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comparison test-data/output_pairs_split.pairs @ 3:060f0fed864e draft

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planemo upload for repository https://github.com/open2c/pairtools commit 162c595b19e442f40be4c2f5434b20b56ade52d4
author iuc
date Tue, 30 Apr 2024 12:02:15 +0000
parents bffcba7ce9b5
children
comparison
equal deleted inserted replaced
2:53d73d58e105 3:060f0fed864e
37 #samheader: @SQ SN:chrXV LN:1091291 37 #samheader: @SQ SN:chrXV LN:1091291
38 #samheader: @SQ SN:chrXVI LN:948066 38 #samheader: @SQ SN:chrXVI LN:948066
39 #samheader: @PG ID:bwa PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane1.00.1.fastq.gz MATalpha_R1.lane1.00.2.fastq.gz 39 #samheader: @PG ID:bwa PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane1.00.1.fastq.gz MATalpha_R1.lane1.00.2.fastq.gz
40 #samheader: @PG ID:pairtools_parse-1.2 PN:pairtools_parse CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam PP:bwa VN:1.0.2 40 #samheader: @PG ID:pairtools_parse-1.2 PN:pairtools_parse CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam PP:bwa VN:1.0.2
41 #samheader: @PG ID:pairtools_sort-1.3 PN:pairtools_sort CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs PP:pairtools_parse-1.2 VN:1.0.2 41 #samheader: @PG ID:pairtools_sort-1.3 PN:pairtools_sort CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs PP:pairtools_parse-1.2 VN:1.0.2
42 #samheader: @PG ID:pairtools_dedup-1.4 PN:pairtools_dedup CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools dedup -o output_dedup_pairs_markdups.pairsam --mark-dups --output-stats output_dedup_pairs.stats output_sorted_pairs.pairsam PP:pairtools_sort-1.3 VN:1.0.2 42 #samheader: @PG ID:pairtools_dedup-1.4 PN:pairtools_dedup CL:/usr/local/bin/pairtools dedup /tmp/tmpp1v7bap4/files/3/7/9/dataset_379f0c04-3329-4201-9b3c-3c3a66e7eec4.dat -o /tmp/tmpp1v7bap4/job_working_directory/000/6/outputs/dataset_6f9ee270-56fb-4c2e-92f4-509340f9eb58.dat --mark-dups --output-stats /tmp/tmpp1v7bap4/job_working_directory/000/6/outputs/dataset_653a5918-ae05-4cfe-8fc9-4ecc516aeaf1.dat --nproc-in 1 --nproc-out 1 PP:pairtools_sort-1.3 VN:1.1.0
43 #samheader: @PG ID:pairtools_split-1.5 PN:pairtools_split CL:/usr/local/bin/pairtools split /tmp/tmpnt_hb134/files/7/4/2/dataset_7420fb9f-e3dd-4326-8cef-1e023c2b5e85.dat --output-pairs /tmp/tmpnt_hb134/job_working_directory/000/2/outputs/dataset_ba891b58-22e9-49f5-83f9-063b56eda346.dat --output-sam ./output.bam --nproc-in 1 --nproc-out 1 PP:pairtools_dedup-1.4 VN:1.0.3 43 #samheader: @PG ID:pairtools_split-1.5 PN:pairtools_split CL:/usr/local/bin/pairtools split /tmp/tmpms_dxt0a/files/8/b/9/dataset_8b97afbd-6770-4cb4-8bf1-fdc78bbce0af.dat --output-pairs /tmp/tmpms_dxt0a/job_working_directory/000/2/outputs/dataset_da90611d-b0d1-447c-ae61-f9ac7147d51d.dat --output-sam ./output.bam --nproc-in 1 --nproc-out 1 PP:pairtools_dedup-1.4 VN:1.1.0
44 #samheader: @PG ID:bwa-2CCE5976 PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane1.01.1.fastq.gz MATalpha_R1.lane1.01.2.fastq.gz 44 #samheader: @PG ID:bwa-2CCE5976 PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane1.01.1.fastq.gz MATalpha_R1.lane1.01.2.fastq.gz
45 #samheader: @PG ID:pairtools_parse-2.2 PN:pairtools_parse CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam PP:bwa-2CCE5976 VN:1.0.2 45 #samheader: @PG ID:pairtools_parse-2.2 PN:pairtools_parse CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam PP:bwa-2CCE5976 VN:1.0.2
46 #samheader: @PG ID:pairtools_sort-2.3 PN:pairtools_sort CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs PP:pairtools_parse-2.2 VN:1.0.2 46 #samheader: @PG ID:pairtools_sort-2.3 PN:pairtools_sort CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs PP:pairtools_parse-2.2 VN:1.0.2
