Created by Bpipe, Sat Dec 03 12:08:01 COT 2016
Total Runtime = 17 hours, 7 minutes, 50.519 seconds
Creates directories for organizing files from all pipeline stages.
| Author | nfranco@eafit.edu.co |
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| Commands | mkdir prot_seqs alignments alignments/prot alignments/dna partitionfinder phylo_analyses phylo_analyses/mrbayes phylo_analyses/garli phylo_analyses/raxml |
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| Execution Time | 2016-12-2 19:0:10 (0.304 seconds) |
Looks for identifiers in input filenames in order to redirect files properly according their status (coding sequence '_cds.fasta', provided alignment '_al.fasta' and noncoding sequence).
| Author | nfranco@eafit.edu.co |
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| Execution Time | 2016-12-2 19:0:11 (0.031 seconds) |
Translates protein coding sequences to amino acid sequences given the appropiate genetic code table (default: 1).
| Author | nfranco@eafit.edu.co |
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| Execution Time | 2016-12-2 19:0:11 (0.030 seconds) |
This stage aligns FASTA files (nucleotide or amino acid sequences) if required according input file status.
| Author | nfranco@eafit.edu.co |
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| Commands | /home/bio/phypipe/scripts/apps/mafft/bin/mafft --quiet --auto 18s.fasta > alignments/dna/18s.DNA.alignment.fasta |
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| Execution Time | 2016-12-2 19:0:11 - 2016-12-2 19:0:40 (28.396 seconds) |
This stage transforms FASTA amino acid alignment file to nucleotide alignment matrix.
| Author | nfranco@eafit.edu.co |
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| Execution Time | 2016-12-2 19:0:40 (0.006 seconds) |
Looks for identifiers in input filenames in order to redirect files properly according their status (coding sequence '_cds.fasta', provided alignment '_al.fasta' and noncoding sequence).
| Author | nfranco@eafit.edu.co |
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| Execution Time | 2016-12-2 19:0:11 (0.050 seconds) |
Translates protein coding sequences to amino acid sequences given the appropiate genetic code table (default: 1).
| Author | nfranco@eafit.edu.co |
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| Execution Time | 2016-12-2 19:0:11 (0.044 seconds) |
This stage aligns FASTA files (nucleotide or amino acid sequences) if required according input file status.
| Author | nfranco@eafit.edu.co |
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| Commands | /home/bio/phypipe/scripts/apps/mafft/bin/mafft --quiet --auto 28s.fasta > alignments/dna/28s.DNA.alignment.fasta |
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| Execution Time | 2016-12-2 19:0:11 (0.893 seconds) |
This stage transforms FASTA amino acid alignment file to nucleotide alignment matrix.
| Author | nfranco@eafit.edu.co |
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| Execution Time | 2016-12-2 19:0:12 (0.011 seconds) |
Looks for identifiers in input filenames in order to redirect files properly according their status (coding sequence '_cds.fasta', provided alignment '_al.fasta' and noncoding sequence).
| Author | nfranco@eafit.edu.co |
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| Execution Time | 2016-12-2 19:0:11 (0.104 seconds) |
Translates protein coding sequences to amino acid sequences given the appropiate genetic code table (default: 1).
| Author | nfranco@eafit.edu.co |
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| Execution Time | 2016-12-2 19:0:11 (0.054 seconds) |
This stage aligns FASTA files (nucleotide or amino acid sequences) if required according input file status.
| Author | nfranco@eafit.edu.co |
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| Commands | /home/bio/phypipe/scripts/apps/mafft/bin/mafft --quiet --auto 58s.fasta > alignments/dna/58s.DNA.alignment.fasta |
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| Execution Time | 2016-12-2 19:0:11 (0.947 seconds) |
This stage transforms FASTA amino acid alignment file to nucleotide alignment matrix.
| Author | nfranco@eafit.edu.co |
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| Execution Time | 2016-12-2 19:0:12 (0.013 seconds) |
Looks for identifiers in input filenames in order to redirect files properly according their status (coding sequence '_cds.fasta', provided alignment '_al.fasta' and noncoding sequence).
| Author | nfranco@eafit.edu.co |
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| Execution Time | 2016-12-2 19:0:11 (0.035 seconds) |
Translates protein coding sequences to amino acid sequences given the appropiate genetic code table (default: 1).
| Author | nfranco@eafit.edu.co |
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| Execution Time | 2016-12-2 19:0:11 (0.048 seconds) |
This stage aligns FASTA files (nucleotide or amino acid sequences) if required according input file status.
| Author | nfranco@eafit.edu.co |
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| Commands | /home/bio/phypipe/scripts/apps/mafft/bin/mafft --quiet --auto ITS1.fasta > alignments/dna/ITS1.DNA.alignment.fasta |
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| Execution Time | 2016-12-2 19:0:11 - 2016-12-2 19:0:13 (1.944 seconds) |
This stage transforms FASTA amino acid alignment file to nucleotide alignment matrix.
