BSP_pipeline.pl Version = 2.0 Copyright Floragenex, Inc. 2011 Parameters / Options: Fasta reference file: Genome/Deagle_KrillTest_Test01SbfI_sequence_1_RAD_unitags.fasta Directory with raw sequence data: Raw_Illumina_Sequence SR / PE alignment mode: 1 SAM_BAM_Pileup output folder: SAM_BAM_Pileups_krilltest_sbfI Bowtie alignment options: Number of threads for bowtie alignment: 7 Number of mismatches permitted per alignment: 3 Maximum number of alignments permissable per read: 1 Illumina quality score type: SANGER 5' end sequence trimming: 0 BSP_pipeline.pl Version = 2.0 Copyright Floragenex, Inc. 2011 Parameters / Options: Fasta reference file: Genome/Deagle_KrillTest_Test01SbfI_sequence_1_RAD_unitags.fasta Directory with raw sequence data: Raw_Illumina_Sequence SR / PE alignment mode: 1 SAM_BAM_Pileup output folder: SAM_BAM_Pileups_krilltest_sbfI Bowtie alignment options: Number of threads for bowtie alignment: 7 Number of mismatches permitted per alignment: 3 Maximum number of alignments permissable per read: 1 Illumina quality score type: SANGER 5' end sequence trimming: 0 Reads trimmed to length 90 during alignment Aligning file Deagle_KrillTest_Test02SbfI_sequence_1.txt to fasta reference... Aligning file Deagle_KrillTest_Test01SbfI_sequence_1.txt to fasta reference... Aligning file Deagle_KrillTest_S2M12SbfI_sequence_1.txt to fasta reference... Aligning file Deagle_KrillTest_Test03SbfI_sequence_1.txt to fasta reference... Aligning file Deagle_KrillTest_Test04SbfI_sequence_1.txt to fasta reference... Aligning file Deagle_KrillTest_S2F12SbfI_sequence_1.txt to fasta reference... Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201208/SAM_BAM_Pileups_krilltest_sbfI/Deagle_KrillTest_Test03SbfI_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201208/SAM_BAM_Pileups_krilltest_sbfI/Deagle_KrillTest_Test04SbfI_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201208/SAM_BAM_Pileups_krilltest_sbfI/Deagle_KrillTest_Test01SbfI_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201208/SAM_BAM_Pileups_krilltest_sbfI/Deagle_KrillTest_Test02SbfI_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201208/SAM_BAM_Pileups_krilltest_sbfI/Deagle_KrillTest_S2M12SbfI_sequence_1_sort.bam...completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201208/SAM_BAM_Pileups_krilltest_sbfI/Deagle_KrillTest_S2F12SbfI_sequence_1_sort.bam...completed completed completed Total BSP runtime: 04:25:01 BSP_pipeline.pl Version = 2.0 Copyright Floragenex, Inc. 2011 Parameters / Options: Fasta reference file: Genome/Deagle_Krill_16_sequence_1_RAD_unitags.fasta Directory with raw sequence data: Raw_Illumina_Sequence SR / PE alignment mode: 1 SAM_BAM_Pileup output folder: SAM_BAM_Pileups_vs_16 Bowtie alignment options: Number of threads for bowtie alignment: 7 Number of mismatches permitted per alignment: 3 Maximum number of alignments permissable per read: 1 Illumina quality score type: SANGER 5' end sequence trimming: 0 Reads trimmed to length 90 during alignment Aligning file Deagle_KrillTest_Test02SbfI_sequence_1.txt to fasta reference... Aligning file Deagle_KrillTest_Test01SbfI_sequence_1.txt to fasta reference... Aligning file Deagle_KrillTest_S2M12SbfI_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM03_sequence_1.txt to fasta reference... Aligning file Deagle_KrillTest_Test03SbfI_sequence_1.txt to fasta reference... Aligning file Deagle_KrillTest_Test04SbfI_sequence_1.txt to fasta reference... Aligning file Deagle_KrillTest_S2F12SbfI_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM09_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE25_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM02b_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_4_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM12_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_2_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM06_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM01_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_16_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF11_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE03_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM08_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_8_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE26_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF02_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM05_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPB08_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_7_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPB02_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPB09_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_17_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF05_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM09_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPPS2_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPB04_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAP14_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPB11_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_9_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF01_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM11_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_1a_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM10_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM07_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S4MawE10_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF11_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPA02_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_20_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_6_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_15_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM07_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPPS1_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE01_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM10_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF03_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_18_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S4MawE13_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_2c_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF04_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF02_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_3c_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF08_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_10_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM04_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_3_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPA05_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM03_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_23_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_12_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAP16_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPA01_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_5_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF05_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE02_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_25_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPB13_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_21_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE06_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S4MawE03_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAP15_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF08_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF14_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE10_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF12_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_13_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM06_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE12_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE16_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_11_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM08_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM02_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPB01_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF13_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_19_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S4MawE12_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAP11_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPA06_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM04_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF10_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF10_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF09_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE14_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF07_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM13_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAP12_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF06_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPA07_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF01_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM01_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM14_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF09_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF07_sequence_1.txt to fasta reference... Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16/Deagle_KrillTest_Test02SbfI_sequence_1_sort.bam...completed BSP_pipeline.pl Version = 2.0 Copyright Floragenex, Inc. 2011 Parameters / Options: Fasta reference file: Genome/Deagle_Krill_16_sequence_1_RAD_unitags.fasta Directory with raw sequence data: Raw_Illumina_Sequence SR / PE alignment mode: 1 SAM_BAM_Pileup output folder: SAM_BAM_Pileups_vs_16 Bowtie alignment options: Number of threads for bowtie alignment: 7 Number of mismatches permitted per alignment: 3 Maximum number of alignments permissable per read: 1 Illumina quality score type: SANGER 5' end sequence trimming: 0 Reads trimmed to length 90 during alignment Aligning file Deagle_KrillTest_Test02SbfI_sequence_1.txt to fasta reference... Aligning file Deagle_KrillTest_Test01SbfI_sequence_1.txt to fasta reference... Aligning file Deagle_KrillTest_S2M12SbfI_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM03_sequence_1.txt to fasta reference... Aligning file Deagle_KrillTest_Test03SbfI_sequence_1.txt to fasta reference... Aligning file Deagle_KrillTest_Test04SbfI_sequence_1.txt to fasta reference... Aligning file Deagle_KrillTest_S2F12SbfI_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM09_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE25_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM02b_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_4_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM12_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_2_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM06_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM01_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_16_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF11_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE03_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM08_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_8_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE26_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF02_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM05_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPB08_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_7_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPB02_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPB09_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_17_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF05_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM09_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPPS2_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPB04_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAP14_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPB11_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_9_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF01_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM11_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_1a_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM10_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM07_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S4MawE10_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF11_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPA02_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_20_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_6_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_15_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM07_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPPS1_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE01_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM10_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF03_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_18_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S4MawE13_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_2c_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF04_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF02_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_3c_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF08_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_10_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM04_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_3_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPA05_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM03_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_23_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_12_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAP16_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPA01_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_5_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF05_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE02_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_25_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPB13_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_21_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE06_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S4MawE03_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAP15_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF08_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF14_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE10_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF12_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_13_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM06_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE12_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE16_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_11_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM08_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM02_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPB01_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF13_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_19_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S4MawE12_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAP11_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPA06_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM04_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF10_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF10_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF09_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE14_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF07_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM13_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAP12_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF06_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPA07_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF01_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM01_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM14_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF09_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF07_sequence_1.txt to fasta reference... Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16/Deagle_Krill_S1CasM03_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16/Deagle_KrillTest_Test01SbfI_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16/Deagle_KrillTest_S2M12SbfI_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16/Deagle_KrillTest_Test02SbfI_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16/Deagle_KrillTest_Test03SbfI_sequence_1_sort.bam...completed completed completed completed completed BSP_pipeline.pl Version = 2.0 Copyright Floragenex, Inc. 2011 Parameters / Options: Fasta reference file: Genome/Deagle_Krill_16_sequence_1_RAD_unitags.fasta Directory with raw sequence data: Raw_Illumina_Sequence SR / PE alignment mode: 1 SAM_BAM_Pileup output folder: SAM_BAM_Pileups_vs_16/ Bowtie alignment options: Number of threads for bowtie alignment: 30 Number of mismatches permitted per alignment: 3 Maximum number of alignments permissable per read: 1 Illumina quality score type: SANGER 5' end sequence trimming: 0 Reads trimmed to length 85 during alignment Aligning file Deagle_KrillTest_Test02SbfI_sequence_1.txt to fasta reference... Aligning file Deagle_KrillTest_Test01SbfI_sequence_1.txt to fasta reference... Aligning file Deagle_KrillTest_S2M12SbfI_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM03_sequence_1.txt to fasta reference... Aligning file Deagle_KrillTest_Test03SbfI_sequence_1.txt to fasta reference... Aligning file Deagle_KrillTest_Test04SbfI_sequence_1.txt to fasta reference... Aligning file Deagle_KrillTest_S2F12SbfI_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM09_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE25_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM02b_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_4_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM12_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_2_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM06_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM01_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_16_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF11_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE03_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM08_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_8_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE26_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF02_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM05_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPB08_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_7_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPB02_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPB09_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_17_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF05_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM09_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPPS2_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPB04_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAP14_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPB11_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_9_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF01_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM11_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_1a_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM10_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM07_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S4MawE10_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF11_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPA02_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_20_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_6_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_15_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM07_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPPS1_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE01_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM10_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF03_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_18_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S4MawE13_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_2c_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF04_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF02_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_3c_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF08_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_10_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM04_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_3_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPA05_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM03_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_23_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_12_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAP16_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPA01_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_5_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF05_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE02_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_25_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPB13_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_21_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE06_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S4MawE03_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAP15_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF08_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF14_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE10_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF12_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_13_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM06_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE12_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE16_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_11_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM08_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM02_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPB01_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF13_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_19_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S4MawE12_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAP11_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPA06_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM04_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF10_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF10_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF09_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE14_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF07_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM13_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAP12_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF06_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPA07_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF01_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM01_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM14_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF09_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF07_sequence_1.txt to fasta reference... Total BSP runtime: 00:01:16 BSP_pipeline.pl Version = 2.0 Copyright Floragenex, Inc. 2011 Parameters / Options: Fasta reference file: Genome/Deagle_Krill_16_sequence_1_RAD_unitags.fasta Directory with raw sequence data: Raw_Illumina_Sequence SR / PE alignment mode: 1 SAM_BAM_Pileup output folder: SAM_BAM_Pileups_vs_16/ Bowtie alignment options: Number of threads for bowtie alignment: 7 Number of mismatches permitted per alignment: 3 Maximum number of alignments permissable per read: 1 Illumina quality score type: SANGER 5' end sequence trimming: 0 Reads trimmed to length 85 during alignment Aligning file Deagle_KrillTest_Test02SbfI_sequence_1.txt to fasta reference... Aligning file Deagle_KrillTest_Test01SbfI_sequence_1.txt to fasta reference... Aligning file Deagle_KrillTest_S2M12SbfI_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM03_sequence_1.txt to fasta reference... Aligning file Deagle_KrillTest_Test03SbfI_sequence_1.txt to fasta reference... Aligning file Deagle_KrillTest_Test04SbfI_sequence_1.txt to fasta reference... Aligning file Deagle_KrillTest_S2F12SbfI_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM09_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE25_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM02b_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_4_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM12_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_2_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM06_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM01_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_16_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF11_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE03_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM08_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_8_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE26_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF02_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM05_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPB08_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_7_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPB02_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPB09_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_17_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF05_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM09_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPPS2_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPB04_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAP14_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPB11_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_9_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF01_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM11_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_1a_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM10_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM07_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S4MawE10_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF11_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPA02_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_20_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_6_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_15_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM07_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPPS1_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE01_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM10_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF03_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_18_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S4MawE13_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_2c_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF04_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF02_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_3c_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF08_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_10_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM04_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_3_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPA05_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM03_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_23_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_12_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAP16_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPA01_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_5_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF05_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE02_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_25_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPB13_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_21_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE06_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S4MawE03_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAP15_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF08_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF14_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE10_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF12_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_13_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM06_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE12_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE16_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_11_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM08_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM02_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPB01_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF13_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_19_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S4MawE12_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAP11_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPA06_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM04_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF10_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF10_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF09_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE14_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF07_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM13_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAP12_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF06_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPA07_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF01_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM01_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM14_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF09_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF07_sequence_1.txt to fasta reference... Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_KrillTest_Test03SbfI_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S1CasM03_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_KrillTest_S2M12SbfI_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_KrillTest_Test02SbfI_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_KrillTest_Test01SbfI_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S2MawM02b_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S3LazE25_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S2MawM09_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_KrillTest_Test04SbfI_sequence_1_sort.bam...completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_KrillTest_S2F12SbfI_sequence_1_sort.bam...completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S1CasM12_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_4_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_2_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S1CasM06_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S1CasM01_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_16_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S1CasF11_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S1CasM08_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S3LazE03_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_8_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S3LazE26_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S6WAPB08_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S1CasF02_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S2MawM05_sequence_1_sort.bam...completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_7_sequence_1_sort.bam...completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S6WAPB02_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S6WAPB09_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S1CasF05_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_17_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S1CasM09_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S6WAPPS2_sequence_1_sort.bam...completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S6WAP14_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S6WAPB04_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S6WAPB11_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_9_sequence_1_sort.bam...completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S1CasF01_sequence_1_sort.bam...completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S2MawM07_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S2MawM11_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S1CasM10_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S4MawE10_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_1a_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S6WAPA02_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_20_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_15_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_6_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S2MawF11_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S2MawM10_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S2MawF03_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S3LazE01_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S6WAPPS1_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S1CasM07_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S2MawF02_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S2MawF04_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_2c_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_18_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S4MawE13_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_3c_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S1CasM04_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_10_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_3_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S1CasF08_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_12_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S6WAP16_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_23_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S6WAPA05_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S2MawM03_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_25_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S2MawF05_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S3LazE02_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_5_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S6WAPA01_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S6WAP15_sequence_1_sort.bam...completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S4MawE03_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_21_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S3LazE06_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S6WAPB13_sequence_1_sort.bam...completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S2MawF08_sequence_1_sort.bam...completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S2MawM06_sequence_1_sort.bam...completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_13_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S1CasF12_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S1CasF14_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S3LazE10_sequence_1_sort.bam...completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S3LazE12_sequence_1_sort.bam...completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S2MawM02_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S2MawM08_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S3LazE16_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_11_sequence_1_sort.bam...completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S6WAPB01_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S4MawE12_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S6WAP11_sequence_1_sort.bam...completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_19_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S1CasF13_sequence_1_sort.bam...completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S6WAPA06_sequence_1_sort.bam...completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S1CasF09_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S2MawF10_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S1CasF10_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S2MawM04_sequence_1_sort.bam...completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S3LazE14_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S2MawF07_sequence_1_sort.bam...completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S1CasM13_sequence_1_sort.bam...completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S6WAP12_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S2MawF06_sequence_1_sort.bam...completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S6WAPA07_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S2MawM01_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S2MawF01_sequence_1_sort.bam...completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S2MawF09_sequence_1_sort.bam...completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S1CasM14_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201212/SAM_BAM_Pileups_vs_16//Deagle_Krill_S1CasF07_sequence_1_sort.bam...completed completed completed Total BSP runtime: 22:13:26 BSP_pipeline.pl Version = 2.0 Copyright Floragenex, Inc. 2011 Parameters / Options: Fasta reference file: Genome/Deagle_Krill_S1CasM03_sequence_1_RAD_unitags.fasta Directory with raw sequence data: Raw_Illumina_Sequence SR / PE alignment mode: 1 SAM_BAM_Pileup output folder: SAM_BAM_Pileups_All_vs_S1CasM03_201310 Bowtie alignment options: Number of threads for bowtie alignment: 30 Number of mismatches permitted per alignment: 3 Maximum number of alignments permissable per read: 1 Illumina quality score type: SANGER 5' end sequence trimming: 0 Reads trimmed to length 90 during alignment Aligning file Deagle_KrillTest_Test02SbfI_sequence_1.txt to fasta reference... Aligning file Deagle_KrillTest_Test01SbfI_sequence_1.txt to fasta reference... Aligning file Deagle_KrillTest_S2M12SbfI_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM03_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF01b_sequence_1.txt to fasta reference... Aligning file Deagle_KrillTest_Test03SbfI_sequence_1.txt to fasta reference... Aligning file Deagle_KrillTest_Test04SbfI_sequence_1.txt to fasta reference... Aligning file Deagle_KrillTest_S2F12SbfI_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF07b_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPPS4_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_Test02b_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS23_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM09_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS18_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM13b_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF10b_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS13_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS27_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS29_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPA07b_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE25_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM02b_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS06_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS22_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPA16b_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS21_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF10b_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS37_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS36_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM14b_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS31b_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS26_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_4_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS32_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM12_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS31_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_2_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS43_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM06_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPPS3_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM01_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS28_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS34_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_16_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF11_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE03_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS25_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM08_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS30_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS33_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_8_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE26_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF02_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM05_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPB08_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_7_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPB02_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS17_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS05_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPB09_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_17_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF05_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM09_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPPS2_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPB04_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAP14_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPB11_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_9_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF01_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS24_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM11_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_1a_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM10_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPPS5_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM07_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S4MawE10_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS20_