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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:"/panfs/roc/galaxy/shared/miniconda3/envs/mulled-v1-e7321ba46fa5ea4c6b9a06b78e6cd5182b33c0a47c2c86b5d610e1361f8b1686/bin/hisat2-align-s --wrapper basic-0 -p 4 -x /panfs/roc/risdb/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:"/panfs/roc/galaxy/shared/miniconda3/envs/mulled-v1-e7321ba46fa5ea4c6b9a06b78e6cd5182b33c0a47c2c86b5d610e1361f8b1686/bin/hisat2-align-s --wrapper basic-0 -p 4 -x /panfs/roc/risdb/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_1075444.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_1075450.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_1075450.dat 0.sam 1.sam
@PG	ID:hisat2-6ADB4A65	PN:hisat2	VN:2.1.0	CL:"/panfs/roc/galaxy/shared/miniconda3/envs/mulled-v1-e7321ba46fa5ea4c6b9a06b78e6cd5182b33c0a47c2c86b5d610e1361f8b1686/bin/hisat2-align-s --wrapper basic-0 -p 4 -x /panfs/roc/risdb/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_1075454.dat /panfs/roc/galaxy/PRODUCTION/database/files/001/075/dataset_1075523.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_1075454.dat /panfs/roc/galaxy/PRODUCTION/database/files/001/075/dataset_1075523.dat 0.sam 1.sam
NB500964:249:HHLFNBGX7:1:12312:5087:3846	163	6	52995649	60	75M	=	52995848	274	TGTCACCCCATTGATCGCCAGGGTTGATTCGGCTGATCTGGCTGGCTAGGCGGGTGTCCCCTTCCTCCCTCACCG	AAAA/EEEE6EEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEE6EEEEEEEE/EEEEEEEEEEEEEEEEEE/EE/	AS:i:0	MD:Z:75	NM:i:0	NH:i:1	XN:i:0	XM:i:0	ZS:i:-1	XO:i:0	XG:i:0	YS:i:-2	YT:Z:CP
NB500964:249:HHLFNBGX7:2:23304:14989:7965	129	6	52995665	1	75M	2	32916255	0	GCCAGGGTTGATTCGGCTGATCTGGCTGGCTAGGCGGGTGTCCCCTTCCTCCCTCACCGCTCCATGTGCGTCCCT	AAAAAEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEE<AE	AS:i:0	MD:Z:75	NM:i:0	NH:i:2	XN:i:0	XM:i:0	ZS:i:0	XO:i:0	XG:i:0	YT:Z:UP
NB500964:249:HHLFNBGX7:4:13611:22454:15447	419	6	52995667	1	75M	=	52995712	120	CAGGGTTGATTCGGCTGATCTGGCTGGCTAGGCGGGTGTCCCCTTCCTCCCTCACCGCTCCATGTGCGTCCCTCC	AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEEEE	AS:i:0	MD:Z:75	NM:i:0	NH:i:2	XN:i:0	XM:i:0	ZS:i:0	XO:i:0	XG:i:0	YS:i:0	YT:Z:CP