47 #samheader: @PG ID:pairtools_dedup-2.4 PN:pairtools_dedup CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools dedup -o output_dedup_pairs_markdups.pairsam --mark-dups --output-stats output_dedup_pairs.stats output_sorted_pairs.pairsam PP:pairtools_sort-2.3 VN:1.0.2 47 #samheader: @PG ID:pairtools_dedup-2.4 PN:pairtools_dedup CL:/usr/local/bin/pairtools dedup /tmp/tmpp1v7bap4/files/3/7/9/dataset_379f0c04-3329-4201-9b3c-3c3a66e7eec4.dat -o /tmp/tmpp1v7bap4/job_working_directory/000/6/outputs/dataset_6f9ee270-56fb-4c2e-92f4-509340f9eb58.dat --mark-dups --output-stats /tmp/tmpp1v7bap4/job_working_directory/000/6/outputs/dataset_653a5918-ae05-4cfe-8fc9-4ecc516aeaf1.dat --nproc-in 1 --nproc-out 1 PP:pairtools_sort-2.3 VN:1.1.0
48 #samheader: @PG ID:pairtools_split-2.5 PN:pairtools_split CL:/usr/local/bin/pairtools split /tmp/tmpnt_hb134/files/7/4/2/dataset_7420fb9f-e3dd-4326-8cef-1e023c2b5e85.dat --output-pairs /tmp/tmpnt_hb134/job_working_directory/000/2/outputs/dataset_ba891b58-22e9-49f5-83f9-063b56eda346.dat --output-sam ./output.bam --nproc-in 1 --nproc-out 1 PP:pairtools_dedup-2.4 VN:1.0.3 48 #samheader: @PG ID:pairtools_split-2.5 PN:pairtools_split CL:/usr/local/bin/pairtools split /tmp/tmpms_dxt0a/files/8/b/9/dataset_8b97afbd-6770-4cb4-8bf1-fdc78bbce0af.dat --output-pairs /tmp/tmpms_dxt0a/job_working_directory/000/2/outputs/dataset_da90611d-b0d1-447c-ae61-f9ac7147d51d.dat --output-sam ./output.bam --nproc-in 1 --nproc-out 1 PP:pairtools_dedup-2.4 VN:1.1.0
49 #samheader: @PG ID:bwa-3CAFD9D9 PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane2.00.1.fastq.gz MATalpha_R1.lane2.00.2.fastq.gz 49 #samheader: @PG ID:bwa-3CAFD9D9 PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane2.00.1.fastq.gz MATalpha_R1.lane2.00.2.fastq.gz
50 #samheader: @PG ID:pairtools_parse-3.2 PN:pairtools_parse CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam PP:bwa-3CAFD9D9 VN:1.0.2 50 #samheader: @PG ID:pairtools_parse-3.2 PN:pairtools_parse CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam PP:bwa-3CAFD9D9 VN:1.0.2
51 #samheader: @PG ID:pairtools_sort-3.3 PN:pairtools_sort CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs PP:pairtools_parse-3.2 VN:1.0.2 51 #samheader: @PG ID:pairtools_sort-3.3 PN:pairtools_sort CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs PP:pairtools_parse-3.2 VN:1.0.2
52 #samheader: @PG ID:pairtools_dedup-3.4 PN:pairtools_dedup CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools dedup -o output_dedup_pairs_markdups.pairsam --mark-dups --output-stats output_dedup_pairs.stats output_sorted_pairs.pairsam PP:pairtools_sort-3.3 VN:1.0.2 52 #samheader: @PG ID:pairtools_dedup-3.4 PN:pairtools_dedup CL:/usr/local/bin/pairtools dedup /tmp/tmpp1v7bap4/files/3/7/9/dataset_379f0c04-3329-4201-9b3c-3c3a66e7eec4.dat -o /tmp/tmpp1v7bap4/job_working_directory/000/6/outputs/dataset_6f9ee270-56fb-4c2e-92f4-509340f9eb58.dat --mark-dups --output-stats /tmp/tmpp1v7bap4/job_working_directory/000/6/outputs/dataset_653a5918-ae05-4cfe-8fc9-4ecc516aeaf1.dat --nproc-in 1 --nproc-out 1 PP:pairtools_sort-3.3 VN:1.1.0
53 #samheader: @PG ID:pairtools_split-3.5 PN:pairtools_split CL:/usr/local/bin/pairtools split /tmp/tmpnt_hb134/files/7/4/2/dataset_7420fb9f-e3dd-4326-8cef-1e023c2b5e85.dat --output-pairs /tmp/tmpnt_hb134/job_working_directory/000/2/outputs/dataset_ba891b58-22e9-49f5-83f9-063b56eda346.dat --output-sam ./output.bam --nproc-in 1 --nproc-out 1 PP:pairtools_dedup-3.4 VN:1.0.3 53 #samheader: @PG ID:pairtools_split-3.5 PN:pairtools_split CL:/usr/local/bin/pairtools split /tmp/tmpms_dxt0a/files/8/b/9/dataset_8b97afbd-6770-4cb4-8bf1-fdc78bbce0af.dat --output-pairs /tmp/tmpms_dxt0a/job_working_directory/000/2/outputs/dataset_da90611d-b0d1-447c-ae61-f9ac7147d51d.dat --output-sam ./output.bam --nproc-in 1 --nproc-out 1 PP:pairtools_dedup-3.4 VN:1.1.0