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF11_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPA02_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_20_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_6_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_15_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM07_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPPS1_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE01_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM10_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF03_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_18_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S4MawE13_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPA06b_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_2c_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF04_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF02_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_3c_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF08_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_10_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM04_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_3_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPA05_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM03_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_23_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_12_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAP16_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPA01_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_5_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF05_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE02_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_25_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPB13_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_21_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE06_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S4MawE03_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAP15_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF08_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF14_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE10_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF12_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_13_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM06_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE12_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE16_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_11_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM08_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM02_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPB01_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF13_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_19_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S4MawE12_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAP11_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPA06_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM04_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF10_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF10_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF09_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE14_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF07_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS31c_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM13_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAP12_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF06_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPA07_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF01_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPA11b_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM01_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM14_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF09_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS49_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF07_sequence_1.txt to fasta reference... Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S2MawF01b_sequence_1_sort.bam...completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S1CasM03_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_KrillTest_Test02SbfI_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_KrillTest_S2M12SbfI_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_KrillTest_Test01SbfI_sequence_1_sort.bam...completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S1CasF07b_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S6WAPPS4_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_KrillTest_S2F12SbfI_sequence_1_sort.bam...completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_KrillTest_Test03SbfI_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_KrillTest_Test04SbfI_sequence_1_sort.bam...completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S1CasM13b_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S7RS18_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S2MawM09_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S7RS23_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_Test02b_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S6WAPA07b_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S7RS29_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S2MawF10b_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S7RS27_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S7RS13_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S3LazE25_sequence_1_sort.bam...completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S6WAPA16b_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S7RS22_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S2MawM02b_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S7RS06_sequence_1_sort.bam...completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S7RS21_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S7RS36_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S1CasM14b_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S7RS37_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S1CasF10b_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S7RS31b_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S1CasM12_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S7RS32_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S7RS26_sequence_1_sort.bam...completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_4_sequence_1_sort.bam...completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S7RS31_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_2_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S6WAPPS3_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S7RS43_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S1CasM06_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S7RS28_sequence_1_sort.bam...completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S1CasM01_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_16_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S1CasF11_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S7RS34_sequence_1_sort.bam...completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S7RS33_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S7RS30_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S3LazE03_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S1CasM08_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S7RS25_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S2MawM05_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S6WAPB08_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S1CasF02_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_8_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S3LazE26_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S6WAPB09_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S7RS05_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S7RS17_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_7_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S6WAPB02_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_17_sequence_1_sort.bam...completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S6WAPPS2_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S6WAPB04_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S1CasM09_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S1CasF05_sequence_1_sort.bam...completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S6WAP14_sequence_1_sort.bam...completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S7RS24_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S1CasF01_sequence_1_sort.bam...completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S6WAPB11_sequence_1_sort.bam...completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_9_sequence_1_sort.bam...completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S2MawM11_sequence_1_sort.bam...completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_1a_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S2MawM07_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S6WAPPS5_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S1CasM10_sequence_1_sort.bam...completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S4MawE10_sequence_1_sort.bam...completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S6WAPA02_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_20_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S2MawF11_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S7RS20_sequence_1_sort.bam...completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_6_sequence_1_sort.bam...completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S6WAPPS1_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S1CasM07_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S3LazE01_sequence_1_sort.bam...completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_15_sequence_1_sort.bam...completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S2MawM10_sequence_1_sort.bam...completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_18_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S4MawE13_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S2MawF03_sequence_1_sort.bam...completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_2c_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S6WAPA06b_sequence_1_sort.bam...completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_3c_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_10_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S2MawF04_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S2MawF02_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S1CasF08_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S6WAPA05_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S1CasM04_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S2MawM03_sequence_1_sort.bam...completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_23_sequence_1_sort.bam...completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_3_sequence_1_sort.bam...completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S6WAPA01_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_12_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S6WAP16_sequence_1_sort.bam...completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_5_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S2MawF05_sequence_1_sort.bam...completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_25_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S6WAPB13_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S3LazE02_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_21_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S3LazE06_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S6WAP15_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S2MawF08_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S3LazE10_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S1CasF14_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S4MawE03_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S3LazE16_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S3LazE12_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S2MawM06_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_13_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S1CasF12_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S6WAPB01_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S1CasF13_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S2MawM02_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S2MawM08_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_11_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S2MawM04_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S6WAP11_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S6WAPA06_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S4MawE12_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_19_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S2MawF07_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S3LazE14_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S1CasF09_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S2MawF10_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S1CasF10_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S6WAPA07_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S6WAP12_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S2MawF06_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S1CasM13_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S7RS31c_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S2MawF09_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S1CasM14_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S2MawM01_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S6WAPA11b_sequence_1_sort.bam...completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S2MawF01_sequence_1_sort.bam...completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S1CasF07_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S1CasM03_201310/Deagle_Krill_S7RS49_sequence_1_sort.bam...completed completed Total BSP runtime: 13:55:48 BSP_pipeline.pl Version = 2.0 Copyright Floragenex, Inc. 2011 Parameters / Options: Fasta reference file: Genome/Deagle_Krill_S2MawF01b_sequence_1_RAD_unitags.fasta