Picard update v.3.1.0 #5348

gallardoalba · 2023-06-06T18:48:29Z

FOR CONTRIBUTOR:

- I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
- License permits unrestricted use (educational + commercial)
- This PR adds a new tool or tool collection
- This PR updates an existing tool or tool collection
- This PR does something else (explain below)

gallardoalba · 2023-09-01T15:35:40Z

~~Everything seems to be fine, except the wrapper piccardCollectRnaSeqMetrics.xml, which shows the following error:~~

Job in error state.. tool_id: picard_CollectRnaSeqMetrics, exit_code: 127, stderr: /tmp/tmp4rglmtho/job_working_directory/000/8/tool_script.sh: line 9: picard: command not found
~~Could you have a look? @bgruening @bernt-matthias? I reviewed it, but I'm not able to find the problem. Thanks a lot!~~

tools/picard/picard_AddOrReplaceReadGroups.xml

https://github.com/bioconda/bioconda-recipes/blob/master/recipes/picard/meta.yaml#L21 I hope that helps the solver and fixes 4 of our 5 problems. The 5th problem is a simsize of BAM files, you should not use simsize here, just diff.

…to Update_piccard

bgruening · 2023-09-07T06:20:34Z

tools/picard/test-data/picard_CASM_test1.tab


+## HISTOGRAM	java.lang.Integer


That file does not look like a .tab anymore. Or it looks like 2 files in one. Is that expected?

bgruening · 2023-09-07T06:21:18Z

tools/picard/test-data/picard_CollectWgsMetrics_test1.tab

-16568	2.915862	3.835741	2	2	0	0	0	0.000041	0.008069	0	0.00811	0.684633	0.240464	0.055831	0.02541	0.010985	0	0	0	0	0	0	0	0	0	0.544024	3
+## METRICS CLASS	picard.analysis.WgsMetrics
+GENOME_TERRITORY	MEAN_COVERAGE	SD_COVERAGE	MEDIAN_COVERAGE	MAD_COVERAGE	PCT_EXC_ADAPTER	PCT_EXC_MAPQ	PCT_EXC_DUPE	PCT_EXC_UNPAIRED	PCT_EXC_BASEQ	PCT_EXC_OVERLAP	PCT_EXC_CAPPED	PCT_EXC_TOTAL	PCT_1X	PCT_5X	PCT_10X	PCT_15X	PCT_20X	PCT_25X	PCT_30X	PCT_40X	PCT_50X	PCT_60X	PCT_70X	PCT_80X	PCT_90X	PCT_100X	FOLD_80_BASE_PENALTY	FOLD_90_BASE_PENALTY	FOLD_95_BASE_PENALTY	HET_SNP_SENSITIVITY	HET_SNP_Q
+16568	2.915862	3.835741	2	2	0	0	0	0	0.000041	0.008069	0	0.00811	0.684633	0.240464	0.055831	0.02541	0.010985	0	0	0	0	0	0	0	0	0	?	?	?	0.544024	3


Are those ? expected?

bgruening · 2023-09-07T06:22:35Z

tools/picard/test-data/pos_details

-sample-a	tumor-a	A	T	AAG	52	0	265	0	0	0	0	100
-sample-a	tumor-a	A	T	AAT	240	0	1358	0	0	0	0	100
-sample-a	tumor-a	A	T	CAA	101	0	573	0	0	0	0	100
+picard_ARRG.bam	picard_ARRG.bam	A	C	AAA	58	0	857	0	0	0	0	100


sample-a tumar-a looked better in the last version as two times the file-name, do we know why this is happening?

bgruening · 2023-09-07T06:22:45Z

tools/picard/test-data/pos_summary

-sample-a	tumor-a	T	A	100	ATA	100	ATN	100	NTA	100	NA
-sample-a	tumor-a	T	C	100	GTA	24	CTN	29	NTG	30	NA
-sample-a	tumor-a	T	G	100	ATA	100	ATN	100	NTA	100	NA
+picard_ARRG.bam	picard_ARRG.bam	A	C	35	TAA	26	CAN	34	NAA	28	NA


tools/picard/picard_macros.xml

bgruening · 2023-09-07T10:19:41Z

Lets try the 3.1 version. If it fails, feel free to revert it.

bernt-matthias · 2023-09-08T13:13:12Z

Picard uses format="sam,bam" at many places. This should probably be sam,unsorted.bam.

mvdbeek · 2023-09-09T13:09:01Z

This should probably be sam,unsorted.bam.

