 ./roast --supertranscript_assembly /home/madiha/Documents/data/arabidopsis_testdata/AT_test_ST.fasta --fastq_1 /home/madiha/Documents/data/arabidopsis_testdata/AT_test_1.fastq.gz --fastq_2 /home/madiha/Documents/data/arabidopsis_testdata/AT_test_2.fastq.gz --threads 3 --threadsForSamSort 2 --output_dir /home/madiha/Documents/data/arabidopsis_testdata/ROAST

No. of contigs in initial assembly: 
8329
Outer iteration:1 started.
Inner iteration:1 started.
1-1: Alignment started for fragmented and partial contigs process using soft-clipping

Alignment ended

read length of this data is: 101
1-1: Assembly extension using soft clipped reads started
Extended incomplete contigs using soft-clipping at iteration 1-1: 2597
Assembly extension using soft clipped reads ended

1-1: Fastq files filtering process started.
Fastq file filtering step ended

Inner iteration:2 started.
1-2: Alignment started for fragmented and partial contigs process using soft-clipping

Alignment ended

1-2: Assembly extension using soft clipped reads started
Extended incomplete contigs using soft-clipping at iteration 1-2: 7
Assembly extension using soft clipped reads ended

1-2: Fastq files filtering process started.
Fastq file filtering step ended

Inner iteration:3 started.
1-3: Alignment started for fragmented and partial contigs process using soft-clipping

Alignment ended

1-3: Assembly extension using soft clipped reads started
Extended incomplete contigs using soft-clipping at iteration 1-3: 0
Assembly extension using soft clipped reads ended

1-3: Fastq files filtering process started.
Fastq file filtering step ended

***** Assembly merging using soft-clipped-extended ends: Process started *****

Merged incomplete contigs using Soft-clipping at iteration 1-4: 104
***** Assembly extension and merging using soft clipped reads: Process completed *****

1: Re-alignment on updated assembly for fragmented and partial contigs process using Unmapped and discordantly mapped reads

1: Assembly extension and merging using Unmapped and discordantly mapped reads: process started
No. of extended contigs by Cap3 at iteration : 49
Merged fragmented contigs using Reads Islands at iteration 1: 74

*****  Assembly extension and merging using Unmapped and discordantly mapped reads: process completed  *****

1: Re-alignment on updated assembly for Local mis-assemblies/false chimeras identification process

1: Identification of Local mis-assemblies/false chimeras: Process started
Number of split chimeric contigs in iteration 1: 538
Number of updated contigs for local mis-assemblies in iteration 1: 989
*****  Identification of Local mis-assemblies/false chimeras: Process completed  *****

Outer iteration:2 started.
Inner iteration:1 started.
2-1: Alignment started for fragmented and partial contigs process using soft-clipping

Alignment ended

2-1: Assembly extension using soft clipped reads started
Extended incomplete contigs using soft-clipping at iteration 2-1: 1024
Assembly extension using soft clipped reads ended

2-1: Fastq files filtering process started.
Fastq file filtering step ended

Inner iteration:2 started.
2-2: Alignment started for fragmented and partial contigs process using soft-clipping

Alignment ended

2-2: Assembly extension using soft clipped reads started
Extended incomplete contigs using soft-clipping at iteration 2-2: 3
Assembly extension using soft clipped reads ended

2-2: Fastq files filtering process started.
Fastq file filtering step ended

Inner iteration:3 started.
2-3: Alignment started for fragmented and partial contigs process using soft-clipping

Alignment ended

2-3: Assembly extension using soft clipped reads started
Extended incomplete contigs using soft-clipping at iteration 2-3: 0
Assembly extension using soft clipped reads ended

2-3: Fastq files filtering process started.
Fastq file filtering step ended

***** Assembly merging using soft-clipped-extended ends: Process started *****

Merged incomplete contigs using Soft-clipping at iteration 2-4: 21
***** Assembly extension and merging using soft clipped reads: Process completed *****

2: Re-alignment on updated assembly for fragmented and partial contigs process using Unmapped and discordantly mapped reads

2: Assembly extension and merging using Unmapped and discordantly mapped reads: process started
No. of extended contigs by Cap3 at iteration : 3
Merged fragmented contigs using Reads Islands at iteration 2: 27

*****  Assembly extension and merging using Unmapped and discordantly mapped reads: process completed  *****

2: Re-alignment on updated assembly for Local mis-assemblies/false chimeras identification process

2: Identification of Local mis-assemblies/false chimeras: Process started
Number of split chimeric contigs in iteration 2: 188
Number of updated contigs for local mis-assemblies in iteration 2: 167
*****  Identification of Local mis-assemblies/false chimeras: Process completed  *****