Directory with raw sequence data: Raw_Illumina_Sequence SR / PE alignment mode: 1 SAM_BAM_Pileup output folder: SAM_BAM_Pileups_All_vs_S2MawF01b_201310 Bowtie alignment options: Number of threads for bowtie alignment: 30 Number of mismatches permitted per alignment: 3 Maximum number of alignments permissable per read: 1 Illumina quality score type: SANGER 5' end sequence trimming: 0 Reads trimmed to length 90 during alignment Aligning file Deagle_KrillTest_Test02SbfI_sequence_1.txt to fasta reference... Aligning file Deagle_KrillTest_Test01SbfI_sequence_1.txt to fasta reference... Aligning file Deagle_KrillTest_S2M12SbfI_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM03_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF01b_sequence_1.txt to fasta reference... Aligning file Deagle_KrillTest_Test03SbfI_sequence_1.txt to fasta reference... Aligning file Deagle_KrillTest_Test04SbfI_sequence_1.txt to fasta reference... Aligning file Deagle_KrillTest_S2F12SbfI_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF07b_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPPS4_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_Test02b_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS23_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM09_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS18_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM13b_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF10b_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS13_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS27_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS29_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPA07b_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE25_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM02b_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS06_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS22_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPA16b_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS21_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF10b_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS37_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS36_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM14b_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS31b_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS26_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_4_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS32_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM12_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS31_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_2_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS43_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM06_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPPS3_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM01_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS28_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS34_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_16_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF11_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE03_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS25_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM08_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS30_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS33_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_8_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE26_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF02_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM05_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPB08_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_7_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPB02_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS17_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS05_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPB09_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_17_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF05_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM09_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPPS2_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPB04_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAP14_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPB11_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_9_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF01_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS24_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM11_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_1a_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM10_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPPS5_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM07_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S4MawE10_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS20_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF11_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPA02_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_20_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_6_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_15_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM07_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPPS1_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE01_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM10_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF03_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_18_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S4MawE13_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPA06b_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_2c_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF04_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF02_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_3c_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF08_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_10_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM04_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_3_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPA05_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM03_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_23_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_12_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAP16_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPA01_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_5_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF05_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE02_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_25_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPB13_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_21_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE06_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S4MawE03_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAP15_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF08_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF14_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE10_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF12_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_13_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM06_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE12_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE16_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_11_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM08_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM02_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPB01_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF13_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_19_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S4MawE12_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAP11_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPA06_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM04_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF10_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF10_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF09_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE14_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF07_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS31c_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM13_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAP12_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF06_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPA07_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF01_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPA11b_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM01_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM14_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF09_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS49_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF07_sequence_1.txt to fasta reference... Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S2MawF01b_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S1CasM03_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_KrillTest_Test01SbfI_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_KrillTest_S2M12SbfI_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_KrillTest_Test02SbfI_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S6WAPPS4_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S1CasF07b_sequence_1_sort.bam...completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_KrillTest_S2F12SbfI_sequence_1_sort.bam...completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_KrillTest_Test04SbfI_sequence_1_sort.bam...completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_KrillTest_Test03SbfI_sequence_1_sort.bam...completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_Test02b_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S7RS23_sequence_1_sort.bam...completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S1CasM13b_sequence_1_sort.bam...completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S7RS18_sequence_1_sort.bam...completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S2MawM09_sequence_1_sort.bam...completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S6WAPA07b_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S7RS13_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S7RS29_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S2MawF10b_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S7RS27_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S7RS22_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S7RS06_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S3LazE25_sequence_1_sort.bam...completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S2MawM02b_sequence_1_sort.bam...completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S6WAPA16b_sequence_1_sort.bam...completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S1CasF10b_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S7RS21_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S7RS37_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S1CasM14b_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S7RS36_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S7RS31b_sequence_1_sort.bam...completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S1CasM12_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S7RS26_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S7RS32_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_4_sequence_1_sort.bam...completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_2_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S7RS31_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S6WAPPS3_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S7RS43_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S1CasM06_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S7RS28_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_16_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S1CasM01_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S1CasF11_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S7RS34_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S7RS33_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S7RS30_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S1CasM08_sequence_1_sort.bam...completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S7RS25_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S3LazE03_sequence_1_sort.bam...completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S6WAPB08_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S2MawM05_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S1CasF02_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_8_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S3LazE26_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S6WAPB09_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S7RS05_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S7RS17_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S6WAPB02_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_7_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S6WAPB04_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S6WAPPS2_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S1CasM09_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S1CasF05_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_17_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S6WAP14_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S6WAPB11_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S7RS24_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S1CasF01_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_9_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S2MawM11_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_1a_sequence_1_sort.bam...completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S1CasM10_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S6WAPPS5_sequence_1_sort.bam...completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S2MawM07_sequence_1_sort.bam...completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S4MawE10_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S7RS20_sequence_1_sort.bam...completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S2MawF11_sequence_1_sort.bam...completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S6WAPA02_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_20_sequence_1_sort.bam...completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_15_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_6_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S1CasM07_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S3LazE01_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S6WAPPS1_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S2MawM10_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S4MawE13_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_18_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S6WAPA06b_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S2MawF03_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_3c_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S2MawF04_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S1CasF08_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S2MawF02_sequence_1_sort.bam...completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_2c_sequence_1_sort.bam...completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S6WAPA05_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_10_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S2MawM03_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S1CasM04_sequence_1_sort.bam...completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_3_sequence_1_sort.bam...completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_23_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_5_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S6WAPA01_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_12_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S6WAP16_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S2MawF05_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_21_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_25_sequence_1_sort.bam...completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S6WAPB13_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S3LazE02_sequence_1_sort.bam...completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S6WAP15_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S1CasF14_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S2MawF08_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S4MawE03_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S3LazE06_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_13_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S1CasF12_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S3LazE12_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S2MawM06_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S3LazE10_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S6WAPB01_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S2MawM08_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S2MawM02_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S3LazE16_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_11_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S6WAPA06_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S6WAP11_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_19_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S4MawE12_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S1CasF13_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S1CasF09_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S3LazE14_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S2MawF10_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S1CasF10_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S2MawM04_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S6WAP12_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S2MawF06_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S1CasM13_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S2MawF07_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S7RS31c_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S1CasM14_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S2MawM01_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S6WAPA11b_sequence_1_sort.bam...completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S6WAPA07_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S2MawF01_sequence_1_sort.bam...completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S1CasF07_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S7RS49_sequence_1_sort.bam...completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_All_vs_S2MawF01b_201310/Deagle_Krill_S2MawF09_sequence_1_sort.bam...completed Total BSP runtime: 11:26:30 BSP_pipeline.pl Version = 2.0 Copyright Floragenex, Inc. 2011 Parameters / Options: Fasta reference file: Genome/Deagle_Krill_S1CasM03_sequence_1_RAD_unitags.fasta Directory with raw sequence data: Raw_Illumina_Sequence SR / PE alignment mode: 1 SAM_BAM_Pileup output folder: SAM_BAM_Pileups_vs_S1CasM03 Bowtie alignment options: Number of threads for bowtie alignment: 31 Number of mismatches permitted per alignment: 3 Maximum number of alignments permissable per read: 1 Illumina quality score type: SANGER 5' end sequence trimming: 0 Reads trimmed to length 90 during alignment Aligning file Deagle_KrillTest_Test02SbfI_sequence_1.txt to fasta reference... Aligning file Deagle_KrillTest_Test01SbfI_sequence_1.txt to fasta reference... Aligning file Deagle_KrillTest_S2M12SbfI_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM03_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF01b_sequence_1.txt to fasta reference... Aligning file Deagle_KrillTest_Test03SbfI_sequence_1.txt to fasta reference... Aligning file Deagle_KrillTest_Test04SbfI_sequence_1.txt to fasta reference... Aligning file Deagle_KrillTest_S2F12SbfI_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF07b_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPPS4_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_Test02b_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS23_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM09_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS18_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM13b_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF10b_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS13_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS27_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS29_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPA07b_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE25_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM02b_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS06_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS22_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPA16b_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS21_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF10b_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS37_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS36_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM14b_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS31b_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS26_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_4_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS32_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM12_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS31_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_2_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS43_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM06_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPPS3_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM01_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS28_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS34_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_16_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF11_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE03_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS25_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM08_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS30_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS33_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_8_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE26_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF02_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM05_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPB08_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_7_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPB02_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS17_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS05_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPB09_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_17_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF05_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM09_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPPS2_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPB04_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAP14_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPB11_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_9_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF01_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS24_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM11_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_1a_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM10_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPPS5_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM07_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S4MawE10_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS20_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF11_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPA02_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_20_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_6_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_15_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM07_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPPS1_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE01_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM10_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF03_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_18_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S4MawE13_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPA06b_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_2c_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF04_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF02_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_3c_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF08_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_10_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM04_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_3_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPA05_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM03_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_23_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_12_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAP16_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPA01_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_5_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF05_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE02_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_25_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPB13_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_21_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE06_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S4MawE03_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAP15_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF08_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF14_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE10_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF12_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_13_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM06_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE12_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE16_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_11_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM08_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM02_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPB01_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF13_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_19_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S4MawE12_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAP11_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPA06_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM04_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF10_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF10_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF09_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE14_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF07_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS31c_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM13_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAP12_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF06_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPA07_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF01_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPA11b_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM01_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM14_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF09_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS49_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF07_sequence_1.txt to fasta reference... Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S1CasM03_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_KrillTest_S2M12SbfI_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S2MawF01b_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_KrillTest_Test02SbfI_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_KrillTest_Test01SbfI_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S6WAPPS4_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S1CasF07b_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_KrillTest_S2F12SbfI_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_KrillTest_Test04SbfI_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_KrillTest_Test03SbfI_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S7RS18_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S2MawM09_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S7RS23_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S1CasM13b_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_Test02b_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S6WAPA07b_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S7RS29_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S7RS27_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S7RS13_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S2MawF10b_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S3LazE25_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S2MawM02b_sequence_1_sort.bam...completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S6WAPA16b_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S7RS22_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S7RS06_sequence_1_sort.bam...completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S1CasF10b_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S7RS21_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S7RS37_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S1CasM14b_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S7RS36_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_4_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S7RS26_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S7RS31b_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S1CasM12_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S7RS32_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S7RS31_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_2_sequence_1_sort.bam...completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S7RS43_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S6WAPPS3_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S1CasM06_sequence_1_sort.bam...completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S1CasM01_sequence_1_sort.bam...completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_16_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S1CasF11_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S7RS28_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S7RS34_sequence_1_sort.bam...completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S3LazE03_sequence_1_sort.bam...completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S7RS33_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S7RS30_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S1CasM08_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S7RS25_sequence_1_sort.bam...completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_8_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S6WAPB08_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S2MawM05_sequence_1_sort.bam...completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S1CasF02_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S3LazE26_sequence_1_sort.bam...completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_7_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S6WAPB09_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S7RS17_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S7RS05_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S6WAPB02_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S6WAPPS2_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S6WAPB04_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S1CasM09_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S1CasF05_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_17_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S6WAP14_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S1CasF01_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S7RS24_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S6WAPB11_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_9_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S2MawM11_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S2MawM07_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S1CasM10_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S6WAPPS5_sequence_1_sort.bam...completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_1a_sequence_1_sort.bam...completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S4MawE10_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S7RS20_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S6WAPA02_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_20_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S2MawF11_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S1CasM07_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_15_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_6_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S6WAPPS1_sequence_1_sort.bam...completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S3LazE01_sequence_1_sort.bam...completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_18_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S2MawM10_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S2MawF03_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S4MawE13_sequence_1_sort.bam...completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S6WAPA06b_sequence_1_sort.bam...completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S2MawF04_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S2MawF02_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_2c_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_3c_sequence_1_sort.bam...completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S1CasF08_sequence_1_sort.bam...completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S6WAPA05_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_10_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S1CasM04_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_3_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S2MawM03_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_23_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S6WAP16_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_5_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S6WAPA01_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_12_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S2MawF05_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_21_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_25_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S6WAPB13_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S3LazE02_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S3LazE06_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S2MawF08_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S6WAP15_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S1CasF14_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S4MawE03_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S2MawM06_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S3LazE10_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_13_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S1CasF12_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S3LazE12_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S2MawM08_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S6WAPB01_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S2MawM02_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S3LazE16_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_11_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S6WAPA06_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S6WAP11_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_19_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S4MawE12_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S1CasF13_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S3LazE14_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S1CasF09_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S2MawF10_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S1CasF10_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S2MawM04_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S2MawF07_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S6WAP12_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S1CasM13_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S2MawF06_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S7RS31c_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S1CasM14_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S2MawM01_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S6WAPA11b_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S6WAPA07_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S2MawF01_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S1CasF07_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S7RS49_sequence_1_sort.bam...completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S1CasM03/Deagle_Krill_S2MawF09_sequence_1_sort.bam...completed Total BSP runtime: 16:07:33 BSP_pipeline.pl Version = 2.0 Copyright Floragenex, Inc. 2011 Parameters / Options: Fasta reference file: Genome/Deagle_Krill_S2MawF01b_sequence_1_RAD_unitags.fasta Directory with raw sequence data: Raw_Illumina_Sequence SR / PE alignment mode: 1 SAM_BAM_Pileup output folder: SAM_BAM_Pileups_vs_S2MawF01b Bowtie alignment options: Number of threads for bowtie alignment: 31 Number of mismatches permitted per alignment: 3 Maximum number of alignments permissable per read: 1 Illumina quality score type: SANGER 5' end sequence trimming: 0 Reads trimmed to length 90 during alignment Aligning file Deagle_KrillTest_Test02SbfI_sequence_1.txt to fasta reference... Aligning file Deagle_KrillTest_Test01SbfI_sequence_1.txt to fasta reference... Aligning file Deagle_KrillTest_S2M12SbfI_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM03_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF01b_sequence_1.txt to fasta reference... Aligning file Deagle_KrillTest_Test03SbfI_sequence_1.txt to fasta reference... Aligning file Deagle_KrillTest_Test04SbfI_sequence_1.txt to fasta reference... Aligning file Deagle_KrillTest_S2F12SbfI_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF07b_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPPS4_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_Test02b_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS23_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM09_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS18_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM13b_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF10b_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS13_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS27_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS29_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPA07b_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE25_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM02b_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS06_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS22_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPA16b_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS21_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF10b_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS37_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS36_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM14b_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS31b_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS26_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_4_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS32_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM12_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS31_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_2_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS43_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM06_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPPS3_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM01_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS28_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS34_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_16_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF11_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE03_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS25_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM08_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS30_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS33_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_8_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE26_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF02_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM05_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPB08_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_7_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPB02_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS17_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS05_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPB09_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_17_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF05_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM09_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPPS2_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPB04_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAP14_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPB11_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_9_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF01_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS24_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM11_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_1a_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM10_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPPS5_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM07_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S4MawE10_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS20_