Mercurial > repos > jjohnson > bamutil_diff
comparison test-data/diff_only2_in2.sam @ 0:2cafa8420c04 draft default tip
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
| author | jjohnson |
|---|---|
| date | Fri, 26 Mar 2021 13:16:53 +0000 |
| parents | |
| children |
comparison
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| -1:000000000000 | 0:2cafa8420c04 |
|---|---|
| 1 @HD VN:1.0 SO:coordinate | |
| 2 @SQ SN:1 LN:248956422 | |
| 3 @SQ SN:2 LN:242193529 | |
| 4 @SQ SN:3 LN:198295559 | |
| 5 @SQ SN:4 LN:190214555 | |
| 6 @SQ SN:5 LN:181538259 | |
| 7 @SQ SN:6 LN:170805979 | |
| 8 @SQ SN:7 LN:159345973 | |
| 9 @SQ SN:8 LN:145138636 | |
| 10 @SQ SN:9 LN:138394717 | |
| 11 @SQ SN:10 LN:133797422 | |
| 12 @SQ SN:11 LN:135086622 | |
| 13 @SQ SN:12 LN:133275309 | |
| 14 @SQ SN:13 LN:114364328 | |
| 15 @SQ SN:14 LN:107043718 | |
| 16 @SQ SN:15 LN:101991189 | |
| 17 @SQ SN:16 LN:90338345 | |
| 18 @SQ SN:17 LN:83257441 | |
| 19 @SQ SN:18 LN:80373285 | |
| 20 @SQ SN:19 LN:58617616 | |
| 21 @SQ SN:20 LN:64444167 | |
| 22 @SQ SN:21 LN:46709983 | |
| 23 @SQ SN:22 LN:50818468 | |
| 24 @SQ SN:X LN:156040895 | |
| 25 @SQ SN:Y LN:57227415 | |
| 26 @SQ SN:MT LN:16569 | |
| 27 @PG ID:hisat2 PN:hisat2 VN:2.1.0 CL:"/home/galaxy/galaxy/miniconda2/envs/mulled-v1-e7321ba46fa5ea4c6b9a06b78e6cd5182b33c0a47c2c86b5d610e1361f8b1686/bin/hisat2-align-s --wrapper basic-0 -p 4 -x /panfs/roc/rissdb/galaxy/genomes/GRCh38_canon/hisat2_index/GRCh38_canon/GRCh38_canon --pen-cansplice 0 --pen-noncansplice 12 --pen-canintronlen G,-8.0,1.0 --pen-noncanintronlen G,-8.0,1.0 --known-splicesite-infile splice_sites.txt --min-intronlen 20 --max-intronlen 500000 --dta -1 input_f.fastq -2 input_r.fastq" | |
| 28 @PG ID:hisat2-55424A4 PN:hisat2 VN:2.1.0 CL:"/home/galaxy/galaxy/miniconda2/envs/mulled-v1-e7321ba46fa5ea4c6b9a06b78e6cd5182b33c0a47c2c86b5d610e1361f8b1686/bin/hisat2-align-s --wrapper basic-0 -p 4 -x /panfs/roc/rissdb/galaxy/genomes/GRCh38_canon/hisat2_index/GRCh38_canon/GRCh38_canon --pen-cansplice 0 --pen-noncansplice 12 --pen-canintronlen G,-8.0,1.0 --pen-noncanintronlen G,-8.0,1.0 --known-splicesite-infile splice_sites.txt --min-intronlen 20 --max-intronlen 500000 --dta -1 input_f.fastq -2 input_r.fastq" | |