Outer iteration:3 started.
Inner iteration:1 started.
3-1: Alignment started for fragmented and partial contigs process using soft-clipping

Alignment ended

3-1: Assembly extension using soft clipped reads started
Extended incomplete contigs using soft-clipping at iteration 3-1: 286
Assembly extension using soft clipped reads ended

3-1: Fastq files filtering process started.
Fastq file filtering step ended

Inner iteration:2 started.
3-2: Alignment started for fragmented and partial contigs process using soft-clipping

Alignment ended

3-2: Assembly extension using soft clipped reads started
Extended incomplete contigs using soft-clipping at iteration 3-2: 2
Assembly extension using soft clipped reads ended

3-2: Fastq files filtering process started.
Fastq file filtering step ended

Inner iteration:3 started.
3-3: Alignment started for fragmented and partial contigs process using soft-clipping

Alignment ended

3-3: Assembly extension using soft clipped reads started
Extended incomplete contigs using soft-clipping at iteration 3-3: 0
Assembly extension using soft clipped reads ended

3-3: Fastq files filtering process started.
Fastq file filtering step ended

***** Assembly merging using soft-clipped-extended ends: Process started *****

Merged incomplete contigs using Soft-clipping at iteration 3-4: 3
***** Assembly extension and merging using soft clipped reads: Process completed *****

3: Re-alignment on updated assembly for fragmented and partial contigs process using Unmapped and discordantly mapped reads

3: Assembly extension and merging using Unmapped and discordantly mapped reads: process started
No. of extended contigs by Cap3 at iteration : 1
Merged fragmented contigs using Reads Islands at iteration 3: 6

*****  Assembly extension and merging using Unmapped and discordantly mapped reads: process completed  *****

3: Re-alignment on updated assembly for Local mis-assemblies/false chimeras identification process

3: Identification of Local mis-assemblies/false chimeras: Process started
Number of split chimeric contigs in iteration 3: 96
Number of updated contigs for local mis-assemblies in iteration 3: 28
*****  Identification of Local mis-assemblies/false chimeras: Process completed  *****

Outer iteration:4 started.
Inner iteration:1 started.
4-1: Alignment started for fragmented and partial contigs process using soft-clipping

Alignment ended

4-1: Assembly extension using soft clipped reads started
Extended incomplete contigs using soft-clipping at iteration 4-1: 103
Assembly extension using soft clipped reads ended

4-1: Fastq files filtering process started.
Fastq file filtering step ended

Inner iteration:2 started.
4-2: Alignment started for fragmented and partial contigs process using soft-clipping

Alignment ended

4-2: Assembly extension using soft clipped reads started
Extended incomplete contigs using soft-clipping at iteration 4-2: 0
Assembly extension using soft clipped reads ended

4-2: Fastq files filtering process started.
Fastq file filtering step ended

***** Assembly merging using soft-clipped-extended ends: Process started *****

Merged incomplete contigs using Soft-clipping at iteration 4-3: 5
***** Assembly extension and merging using soft clipped reads: Process completed *****

4: Re-alignment on updated assembly for fragmented and partial contigs process using Unmapped and discordantly mapped reads

4: Assembly extension and merging using Unmapped and discordantly mapped reads: process started
No. of extended contigs by Cap3 at iteration : 0
Merged fragmented contigs using Reads Islands at iteration 4: 3

*****  Assembly extension and merging using Unmapped and discordantly mapped reads: process completed  *****

4: Re-alignment on updated assembly for Local mis-assemblies/false chimeras identification process

4: Identification of Local mis-assemblies/false chimeras: Process started
Number of split chimeric contigs in iteration 4: 26
Number of updated contigs for local mis-assemblies in iteration 4: 12
*****  Identification of Local mis-assemblies/false chimeras: Process completed  *****

Outer iteration:5 started.
Inner iteration:1 started.
5-1: Alignment started for fragmented and partial contigs process using soft-clipping

Alignment ended

5-1: Assembly extension using soft clipped reads started
Extended incomplete contigs using soft-clipping at iteration 5-1: 29
Assembly extension using soft clipped reads ended

5-1: Fastq files filtering process started.
Fastq file filtering step ended

Inner iteration:2 started.
5-2: Alignment started for fragmented and partial contigs process using soft-clipping

Alignment ended

5-2: Assembly extension using soft clipped reads started
Extended incomplete contigs using soft-clipping at iteration 5-2: 0
Assembly extension using soft clipped reads ended