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF11_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPA02_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_20_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_6_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_15_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM07_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPPS1_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE01_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM10_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF03_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_18_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S4MawE13_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPA06b_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_2c_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF04_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF02_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_3c_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF08_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_10_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM04_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_3_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPA05_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM03_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_23_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_12_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAP16_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPA01_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_5_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF05_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE02_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_25_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPB13_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_21_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE06_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S4MawE03_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAP15_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF08_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF14_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE10_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF12_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_13_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM06_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE12_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE16_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_11_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM08_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM02_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPB01_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF13_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_19_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S4MawE12_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAP11_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPA06_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM04_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF10_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF10_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF09_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S3LazE14_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF07_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS31c_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM13_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAP12_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF06_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPA07_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF01_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S6WAPA11b_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawM01_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasM14_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S2MawF09_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S7RS49_sequence_1.txt to fasta reference... Aligning file Deagle_Krill_S1CasF07_sequence_1.txt to fasta reference... Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S2MawF01b_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S1CasM03_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_KrillTest_Test02SbfI_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_KrillTest_Test01SbfI_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_KrillTest_S2M12SbfI_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S1CasF07b_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_KrillTest_S2F12SbfI_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S6WAPPS4_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_KrillTest_Test03SbfI_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_KrillTest_Test04SbfI_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S7RS23_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S2MawM09_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_Test02b_sequence_1_sort.bam...completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S1CasM13b_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S7RS18_sequence_1_sort.bam...completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S7RS29_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S6WAPA07b_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S7RS27_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S7RS13_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S2MawF10b_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S6WAPA16b_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S3LazE25_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S7RS06_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S2MawM02b_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S7RS22_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S1CasM14b_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S7RS36_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S7RS37_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S1CasF10b_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S7RS21_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S7RS31b_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S1CasM12_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_4_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S7RS32_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S7RS26_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S7RS31_sequence_1_sort.bam...completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S6WAPPS3_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S7RS43_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_2_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S1CasM06_sequence_1_sort.bam...completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S1CasM01_sequence_1_sort.bam...completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_16_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S1CasF11_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S7RS28_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S7RS34_sequence_1_sort.bam...completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S3LazE03_sequence_1_sort.bam...completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S7RS33_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S1CasM08_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S7RS30_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S7RS25_sequence_1_sort.bam...completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_8_sequence_1_sort.bam...completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S6WAPB08_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S2MawM05_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S1CasF02_sequence_1_sort.bam...completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S3LazE26_sequence_1_sort.bam...completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_7_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S6WAPB02_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S7RS05_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S7RS17_sequence_1_sort.bam...completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S6WAPB09_sequence_1_sort.bam...completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_17_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S1CasF05_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S6WAPPS2_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S1CasM09_sequence_1_sort.bam...completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S6WAPB04_sequence_1_sort.bam...completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S1CasF01_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S6WAP14_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_9_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S6WAPB11_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S7RS24_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S2MawM11_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S1CasM10_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S2MawM07_sequence_1_sort.bam...completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_1a_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S6WAPPS5_sequence_1_sort.bam...completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S4MawE10_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S7RS20_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S2MawF11_sequence_1_sort.bam...completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S6WAPA02_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_20_sequence_1_sort.bam...completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_6_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_15_sequence_1_sort.bam...completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S6WAPPS1_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S1CasM07_sequence_1_sort.bam...completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S3LazE01_sequence_1_sort.bam...completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S2MawM10_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S2MawF03_sequence_1_sort.bam...completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_18_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S6WAPA06b_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S4MawE13_sequence_1_sort.bam...completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S2MawF04_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_2c_sequence_1_sort.bam...completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_3c_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S2MawF02_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S1CasF08_sequence_1_sort.bam...completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_10_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S1CasM04_sequence_1_sort.bam...completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S2MawM03_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S6WAPA05_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_3_sequence_1_sort.bam...completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_23_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_12_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_5_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S6WAP16_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S6WAPA01_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S2MawF05_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_21_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_25_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S6WAPB13_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S3LazE02_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S3LazE06_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S6WAP15_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S1CasF14_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S2MawF08_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S4MawE03_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S3LazE10_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S3LazE12_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S2MawM06_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_13_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S1CasF12_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S2MawM08_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S2MawM02_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S6WAPB01_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S3LazE16_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_11_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S6WAP11_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S6WAPA06_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S4MawE12_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S1CasF13_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_19_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S2MawM04_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S1CasF10_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S1CasF09_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S3LazE14_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S2MawF10_sequence_1_sort.bam...completed completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S2MawF07_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S7RS31c_sequence_1_sort.bam...completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S2MawF06_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S6WAP12_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S1CasM13_sequence_1_sort.bam...completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S2MawF01_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S6WAPA07_sequence_1_sort.bam...completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S1CasM14_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S2MawM01_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S6WAPA11b_sequence_1_sort.bam...completed completed completed completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S7RS49_sequence_1_sort.bam...completed Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S1CasF07_sequence_1_sort.bam...Beginning pileup for /home/data/Project_Folders/Deagle_Krill_201308/SAM_BAM_Pileups_vs_S2MawF01b/Deagle_Krill_S2MawF09_sequence_1_sort.bam...completed completed Total BSP runtime: 15:20:18