| 29 @PG ID:hisat2-55424A4-3A2CCEF5 PN:hisat2 VN:2.1.0 CL:"/home/galaxy/galaxy/miniconda2/envs/mulled-v1-e7321ba46fa5ea4c6b9a06b78e6cd5182b33c0a47c2c86b5d610e1361f8b1686/bin/hisat2-align-s --wrapper basic-0 -p 4 -x /panfs/roc/rissdb/galaxy/genomes/GRCh38_canon/hisat2_index/GRCh38_canon/GRCh38_canon --pen-cansplice 0 --pen-noncansplice 12 --pen-canintronlen G,-8.0,1.0 --pen-noncanintronlen G,-8.0,1.0 --known-splicesite-infile splice_sites.txt --min-intronlen 20 --max-intronlen 500000 --dta -1 input_f.fastq -2 input_r.fastq" | |
| 30 @PG ID:samtools PN:samtools PP:hisat2-55424A4-3A2CCEF5 VN:1.11 CL:samtools sort -@ 1 -m 10240M -T sorttemp -O sam -o 0.sam /panfs/roc/galaxy/PRODUCTION/database/files/001/075/dataset_1075445.dat | |
| 31 @PG ID:hisat2-3A2CCEF5 PN:hisat2 VN:2.1.0 CL:"/home/galaxy/galaxy/miniconda2/envs/mulled-v1-e7321ba46fa5ea4c6b9a06b78e6cd5182b33c0a47c2c86b5d610e1361f8b1686/bin/hisat2-align-s --wrapper basic-0 -p 4 -x /panfs/roc/rissdb/galaxy/genomes/GRCh38_canon/hisat2_index/GRCh38_canon/GRCh38_canon --pen-cansplice 0 --pen-noncansplice 12 --pen-canintronlen G,-8.0,1.0 --pen-noncanintronlen G,-8.0,1.0 --known-splicesite-infile splice_sites.txt --min-intronlen 20 --max-intronlen 500000 --dta -1 input_f.fastq -2 input_r.fastq" | |
| 32 @PG ID:samtools-6ADB4A65 PN:samtools PP:hisat2-3A2CCEF5 VN:1.11 CL:samtools sort -@ 1 -m 10240M -T sorttemp -O sam -o 1.sam /panfs/roc/galaxy/PRODUCTION/database/files/001/075/dataset_1075446.dat | |
| 33 @PG ID:samtools.1 PN:samtools PP:samtools VN:1.11 CL:samtools merge -@ 1 -s 1 -f -h /panfs/roc/galaxy/PRODUCTION/database/files/001/075/dataset_1075446.dat /panfs/roc/galaxy/PRODUCTION/database/files/001/075/dataset_1075449.dat 0.sam 1.sam | |
| 34 @PG ID:samtools.2 PN:samtools PP:samtools-6ADB4A65 VN:1.11 CL:samtools merge -@ 1 -s 1 -f -h /panfs/roc/galaxy/PRODUCTION/database/files/001/075/dataset_1075446.dat /panfs/roc/galaxy/PRODUCTION/database/files/001/075/dataset_1075449.dat 0.sam 1.sam | |
| 35 @PG ID:hisat2-6ADB4A65 PN:hisat2 VN:2.1.0 CL:"/home/galaxy/galaxy/miniconda2/envs/mulled-v1-e7321ba46fa5ea4c6b9a06b78e6cd5182b33c0a47c2c86b5d610e1361f8b1686/bin/hisat2-align-s --wrapper basic-0 -p 4 -x /panfs/roc/rissdb/galaxy/genomes/GRCh38_canon/hisat2_index/GRCh38_canon/GRCh38_canon --pen-cansplice 0 --pen-noncansplice 12 --pen-canintronlen G,-8.0,1.0 --pen-noncanintronlen G,-8.0,1.0 --known-splicesite-infile splice_sites.txt --min-intronlen 20 --max-intronlen 500000 --dta -1 input_f.fastq -2 input_r.fastq" | |