54 #samheader: @PG ID:bwa-4548A671 PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane2.01.1.fastq.gz MATalpha_R1.lane2.01.2.fastq.gz 54 #samheader: @PG ID:bwa-4548A671 PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane2.01.1.fastq.gz MATalpha_R1.lane2.01.2.fastq.gz
55 #samheader: @PG ID:samtools PN:samtools PP:bwa-4548A671 VN:1.19.2 CL:samtools view -s 0.1 -b -@ 4 -o subset.bam test.bam 55 #samheader: @PG ID:samtools PN:samtools PP:bwa-4548A671 VN:1.19.2 CL:samtools view -s 0.1 -b -@ 4 -o subset.bam test.bam
56 #samheader: @PG ID:pairtools_parse-4.3 PN:pairtools_parse CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam PP:samtools VN:1.0.2 56 #samheader: @PG ID:pairtools_parse-4.3 PN:pairtools_parse CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam PP:samtools VN:1.0.2
57 #samheader: @PG ID:pairtools_sort-4.4 PN:pairtools_sort CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs PP:pairtools_parse-4.3 VN:1.0.2 57 #samheader: @PG ID:pairtools_sort-4.4 PN:pairtools_sort CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs PP:pairtools_parse-4.3 VN:1.0.2
58 #samheader: @PG ID:pairtools_dedup-4.5 PN:pairtools_dedup CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools dedup -o output_dedup_pairs_markdups.pairsam --mark-dups --output-stats output_dedup_pairs.stats output_sorted_pairs.pairsam PP:pairtools_sort-4.4 VN:1.0.2 58 #samheader: @PG ID:pairtools_dedup-4.5 PN:pairtools_dedup CL:/usr/local/bin/pairtools dedup /tmp/tmpp1v7bap4/files/3/7/9/dataset_379f0c04-3329-4201-9b3c-3c3a66e7eec4.dat -o /tmp/tmpp1v7bap4/job_working_directory/000/6/outputs/dataset_6f9ee270-56fb-4c2e-92f4-509340f9eb58.dat --mark-dups --output-stats /tmp/tmpp1v7bap4/job_working_directory/000/6/outputs/dataset_653a5918-ae05-4cfe-8fc9-4ecc516aeaf1.dat --nproc-in 1 --nproc-out 1 PP:pairtools_sort-4.4 VN:1.1.0
59 #samheader: @PG ID:pairtools_split-4.6 PN:pairtools_split CL:/usr/local/bin/pairtools split /tmp/tmpnt_hb134/files/7/4/2/dataset_7420fb9f-e3dd-4326-8cef-1e023c2b5e85.dat --output-pairs /tmp/tmpnt_hb134/job_working_directory/000/2/outputs/dataset_ba891b58-22e9-49f5-83f9-063b56eda346.dat --output-sam ./output.bam --nproc-in 1 --nproc-out 1 PP:pairtools_dedup-4.5 VN:1.0.3 59 #samheader: @PG ID:pairtools_split-4.6 PN:pairtools_split CL:/usr/local/bin/pairtools split /tmp/tmpms_dxt0a/files/8/b/9/dataset_8b97afbd-6770-4cb4-8bf1-fdc78bbce0af.dat --output-pairs /tmp/tmpms_dxt0a/job_working_directory/000/2/outputs/dataset_da90611d-b0d1-447c-ae61-f9ac7147d51d.dat --output-sam ./output.bam --nproc-in 1 --nproc-out 1 PP:pairtools_dedup-4.5 VN:1.1.0
60 #columns: readID chrom1 pos1 chrom2 pos2 strand1 strand2 pair_type 60 #columns: readID chrom1 pos1 chrom2 pos2 strand1 strand2 pair_type
61 HWI-ST560:29:B0A7LABXX:2:1101:15566:24141 chrI 3199 chrI 3399 + - UU 61 HWI-ST560:29:B0A7LABXX:2:1101:15566:24141 chrI 3199 chrI 3399 + - UU
62 HWI-ST560:29:B0A7LABXX:2:1101:18861:21891 chrI 35431 chrI 35703 + - UU 62 HWI-ST560:29:B0A7LABXX:2:1101:18861:21891 chrI 35431 chrI 35703 + - UU
63 HWUSI-EAS1533_0033_FC:1:1:2785:5545 chrI 50947 chrI 51201 + - UU 63 HWUSI-EAS1533_0033_FC:1:1:2785:5545 chrI 50947 chrI 51201 + - UU
64 HWI-ST560:29:B0A7LABXX:2:1101:19121:14576 chrI 85708 chrI 85934 + - UU 64 HWI-ST560:29:B0A7LABXX:2:1101:19121:14576 chrI 85708 chrI 85934 + - UU