5-2: Fastq files filtering process started.
Fastq file filtering step ended

***** Assembly merging using soft-clipped-extended ends: Process started *****

Merged incomplete contigs using Soft-clipping at iteration 5-3: 2
***** Assembly extension and merging using soft clipped reads: Process completed *****

5: Re-alignment on updated assembly for fragmented and partial contigs process using Unmapped and discordantly mapped reads

5: Assembly extension and merging using Unmapped and discordantly mapped reads: process started
No. of extended contigs by Cap3 at iteration : 0
Merged fragmented contigs using Reads Islands at iteration 5: 2

*****  Assembly extension and merging using Unmapped and discordantly mapped reads: process completed  *****

5: Re-alignment on updated assembly for Local mis-assemblies/false chimeras identification process

5: Identification of Local mis-assemblies/false chimeras: Process started
Number of split chimeric contigs in iteration 5: 11
Number of updated contigs for local mis-assemblies in iteration 5: 7
*****  Identification of Local mis-assemblies/false chimeras: Process completed  *****

Outer iteration:6 started.
Inner iteration:1 started.
6-1: Alignment started for fragmented and partial contigs process using soft-clipping

Alignment ended

6-1: Assembly extension using soft clipped reads started
Extended incomplete contigs using soft-clipping at iteration 6-1: 13
Assembly extension using soft clipped reads ended

6-1: Fastq files filtering process started.
Fastq file filtering step ended

Inner iteration:2 started.
6-2: Alignment started for fragmented and partial contigs process using soft-clipping

Alignment ended

6-2: Assembly extension using soft clipped reads started
Extended incomplete contigs using soft-clipping at iteration 6-2: 0
Assembly extension using soft clipped reads ended

6-2: Fastq files filtering process started.
Fastq file filtering step ended

***** Assembly merging using soft-clipped-extended ends: Process started *****

Merged incomplete contigs using Soft-clipping at iteration 6-3: 1
***** Assembly extension and merging using soft clipped reads: Process completed *****

6: Re-alignment on updated assembly for fragmented and partial contigs process using Unmapped and discordantly mapped reads

6: Assembly extension and merging using Unmapped and discordantly mapped reads: process started
No. of extended contigs by Cap3 at iteration : 0
Merged fragmented contigs using Reads Islands at iteration 6: 1

*****  Assembly extension and merging using Unmapped and discordantly mapped reads: process completed  *****

6: Re-alignment on updated assembly for Local mis-assemblies/false chimeras identification process

6: Identification of Local mis-assemblies/false chimeras: Process started
Number of split chimeric contigs in iteration 6: 11
Number of updated contigs for local mis-assemblies in iteration 6: 4
*****  Identification of Local mis-assemblies/false chimeras: Process completed  *****

Outer iteration:7 started.
Inner iteration:1 started.
7-1: Alignment started for fragmented and partial contigs process using soft-clipping

Alignment ended

7-1: Assembly extension using soft clipped reads started
Extended incomplete contigs using soft-clipping at iteration 7-1: 12
Assembly extension using soft clipped reads ended

7-1: Fastq files filtering process started.
Fastq file filtering step ended

Inner iteration:2 started.
7-2: Alignment started for fragmented and partial contigs process using soft-clipping

Alignment ended

7-2: Assembly extension using soft clipped reads started
Extended incomplete contigs using soft-clipping at iteration 7-2: 0
Assembly extension using soft clipped reads ended

7-2: Fastq files filtering process started.
Fastq file filtering step ended

***** Assembly merging using soft-clipped-extended ends: Process started *****

Merged incomplete contigs using Soft-clipping at iteration 7-3: 0
***** Assembly extension and merging using soft clipped reads: Process completed *****

7: Re-alignment on updated assembly for fragmented and partial contigs process using Unmapped and discordantly mapped reads

7: Assembly extension and merging using Unmapped and discordantly mapped reads: process started
No. of extended contigs by Cap3 at iteration : 0
Merged fragmented contigs using Reads Islands at iteration 7: 0

*****  Assembly extension and merging using Unmapped and discordantly mapped reads: process completed  *****

7: Re-alignment on updated assembly for Local mis-assemblies/false chimeras identification process

7: Identification of Local mis-assemblies/false chimeras: Process started
Number of split chimeric contigs in iteration 7: 6
Number of updated contigs for local mis-assemblies in iteration 7: 4
*****  Identification of Local mis-assemblies/false chimeras: Process completed  *****

Outer iteration:8 started.
Inner iteration:1 started.
8-1: Alignment started for fragmented and partial contigs process using soft-clipping

Alignment ended

8-1: Assembly extension using soft clipped reads started
Extended incomplete contigs using soft-clipping at iteration 8-1: 3
Assembly extension using soft clipped reads ended