After checking that this doesn't change runtime and memory characteristics negatively (i think there's a good chance it would) this could be done in another PR. I don't think anyone's really using sam anymore, and if so, it's likely old and therefor often small data.

macros/read_group_macros.xml

…to Update_piccard

bgruening

Awesome work @gallardoalba

gallardoalba · 2023-09-26T14:25:10Z

Awesome work @gallardoalba

Test didn't run again at all, not sure why

gallardoalba · 2023-09-26T14:53:20Z

This is the problem:
.. WARNING: Conditional [read_group_lb_conditional] first param of type="boolean" is discouraged, use a select

bgruening · 2023-09-26T14:55:33Z

We can igrnore this lint error.

But this is also failing now:

Output outFile:  different than expected, difference (using diff):
( /tmp/local_bam_converted_to_sam_m_mvyp3v.sam v. /tmp/history_bam_converted_to_sam_61d2szdz.sam )
--- local_file
+++ history_data
@@ -1,345 +1,345 @@
 @HD	VN:1.6	SO:coordinate
 @SQ	SN:gi|251831106|ref|NC_012920.1|	LN:16569
-@RG	ID:picard_ARRG.bam	LB:picard_ARRG.bam	PL:ILLUMINA	SM:picard_ARRG.bam	PU:run-1
+@RG	ID:id-1	LB:tumor-a	PL:ILLUMINA	SM:sample-a	PU:run-1
 @PG	ID:bwa	PN:bwa	VN:0.7.10-r837-dirty	CL:bwa mem -t 1 -v 1 localref.fa /Users/anton/galaxy-central/database/files/000/dataset_526.dat /Users/anton/galaxy-central/database/files/000/dataset_527.dat
-M01368:8:000000000-A3GHV:1:1101:6911:8255	73	gi|251831106|ref|NC_012920.1|	1	60	71S180M	=	1	0	ATCTGGTTCCTACTTCAGGGCCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATT	BCCCCFFFFFFFGGGGGGGGGGGHHHHGHGHHHHHHHHHGGGGGGHHHHGHHHHHHHHHHGHHHHHHGGHGGHHHGHHHHFHHGHHHHHHHHHGHEHEFFGHHEGGCEFGGFHHHBGHHGHHHHGHFHHHGHGHGHGGCDFDDACGGGGGGGAAFFFFFFFFFBAFFFFFB;FFFFFFADDFFFFFFFFFFEFFFFFFFFFFBFFFFFFFFFFFFFFEFFFFFFFFBFEFFFFEFE;DFFFDFBFF/9BFB	SA:Z:gi|251831106|ref|NC_012920.1|,16499,+,71M180S,60,2;	MD:Z:72A107	RG:Z:picard_ARRG.bam	NM:i:1	AS:i:175	XS:i:0
-M01368:8:000000000-A3GHV:1:1101:6911:8255	133	gi|251831106|ref|NC_012920.1|	1	0	*	=	1	0	TCGCCTTACCGCTACTCACCCACGGCGGCCATCAGCCGATACTAAGTTTGGGGTATGGTGGGGGGGATAATGAATTAGGTTGTGGGGGAGGGTTTGTGGTTGAGAGAAACACAAAAAACAATCTTATATATGGGTAGTCGTTTTGTATTGGTTTTTTGTTTTGTTTGTGTTTTGAGTGTCGGTTTAGTTCGGTGTACTAGGGGGGGTGGATGGGGTCGGCTGGTGAGGGGGTCTTAGTGTATTGAGTGTGG	1>11111@11111A111A100000000////011110//>>/12@1@22B/////1@>21/>>/-----9/;////9////--;-;-;-----;--------9/-/-///9-;-------9//////9/////-//-/9-;-;9--/////99-;--9-:-;----/---/-----////---9-/////--;A-//////---------9/-----;-----/-/-----;--;//////////9;///-	RG:Z:picard_ARRG.bam	AS:i:0	XS:i:0