NB500964:249:HHLFNBGX7:3:12409:4568:1161	163	6	52995706	60	75M	=	52995785	154	CCCCTTCCTCCCTCACCGCTCCATGTGCGTCCCTCCCGAAGCTGCGCGCTCGGTCGAAGAGGACGACCATCCCCG	AA/AAEEAEEAAAAEEAEEEEEEEEEEE/EEAEEEEEEEAEEEE<EEAEEEEEEEAA<EEAE<AA/AEAEAEEAA	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:HHLFNBGX7:4:21406:23062:17974	163	6	52995706	60	75M	=	52995825	194	CCCCTTCCTCCCTCACCGCTCCATGTGCGTCCCTCCCGAAGCTGCGCGCTCGGTCGAAGAGGACGACCATCCCCG	AAAAAEEEEEAEEEEAEEEAEEAAEEEEE/AEEEEE<EAEAEEEEEEEEEA/EEEEEEAEEEEAE<EE6E<E6EE	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:HHLFNBGX7:4:13611:22454:15447	339	6	52995712	1	75M	=	52995667	-120	CCTCCCTCACCGCTCCATGTGCGTCCCTCCCGAAGCTGCGCGCTCGGTCGAAGAGGACGACCATCCCCGATAGAG	EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA	AS:i:0	MD:Z:75	NM:i:0	NH:i:2	XN:i:0	XM:i:0	ZS:i:0	XO:i:0	XG:i:0	YS:i:0	YT:Z:CP
NB500964:249:HHLFNBGX7:3:23507:21978:1662	163	6	52995758	60	75M	=	52995835	151	GTCGAAGAGGACGACCATCCCCGATAGAGGAGGACCTGTCTTCGGTCAAGGGTATACTAGTAGCTGCGCTCCCCT	AA/AAEEE6EAEEEAEEEEEEAEEE6EEE/EEA/EA/E/EEEEEEEEEEAEEEEEEE/E/66/<E<A<A6A////	AS:i:-6	MD:Z:36G20G17	NM:i:2	NH:i:1	XN:i:0	XM:i:2	ZS:i:-6	XO:i:0	XG:i:0	YS:i:-8	YT:Z:CP
NB500964:249:HHLFNBGX7:2:11209:14749:12659	163	6	52995766	60	75M	=	52995834	143	GGACGACCATCCCCGATAGAGGAGGACCGGTCTTCGGTCAAGGGTATACGAGTAGCTGCGCTCCCCTGCTAGAAC	AAAAA/EEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEAEAE<EEAEEEEEEE<6E	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:HHLFNBGX7:3:12409:4568:1161	83	6	52995785	60	75M	=	52995706	-154	AGGAGGACCGGTCTTCGGTCAAGGGTATACGAGTAGCTGCGCTCCCCTGCTAGAACCTCCAAACAAGCTCTCAAG	</EA<AEEE/EAAEEAAEAE/EEEEEEEEEAEEEEEEEEAEEAEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAAA	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:HHLFNBGX7:4:21406:23062:17974	83	6	52995825	60	75M	=	52995706	-194	GCTCCCCTGCTAGAACCTCCAAACAAGCTCTCAAGGTCCATTTGTAGGAGAACGTAGGGTAGTCAAGCTTCCAAG	EAEEA<<A/EEEEE/EEEEEEEEEEEEEE/EEAE/EEEEEE/EAEE<AEAEEEEEEEEEEEAAA/EEEEEA6AAA	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:HHLFNBGX7:2:13103:3678:13730	89	6	52995829	60	75M	=	52995829	0	CCCTGCTAGAACCTCCAAACAAGCTCTCAAGGTCCATTTGTAGGAGAACGTAGGGTAGTCAAGCTTCCAAGACTC	EEEEEEEAAEEEEAAEEEEAEAEEEEEEEEEE/EEEEEEEEEEAEEEAEEEEAEEEEEEEE6EAEEEAAEAAAAA	AS:i:0	MD:Z:75	NM:i:0	NH:i:1	XN:i:0	XM:i:0	XO:i:0	XG:i:0	YT:Z:UP
NB500964:249:HHLFNBGX7:2:11209:14749:12659	83	6	52995834	60	75M	=	52995766	-143	CTAGAACCTCCAAACAAGCTCTCAAGGTCCATTTGTAGGAGAACGTAGGGTAGTCAAGCTTCCAAGACTCCAGAC	EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA	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:HHLFNBGX7:3:23507:21978:1662	83	6	52995835	60	1S73M1S	=	52995758	-151	GTAGAACCTCCAAACAATCTCTCAAGGTCCATTTGTAGGAGAACGTAGTGTAGTCAAGCTTCCAAGACTCCAGAA	//E/EE/A/6/E/E/EE//E/E/E/<6EE/EAEE//E<A/EE///EEA/EEEEEEEAE6EEEEAEAE6EEAAA6A	AS:i:-8	MD:Z:16G30G25	NM:i:2	NH:i:1	XN:i:0	XM:i:2	XO:i:0	XG:i:0	YS:i:-6	YT:Z:CP