8-1: Fastq files filtering process started.
Fastq file filtering step ended

Inner iteration:2 started.
8-2: Alignment started for fragmented and partial contigs process using soft-clipping

Alignment ended

8-2: Assembly extension using soft clipped reads started
Extended incomplete contigs using soft-clipping at iteration 8-2: 0
Assembly extension using soft clipped reads ended

8-2: Fastq files filtering process started.
Fastq file filtering step ended

***** Assembly merging using soft-clipped-extended ends: Process started *****

Merged incomplete contigs using Soft-clipping at iteration 8-3: 0
***** Assembly extension and merging using soft clipped reads: Process completed *****

8: Re-alignment on updated assembly for fragmented and partial contigs process using Unmapped and discordantly mapped reads

8: Assembly extension and merging using Unmapped and discordantly mapped reads: process started
No. of extended contigs by Cap3 at iteration : 0
Merged fragmented contigs using Reads Islands at iteration 8: 1

*****  Assembly extension and merging using Unmapped and discordantly mapped reads: process completed  *****

8: Re-alignment on updated assembly for Local mis-assemblies/false chimeras identification process

8: Identification of Local mis-assemblies/false chimeras: Process started
Number of split chimeric contigs in iteration 8: 0
Number of updated contigs for local mis-assemblies in iteration 8: 0
*****  Identification of Local mis-assemblies/false chimeras: Process completed  *****

Outer iteration:9 started.
Inner iteration:1 started.
9-1: Alignment started for fragmented and partial contigs process using soft-clipping

Alignment ended

9-1: Assembly extension using soft clipped reads started
Extended incomplete contigs using soft-clipping at iteration 9-1: 3
Assembly extension using soft clipped reads ended

9-1: Fastq files filtering process started.
Fastq file filtering step ended

Inner iteration:2 started.
9-2: Alignment started for fragmented and partial contigs process using soft-clipping

Alignment ended

9-2: Assembly extension using soft clipped reads started
Extended incomplete contigs using soft-clipping at iteration 9-2: 0
Assembly extension using soft clipped reads ended

9-2: Fastq files filtering process started.
Fastq file filtering step ended

***** Assembly merging using soft-clipped-extended ends: Process started *****

Merged incomplete contigs using Soft-clipping at iteration 9-3: 0
***** Assembly extension and merging using soft clipped reads: Process completed *****

9: Re-alignment on updated assembly for fragmented and partial contigs process using Unmapped and discordantly mapped reads

9: Assembly extension and merging using Unmapped and discordantly mapped reads: process started
No. of extended contigs by Cap3 at iteration : 0
Merged fragmented contigs using Reads Islands at iteration 9: 0

*****  Assembly extension and merging using Unmapped and discordantly mapped reads: process completed  *****

9: Re-alignment on updated assembly for Local mis-assemblies/false chimeras identification process

9: Identification of Local mis-assemblies/false chimeras: Process started
Number of split chimeric contigs in iteration 9: 2
Number of updated contigs for local mis-assemblies in iteration 9: 2
*****  Identification of Local mis-assemblies/false chimeras: Process completed  *****

Outer iteration:10 started.
Inner iteration:1 started.
10-1: Alignment started for fragmented and partial contigs process using soft-clipping

Alignment ended

10-1: Assembly extension using soft clipped reads started
Extended incomplete contigs using soft-clipping at iteration 10-1: 2
Assembly extension using soft clipped reads ended

10-1: Fastq files filtering process started.
Fastq file filtering step ended

Inner iteration:2 started.
10-2: Alignment started for fragmented and partial contigs process using soft-clipping

Alignment ended

10-2: Assembly extension using soft clipped reads started
Extended incomplete contigs using soft-clipping at iteration 10-2: 0
Assembly extension using soft clipped reads ended

10-2: Fastq files filtering process started.
Fastq file filtering step ended

***** Assembly merging using soft-clipped-extended ends: Process started *****

Merged incomplete contigs using Soft-clipping at iteration 10-3: 0
***** Assembly extension and merging using soft clipped reads: Process completed *****

10: Re-alignment on updated assembly for fragmented and partial contigs process using Unmapped and discordantly mapped reads

10: Assembly extension and merging using Unmapped and discordantly mapped reads: process started
No. of extended contigs by Cap3 at iteration : 0
Merged fragmented contigs using Reads Islands at iteration 10: 0

*****  Assembly extension and merging using Unmapped and discordantly mapped reads: process completed  *****

10: Re-alignment on updated assembly for Local mis-assemblies/false chimeras identification process