-M01368:8:000000000-A3GHV:1:1101:14518:9998	163	gi|251831106|ref|NC_012920.1|	1	60	10S241M	=	1	242	CATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATAA	CCCCCFCCCCCFGGGGGGGGGGHHHHHHHHHHHHHHHHGFHHHHGGGGGHGFHHHHHHHHHHHHHHHHHHHGHGGEHGGGGCGGGHHGGCGGGGGHHGHHHGGGGGGGG.BFFFGAGADFGAFDGFGGCFFF;DDFFFFFFFFFFFFFFFFFFEFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFF09FFFE00;BE@;DABBFFFFFBBFB00;F:9;FFBFFF9BFFFFFFFFFFFFF90/::BFFFBF0	MD:Z:72A168	RG:Z:picard_ARRG.bam	NM:i:1	AS:i:236	XS:i:0
-M01368:8:000000000-A3GHV:1:1101:18422:19051	99	gi|251831106|ref|NC_012920.1|	1	60	80S171M	=	1	228	GTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACG	CCCCCFDDDDDFGGGGGGGGGGHHHHHHHHHHHHHHHHGHHHHHHFHHHHGGGGHHHHHHHHHGHHHHHHHHHHHHGGHGGHHHHHHHHHHHHHHHHHHHHHHHHHHHGHHHHHGCGGGHHHHHHHHHHHHHHHHHHHHHHGFDHGFHCFGGGGFGGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF;FFFFFFFFFFFFFFFFFFFFFFFFFFFFEFBFFFFFFFFFF:FFF.	SA:Z:gi|251831106|ref|NC_012920.1|,16490,+,80M171S,60,1;	MD:Z:72A98	RG:Z:picard_ARRG.bam	NM:i:1	AS:i:166	XS:i:0
-M01368:8:000000000-A3GHV:1:1101:25545:21098	163	gi|251831106|ref|NC_012920.1|	1	60	113S138M	=	1	216	GCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTTCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCAACCTATGTCGCAGTATCTGTCTTTGAT	3AAA34BFFFFFGCGGCGGGCGHHHGHHHHCGHFGHFHGFGGCDGGBD5FGFFFHFHGGGHAEBFGHHHEHGGFHBGGFHHHGGGEEFHHHFHFFHDHGHGHHHHFFHHGGFAEGFFFFFBGHHHFFHHHHHHHFHFHHFHGFHGHGA/<@EFHEHH1GGHFFFHG1>=FGHFHGF.GE//-<BB?9.9BFFFB==AA/FFFFFA-@BA.;;D?F9FAB;---./99BFFFBBAE-.9B/BFB9F/9BFBB	SA:Z:gi|251831106|ref|NC_012920.1|,16457,+,113M138S,60,1;	MD:Z:72A1G36C26	RG:Z:picard_ARRG.bam	NM:i:3	AS:i:123	XS:i:0
-M01368:8:000000000-A3GHV:1:1101:5446:12248	163	gi|251831106|ref|NC_012920.1|	1	60	78S173M	=	1	213	ATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTT	CCDDDCCCCFFFGGGGGGGGGGHHHHHGHHHHHHHHGHHHHHHGHHHHGGGGHHHHHHHHHHHHHHHHHHHHHHGGGGGHHHHHHHGFGHHHHHHHHHHHHHHHHHGHHHHHGGGGGHHHHHHHHHHHHHHHGHHHHHHGHGHGHHGGGGGGGGGGGFFFFFFFFFFFFFFAFFFFFFFFFFFFFBFC?.EAFFFFFFFFAFFFFFFFFFFFFFFFEFFFF0FFFFFFF0BFFFFFFFFF?.BDCFFEDA/	SA:Z:gi|251831106|ref|NC_012920.1|,16492,+,78M173S,60,1;	MD:Z:72A100	RG:Z:picard_ARRG.bam	NM:i:1	AS:i:168	XS:i:0