NB500964:249:HHLFNBGX7:4:12611:5420:13168	81	6	52995838	60	74M1S	2	32916257	0	AACCTCCAAACAAGCTCTCAAGGTCCATTTGTAGGAGAACGTAGGGTAGTCAAGCTTCCAAGACTCCAGACACAC	EEEEAEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEAAAAA	AS:i:-1	MD:Z:74	NM:i:0	NH:i:1	XN:i:0	XM:i:0	XO:i:0	XG:i:0	YT:Z:UP
NB500964:249:HHLFNBGX7:1:12312:5087:3846	83	6	52995848	60	73M2S	=	52995649	-274	CAAGCTCTCAAGGTCCATTTGTAGGAGAACGTAGGGTAGTCAAGCTTCCAAGACTCCAGACACATCCAAATGAAG	<EEEEEEEEEEEEAEEEEEEEEAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA	AS:i:-2	MD:Z:73	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:HHLFNBGX7:3:21607:1536:15142	99	6	73518202	60	63M89N12M	=	73518250	118	GTGGCAATCCAATACAGGGGCATAGCCGGCGCTTATTTGGCCTGGATGGTTCAGGATAATCACCTGAGCAGTGAA	AAAAAEEEEEEEEEEEAEEA/EEEEAEAEAEEEEEEEAEEE<EAA/EEEEE<EEAE/EA</A/AAAAAEAA/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:-2	YT:Z:CP	XS:A:-
NB500964:249:HHLFNBGX7:3:21607:1536:15142	147	6	73518250	60	2S15M89N58M	=	73518202	-118	TTGTTCAGGATAATCACCTGAGCAGTGAAGCCAGCTGCTTCCATTGGTGGGTCATTTTTGCTGTCACCAGCAACG	A/<EAEEA//<//EA/AEAEE/EEA//EE<EEE/EEA/AEEEEEAAAEE/E/EEEEEEEEEEE/EEEEEEAAAAA	AS:i:-2	MD:Z:73	NM:i:0	NH:i:1	XN:i:0	XM:i:0	ZS:i:-2	XO:i:0	XG:i:0	YS:i:0	YT:Z:CP	XS:A:-
NB500964:249:HHLFNBGX7:2:21106:19199:5423	99	6	73519036	1	75M	=	73519096	135	CCTTAACAATTTCCTCATATCTCTTCTGGCTGTAGGGTGGCTCAGTGGAATCCATTTTGTTAACACCGACAATTA	AAAAAEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE	AS:i:0	MD:Z:75	NM:i:0	NH:i:3	XN:i:0	XM:i:0	ZS:i:0	XO:i:0	XG:i:0	YS:i:0	YT:Z:CP
NB500964:249:HHLFNBGX7:2:21106:19199:5423	147	6	73519096	1	75M	=	73519036	-135	TAACACCGACAATTAGTTGTTTCACACCCAGTGTGTAAGCCAGAAGGGCATGCTCTCGGGTCTGCCCATTCTTGG	EEEEEEEEEEEEE<EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE/EEEEEEEEEEEEEEEAAAAA	AS:i:0	MD:Z:75	NM:i:0	NH:i:3	XN:i:0	XM:i:0	ZS:i:0	XO:i:0	XG:i:0	YS:i:0	YT:Z:CP
NB500964:249:HHLFNBGX7:1:23112:23126:11688	355	6	73519370	1	75M	=	73519434	139	GTCTCTGTGTCCTGGGGCATCAATGATAGTCACATAGTACTTGCTGGTCTCAAATTTCCACAAGGAGATATCAAT	AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEAEEEEEEEEEEEEEEEE	AS:i:0	MD:Z:75	NM:i:0	NH:i:2	XN:i:0	XM:i:0	ZS:i:0	XO:i:0	XG:i:0	YS:i:0	YT:Z:CP
NB500964:249:HHLFNBGX7:1:23112:23126:11688	403	6	73519434	1	75M	=	73519370	-139	GAGATATCAATGGTGATACCACGTTCACGCTCAGCTTTCAGTTTATCCAAGACCCAGGCATACTTGAAGGAGCCC	EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEAEEEEEEEEEEEEAAAAA	AS:i:0	MD:Z:75	NM:i:0	NH:i:2	XN:i:0	XM:i:0	ZS:i:0	XO:i:0	XG:i:0	YS:i:0	YT:Z:CP