10: Identification of Local mis-assemblies/false chimeras: Process started
Number of split chimeric contigs in iteration 10: 1
Number of updated contigs for local mis-assemblies in iteration 10: 3
*****  Identification of Local mis-assemblies/false chimeras: Process completed  *****

Outer iteration:11 started.
Inner iteration:1 started.
11-1: Alignment started for fragmented and partial contigs process using soft-clipping

Alignment ended

11-1: Assembly extension using soft clipped reads started
Extended incomplete contigs using soft-clipping at iteration 11-1: 0
Assembly extension using soft clipped reads ended

11-1: Fastq files filtering process started.
Fastq file filtering step ended

***** Assembly merging using soft-clipped-extended ends: Process started *****

Merged incomplete contigs using Soft-clipping at iteration 11-2: 0
***** Assembly extension and merging using soft clipped reads: Process completed *****

11: Re-alignment on updated assembly for fragmented and partial contigs process using Unmapped and discordantly mapped reads

11: Assembly extension and merging using Unmapped and discordantly mapped reads: process started
No. of extended contigs by Cap3 at iteration : 0
Merged fragmented contigs using Reads Islands at iteration 11: 1

*****  Assembly extension and merging using Unmapped and discordantly mapped reads: process completed  *****

11: Re-alignment on updated assembly for Local mis-assemblies/false chimeras identification process

11: Identification of Local mis-assemblies/false chimeras: Process started
Number of split chimeric contigs in iteration 11: 0
Number of updated contigs for local mis-assemblies in iteration 11: 0
*****  Identification of Local mis-assemblies/false chimeras: Process completed  *****

Outer iteration:12 started.
Inner iteration:1 started.
12-1: Alignment started for fragmented and partial contigs process using soft-clipping

Alignment ended

12-1: Assembly extension using soft clipped reads started
Extended incomplete contigs using soft-clipping at iteration 12-1: 0
Assembly extension using soft clipped reads ended

12-1: Fastq files filtering process started.
Fastq file filtering step ended

***** Assembly merging using soft-clipped-extended ends: Process started *****

Merged incomplete contigs using Soft-clipping at iteration 12-2: 0
***** Assembly extension and merging using soft clipped reads: Process completed *****

12: Re-alignment on updated assembly for fragmented and partial contigs process using Unmapped and discordantly mapped reads

12: Assembly extension and merging using Unmapped and discordantly mapped reads: process started
No. of extended contigs by Cap3 at iteration : 0
Merged fragmented contigs using Reads Islands at iteration 12: 1

*****  Assembly extension and merging using Unmapped and discordantly mapped reads: process completed  *****

12: Re-alignment on updated assembly for Local mis-assemblies/false chimeras identification process

12: Identification of Local mis-assemblies/false chimeras: Process started
Number of split chimeric contigs in iteration 12: 0
Number of updated contigs for local mis-assemblies in iteration 12: 0
*****  Identification of Local mis-assemblies/false chimeras: Process completed  *****

Outer iteration:13 started.
Inner iteration:1 started.
13-1: Alignment started for fragmented and partial contigs process using soft-clipping

Alignment ended

13-1: Assembly extension using soft clipped reads started
Extended incomplete contigs using soft-clipping at iteration 13-1: 0
Assembly extension using soft clipped reads ended

13-1: Fastq files filtering process started.
Fastq file filtering step ended

***** Assembly merging using soft-clipped-extended ends: Process started *****

Merged incomplete contigs using Soft-clipping at iteration 13-2: 0
***** Assembly extension and merging using soft clipped reads: Process completed *****

13: Re-alignment on updated assembly for fragmented and partial contigs process using Unmapped and discordantly mapped reads

13: Assembly extension and merging using Unmapped and discordantly mapped reads: process started
No. of extended contigs by Cap3 at iteration : 0
Merged fragmented contigs using Reads Islands at iteration 13: 0

*****  Assembly extension and merging using Unmapped and discordantly mapped reads: process completed  *****

13: Re-alignment on updated assembly for Local mis-assemblies/false chimeras identification process

13: Identification of Local mis-assemblies/false chimeras: Process started
Number of split chimeric contigs in iteration 13: 0
Number of updated contigs for local mis-assemblies in iteration 13: 0
*****  Identification of Local mis-assemblies/false chimeras: Process completed  *****



*****************************************************************
                         Process completed                         
*****************************************************************

No. of contigs in initial assembly: 
8330
Total number of merges occurred: 252
Total number of splits occurred: 879
Number of cap3 asemblies merged to main contigs by Ns: 24
No. of contigs in Final assembly: 
8772
Total number of extensions occurred: 4084
Total number of updated sequences: 1216

*****************************************************************
*****************************************************************