| Author | nfranco@eafit.edu.co |
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| Execution Time | 2016-12-2 19:0:13 (0.006 seconds) |
Looks for identifiers in input filenames in order to redirect files properly according their status (coding sequence '_cds.fasta', provided alignment '_al.fasta' and noncoding sequence).
| Author | nfranco@eafit.edu.co |
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| Execution Time | 2016-12-2 19:0:11 (0.038 seconds) |
Translates protein coding sequences to amino acid sequences given the appropiate genetic code table (default: 1).
| Author | nfranco@eafit.edu.co |
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| Execution Time | 2016-12-2 19:0:11 (0.057 seconds) |
This stage aligns FASTA files (nucleotide or amino acid sequences) if required according input file status.
| Author | nfranco@eafit.edu.co |
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| Commands | /home/bio/phypipe/scripts/apps/mafft/bin/mafft --quiet --auto ITS2.fasta > alignments/dna/ITS2.DNA.alignment.fasta |
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| Execution Time | 2016-12-2 19:0:11 - 2016-12-2 19:0:13 (1.513 seconds) |
This stage transforms FASTA amino acid alignment file to nucleotide alignment matrix.
| Author | nfranco@eafit.edu.co |
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| Execution Time | 2016-12-2 19:0:13 (0.025 seconds) |
This stage concatenates FASTA alignments in a single file. It also generates a configuration file for partitionfinder.
| Author | nfranco@eafit.edu.co |
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| Commands | /home/bio/phypipe-run/venv/bin/python /home/bio/phypipe/scripts/concat_fasta_alignments.py /home/bio/Documents/Ctenophora_sequences/Arbol_18s_28s_58s_ITS1_ITS2/Arbol_mr_bayes_3_wi_Mnemiopsis/alignments/dna/18s.DNA.alignment.fasta /home/bio/Documents/Ctenophora_sequences/Arbol_18s_28s_58s_ITS1_ITS2/Arbol_mr_bayes_3_wi_Mnemiopsis/alignments/dna/28s.DNA.alignment.fasta /home/bio/Documents/Ctenophora_sequences/Arbol_18s_28s_58s_ITS1_ITS2/Arbol_mr_bayes_3_wi_Mnemiopsis/alignments/dna/58s.DNA.alignment.fasta /home/bio/Documents/Ctenophora_sequences/Arbol_18s_28s_58s_ITS1_ITS2/Arbol_mr_bayes_3_wi_Mnemiopsis/alignments/dna/ITS1.DNA.alignment.fasta /home/bio/Documents/Ctenophora_sequences/Arbol_18s_28s_58s_ITS1_ITS2/Arbol_mr_bayes_3_wi_Mnemiopsis/alignments/dna/ITS2.DNA.alignment.fasta /home/bio/Documents/Ctenophora_sequences/Arbol_18s_28s_58s_ITS1_ITS2/Arbol_mr_bayes_3_wi_Mnemiopsis/concat_matrix.fasta |
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| Execution Time | 2016-12-2 19:0:40 (0.341 seconds) |
This stage creates NEXUS and Phylip files to be used in the downstream steps.
| Author | nfranco@eafit.edu.co |
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| Commands | /home/bio/phypipe-run/venv/bin/python /home/bio/phypipe/scripts/fasta2nexus.py /home/bio/Documents/Ctenophora_sequences/Arbol_18s_28s_58s_ITS1_ITS2/Arbol_mr_bayes_3_wi_Mnemiopsis/concat_matrix.fasta concat_matrix.nexus |
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| Execution Time | 2016-12-2 19:0:40 (0.365 seconds) |
This stage runs partitionfinder. It also creates MrBayes and garli blocks with best model information for each partition based on partitionfinder results.
| Author | nfranco@eafit.edu.co |
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| Commands | cat concat_matrix.nexus phylo_analyses/garli/garli_pfinder.txt > phylo_analyses/garli/concat_w_partitions.nexus |
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| Execution Time | 2016-12-2 19:0:40 - 2016-12-2 19:14:47 (14 minutes, 6.559 seconds) |
This stage runs MrBayes or garli using files generated through the whole pipeline. It outputs consensus tree (for bayesian analysis) or best tree with bootstrap support (for maximum likelihood analysis)
| Author | nfranco@eafit.edu.co |
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| Commands | mv phylo_analyses/garli/results.tre phylo_analyses/garli/phylo_maxlikelihood.tree |
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| Execution Time | 2016-12-2 19:14:47 - 2016-12-3 12:8:1 (16 hours, 53 minutes, 13.655 seconds) |