-M01368:8:000000000-A3GHV:1:1101:5861:6452	163	gi|251831106|ref|NC_012920.1|	1	60	80S171M	=	1	236	TTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACG	BCCCCFBBCCCFGGGGGGGGGGHHHHHHHHHHHHHHHHGHHHHHHHHHHHGGGGHHHHHHHHGHHHHHHHHHHHHHGGHGGHHHHHHHGHHHHHHHHHHHHHHHHHHHGGHHHHGGGGGGEHGHHHHHHHHHHHGHHHHHHGHGHGHGGGGCGGGGGFFFFFFFFFFFFFFFFFFFFFFFF?FFEAF:DAEF9DEFFFFFFF-A.BFFFFFEFFFFEFFFFFFFF0FFEB0FFFFBFFFFFFADEFCF0/.	SA:Z:gi|251831106|ref|NC_012920.1|,16490,+,80M171S,60,2;	MD:Z:72A98	RG:Z:picard_ARRG.bam	NM:i:1	AS:i:166	XS:i:0
-M01368:8:000000000-A3GHV:1:1102:10403:6021	99	gi|251831106|ref|NC_012920.1|	1	60	121S130M	=	1	151	CGCTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTG	>A@AAAAD2ADDFFGGGGGFGGHA?EAEFBEAGHFABFGG5FDF5DB1EEGAFDFB53FF5FH@G5FFEHGHEFHFFHBE333GF43GCGGGGE@0?BFGGB0B?FHGFDGGHHHBFFDEGGHGFFFDFE@<1>@FFFGHHHHFHEFGDABFFGG/@DCE<CG1<GF0/DD000=<DHGBDFDCECE/:AC?-;-;9B/ABBB-AD9BFB99AB?BDFBAD-.9..@;=;;..9..9/9;BEF;A:9/BFF	SA:Z:gi|251831106|ref|NC_012920.1|,16449,+,121M130S,60,1;	MD:Z:72A57	RG:Z:picard_ARRG.bam	NM:i:1	AS:i:125	XS:i:0
-M01368:8:000000000-A3GHV:1:1102:10677:23253	99	gi|251831106|ref|NC_012920.1|	1	60	22S213M16S	=	1	213	CCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTAATTCTGTCTCTTATACACA	ABBBBFFFFFFFGGGGGGGCGGGHHHHHGHHHHHHHHHGHHHHHHHHHHHGHHHHHGGGGGHGHHHHHHHHHHHHHBGFHHHHGHGHGGHGGGCGGGHHHGGGGGGGHHHGHGGGGGGGGGGGGGGGGGGGGFFFFFFFFFFFFFFDFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFEDBDFFFFFFFEFFFE0F0FBFFFF0FFFFFFFFFFFFFFFFF:	MD:Z:72A140	RG:Z:picard_ARRG.bam	NM:i:1	AS:i:208	XS:i:0
-M01368:8:000000000-A3GHV:1:1102:13809:1733	163	gi|251831106|ref|NC_012920.1|	1	60	50S179M22S	=	1	179	NATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATCTGTCTCTTATACACATCTGAC	#>AABBFFCFFFGGGFGGGGGGGGHHHHHHHHHHHHHHHHHHGHHHGGEGGFFHHHHHHGHGHGHHHHHEHFHGHHHHEFHHGHGGGGGHHHHGHHHHHHHHHGFGHHHHHGHGHGHHGGGCCGGGGFGGGGGGDGGGGFGDGGGFFFFFFEFFFFFFFBAF:9AF//;BEF-DD/FFFFBFFFFFFFFFEBFF?FB;/;//BFFEFFE/::..9;-:B9:FBFFFFFFBFB/9/FFF/B///99/:B///	SA:Z:gi|251831106|ref|NC_012920.1|,16520,+,50M201S,60,2;	MD:Z:72A106	RG:Z:picard_ARRG.bam	NM:i:1	AS:i:174	XS:i:0
