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"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
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@HD	VN:1.0	SO:coordinate
@SQ	SN:1	LN:248956422
@SQ	SN:2	LN:242193529
@SQ	SN:3	LN:198295559
@SQ	SN:4	LN:190214555
@SQ	SN:5	LN:181538259
@SQ	SN:6	LN:170805979
@SQ	SN:7	LN:159345973
@SQ	SN:8	LN:145138636
@SQ	SN:9	LN:138394717
@SQ	SN:10	LN:133797422
@SQ	SN:11	LN:135086622
@SQ	SN:12	LN:133275309
@SQ	SN:13	LN:114364328
@SQ	SN:14	LN:107043718
@SQ	SN:15	LN:101991189
@SQ	SN:16	LN:90338345
@SQ	SN:17	LN:83257441
@SQ	SN:18	LN:80373285
@SQ	SN:19	LN:58617616
@SQ	SN:20	LN:64444167
@SQ	SN:21	LN:46709983
@SQ	SN:22	LN:50818468
@SQ	SN:X	LN:156040895
@SQ	SN:Y	LN:57227415
@SQ	SN:MT	LN:16569
@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"
@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"
@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"
@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
@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"
@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
@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
@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
@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"
@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
@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
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
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
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
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
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
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
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
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
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
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
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
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
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:-
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