| 36 @PG ID:samtools.3 PN:samtools PP:samtools.1 VN:1.11 CL:samtools merge -@ 1 -s 1 -f -h /panfs/roc/galaxy/PRODUCTION/database/files/001/075/dataset_1075453.dat /panfs/roc/galaxy/PRODUCTION/database/files/001/075/dataset_1075522.dat 0.sam 1.sam | |
| 37 @PG ID:samtools.4 PN:samtools PP:samtools.2 VN:1.11 CL:samtools merge -@ 1 -s 1 -f -h /panfs/roc/galaxy/PRODUCTION/database/files/001/075/dataset_1075453.dat /panfs/roc/galaxy/PRODUCTION/database/files/001/075/dataset_1075522.dat 0.sam 1.sam | |
| 38 NB500964:249:HHLFNBGX7:4:11510:10074:3541 163 6 52995646 60 75M = 52995715 144 ATCTGTCACCCCATTGATCGCCAGGGTTGATTCGGCTGATCTGGCTGGCTAGGCGGGTGTCCCCTTCCTCCCTCA AAAAAEE/EEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEAEE/ AS:i:0 MD:Z:75 NM:i:0 NH:i:1 XN:i:0 XM:i:0 ZS:i:0 XO:i:0 XG:i:0 YS:i:0 YT:Z:CP | |
| 39 NB500964:249:HHLFNBGX7:2:13209:7691:13203 163 6 52995675 60 75M = 52995789 189 ATTCGGCTGATCTGGCTGGCTAGGCGGGTGTCCCCTTCCTCCCTCACCGCTCCATGTGCGTCCCTCCCGAAGCTG AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEEEEEEAEEEEE AS:i:0 MD:Z:75 NM:i:0 NH:i:1 XN:i:0 XM:i:0 ZS:i:0 XO:i:0 XG:i:0 YS:i:0 YT:Z:CP | |
| 40 NB500964:249:HHLFNBGX7:4:11510:10074:3541 83 6 52995715 60 75M = 52995646 -144 CCCTCACCGCTCCATGTGCGTCCCTCCCGAAGCTGCGCGCTCGGTCGAAGAGGACGACCATCCCCGATAGAGGAG EEEAEEE/EAEAEEEAEEE<EAEEEEEEEEEEEEEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEAAAAA AS:i:0 MD:Z:75 NM:i:0 NH:i:1 XN:i:0 XM:i:0 ZS:i:0 XO:i:0 XG:i:0 YS:i:0 YT:Z:CP | |
| 41 NB500964:249:HHLFNBGX7:3:21512:8039:1524 163 6 52995730 60 75M = 52995836 181 GTGCGTCCCTCCCGAAGCTGCGCGCTCGGTCGAAGAGGACGACCATCCCCGATAGAGGAGGACCGGTCTTCGGTC AAAAAEEAEEEEEEEEEEEEEAE/EEE/EEEEEEEAEEEEE/EEEEEEEEEE/EAEEEEAEEEEEAEAEAA/EEE AS:i:0 MD:Z:75 NM:i:0 NH:i:1 XN:i:0 XM:i:0 ZS:i:0 XO:i:0 XG:i:0 YS:i:0 YT:Z:CP | |
| 42 NB500964:249:HHLFNBGX7:2:13209:7691:13203 83 6 52995789 60 75M = 52995675 -189 GGACCGGTCTTCGGTCAAGGGTATACGAGTAGCTGCGCTCCCCTGCTAGAACCTCCAAACAAGCTCTCAAGGTCC EAAAA<<AEEAEEEEEAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA AS:i:0 MD:Z:75 NM:i:0 NH:i:1 XN:i:0 XM:i:0 ZS:i:0 XO:i:0 XG:i:0 YS:i:0 YT:Z:CP | |
| 43 NB500964:249:HHLFNBGX7:4:21507:2226:9226 163 6 52995797 60 75M = 52995834 112 CTTCGGTCAAGGGTATACGAGTAGCTGCGCTCCCCTGCTAGAACCTCCAAACAAGCTCTCAAGGTCCATTTGTAG AAAAAEEEEEEEEEEE/EEAEEEEEEEE/EEEEE/EEEEEAA//EEEE/E/EE/EEEE/E<E/AEE/6EEEEE/E AS:i:0 MD:Z:75 NM:i:0 NH:i:1 XN:i:0 XM:i:0 ZS:i:0 XO:i:0 XG:i:0 YS:i:-3 YT:Z:CP | |
| 44 NB500964:249:HHLFNBGX7:4:21602:10644:5676 163 6 52995802 60 75M = 52995834 107 GTCAAGGGTATACGAGTAGCTGCGCTCCCCTGCTAGAACCTCCAAACAAGCTCTCAAGGTCCATTTGTAGGAGAA AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE AS:i:0 MD:Z:75 NM:i:0 NH:i:1 XN:i:0 XM:i:0 ZS:i:0 XO:i:0 XG:i:0 YS:i:0 YT:Z:CP | |
| 45 NB500964:249:HHLFNBGX7:4:21507:2226:9226 83 6 52995834 60 75M = 52995797 -112 CTAGAACCTCCAAACAACCTCTCAAGGTCCATTTGTAGGAGAACGTAGGGTAGTCAAGCTTCCAAGACTCCAGAC AEEEEE<EEEEEEEAEA/<A//EEEEEEEEEEEAEE/EEAAE/EAE/EE</AE/EEEEAEEEEEEEEEEEAAAAA AS:i:-3 MD:Z:17G57 NM:i:1 NH:i:1 XN:i:0 XM:i:1 XO:i:0 XG:i:0 YS:i:0 YT:Z:CP | |
| 46 NB500964:249:HHLFNBGX7:4:21602:10644:5676 83 6 52995834 60 75M = 52995802 -107 CTAGAACCTCCAAACAAGCTCTCAAGGTCCATTTGTAGGAGAACGTAGGGTAGTCAAGCTTCCAAGACTCCAGAC EEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE6AAAA AS:i:0 MD:Z:75 NM:i:0 NH:i:1 XN:i:0 XM:i:0 XO:i:0 XG:i:0 YS:i:0 YT:Z:CP | |
| 47 NB500964:249:HHLFNBGX7:3:21512:8039:1524 83 6 52995836 60 75M = 52995730 -181 AGAACCTCCAAACAAGCTCTCAAGGTCCATTTGTAGGAGAACGTAGGGTAGTCAAGCTTCCAAGACTCCAGACAC /EA/EEEEAE/E/A</E/E/6/EEEEEEEE/EEEEE/EEEEEAEEEEEEEE6EEEEAE6EEEEEEEEEEEAAAAA AS:i:0 MD:Z:75 NM:i:0 NH:i:1 XN:i:0 XM:i:0 XO:i:0 XG:i:0 YS:i:0 YT:Z:CP | |
| 48 NB500964:249:HHLFNBGX7:3:13604:19654:15542 99 6 53004731 60 75M = 53004936 280 CTTAAATTGCACCCCTGTTGCAATACTGCATTAATATTATTACATTTTTCAAAATCTGTAGAAAATATTATCTGG AAAAAEEEEEEEA//EEEEEEEEEEEEEEAEEEEEEEEEEEEAEE/EEEEEEEEEEEEEEEEE/EEEEEEE/EEE AS:i:0 MD:Z:75 NM:i:0 NH:i:1 XN:i:0 XM:i:0 XO:i:0 XG:i:0 YS:i:0 YT:Z:CP | |
| 49 NB500964:249:HHLFNBGX7:3:13604:19654:15542 147 6 53004936 60 75M = 53004731 -280 AATAATTTTATACAAAAAAGCCTACTGCATTCAAATCAATATTTTAAAAAAAAACTTTAAAAAAGAATATTGACA EEEEEAEEEEEEEEEEEEEAEE/EAEEEEEEEEEEEEEEEEEEEEEEEEEEAEAAEEAEEEEAAEEEEEEAAAAA AS:i:0 MD:Z:75 NM:i:0 NH:i:1 XN:i:0 XM:i:0 XO:i:0 XG:i:0 YS:i:0 YT:Z:CP | |
| 50 NB500964:249:HHLFNBGX7:3:12402:8344:2452 99 6 73519463 60 54M366N21M = 73519916 162 CTCAGCTTTCAGTTTATCCAAGACCCAGGCATACTTGAAGGAGCCCTTTCGCATCTCAGCAGCCTCCTTCTCAAA A6AAAEE6EEE6/EEEE/<EEEE/<EEEEEEEEEEEE//EEE/E<E/////<E/A/AA///AAEEE<//E</</A AS:i:-3 MD:Z:50C24 NM:i:1 NH:i:1 XN:i:0 XM:i:1 ZS:i:-3 XO:i:0 XG:i:0 YS:i:-9 YT:Z:CP XS:A:- | |
| 51 NB500964:249:HHLFNBGX7:3:12402:8344:2452 147 6 73519916 60 75M = 73519463 -162 TCTTTTGGCGATGCCACCGCATTTATAGATCAGATGGCCAGTAGTGGTGGACTTGCCCGAAGCTACGGGTCCAAT /EEAE6</EE//EEE//AEEEA/EE/<//AE/EE/E//AEAA/EAAAA/AE6EE///E//A/EAE6E/EE/AAAA AS:i:-9 MD:Z:7T53T5T7 NM:i:3 NH:i:1 XN:i:0 XM:i:3 ZS:i:-9 XO:i:0 XG:i:0 YS:i:-3 YT:Z:CP |