-M01368:8:000000000-A3GHV:1:1102:17584:10050	163	gi|251831106|ref|NC_012920.1|	1	60	52S138M61S	=	1	138	GTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGATCTAGTGGAGATCTTGGGGGGTGG	ABCCCFFFFFCFGGGGGGGGGGGGGGHHHHHHHHHHHHHHHHGHHHFHGGHGGHHHHHHHHHHHHHHGHHHGGHHHHHHHGGHHHHGGGGGHHHHHHHHHHHHHHGGHHHHHHGHGHGGHGGFGGGGGGGGGGFGGFGGGGGGGGGFFFFFFFFFFEFFCFAAFEFEFFFFFFFCFDFFFFFFEFFFFFFFFFFBFFFFFFF/:BFFFFFFFFFFFFFFFFAFC=@-.;A///B././//////.-9----	SA:Z:gi|251831106|ref|NC_012920.1|,16518,+,52M199S,60,1;	MD:Z:72A65	RG:Z:picard_ARRG.bam	NM:i:1	AS:i:133	XS:i:0
-M01368:8:000000000-A3GHV:1:1102:18842:24844	99	gi|251831106|ref|NC_012920.1|	1	60	105S146M	=	1	228	CACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCT	BBBCBFF@CCBBGGGGGGGGGGHHGHGGHHHGGGGGHHHHHHHHHHHHHHHHHHHHHHHHHHHGHHHHHHFHHHHGGGGGHHHHHHHHHHHHHHHHHHHHGGGHGGHHHHHHGHBFGHHHHHHHHBGHHHHHHGHGGGHFGCGGFHHFHFFHHBHHHHFFHFHHHHGGDHGGBC?;@DFBFFFFFFFFFBFFFFFFFFFFFFFF.B?FB.@;;DFFFFFFFFFFFEE-A./BBBFBFBFFF//BFB/BFF/	SA:Z:gi|251831106|ref|NC_012920.1|,16465,+,105M146S,60,1;	MD:Z:72A73	RG:Z:picard_ARRG.bam	NM:i:1	AS:i:141	XS:i:0
-M01368:8:000000000-A3GHV:1:1102:21788:11027	99	gi|251831106|ref|NC_012920.1|	1	60	35S213M3S	=	1	213	GCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTAATTCTG	ABCCBCCBBFFFGGGGGGGGGGGHGHHHHHHGGHGGHHHHHHHHGHHHHHHHHHHHHHHHHHHGHHHHHFGGGGHHHHHHHHHHHHHHHHHHHHHHGHGHGGFCGGCGGGHHHGGGGGGGGGGGGGGGGGGGGGGGGGFFFFFFFFFFFFFFFFFFFFFDFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFEF9EFFFFFFFFFFFBFF0FFBBBBFBFBFFFF0	SA:Z:gi|251831106|ref|NC_012920.1|,16535,+,35M216S,60,0;	MD:Z:72A140	RG:Z:picard_ARRG.bam	NM:i:1	AS:i:208	XS:i:0
-M01368:8:000000000-A3GHV:1:1102:5728:8777	163	gi|251831106|ref|NC_012920.1|	1	60	105S146M	=	1	179	CACTTGGGAGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCC	BBBBBFFBBBBFGGGGGGGDGGHHHHHFHHHGGGGGHHGFHFHHFHHHGGHHHHHHHHHHHHHGHHHHHHFGHHHGGGGHHHHHHHHHGHHHGHHHHFHHHGGHGGHFFHHHHGFHHHHHHHHHHFHFHHHFHFHHHHHGGGGGHGHHHHHGHHHHHHH/FHHHHHGHGGGHHGGFBFFFFFFFFFF;DDFFFFFFF;;BA.=DDBFFFFF;-DFF.EDFFFFFFEF-AFFFFFB;FBFFFBFFFFB9B..	SA:Z:gi|251831106|ref|NC_012920.1|,16465,+,105M146S,60,2;	MD:Z:72A72T0	RG:Z:picard_ARRG.bam	NM:i:2	AS:i:140	XS:i:0
-M01368:8:000000000-A3GHV:1:1102:5983:21093	99	gi|251831106|ref|NC_012920.1|	1	60	80S171M	=	1	177	GTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACG	AAABCFCABBCFGGGGGGGGGGHHHHHHGFHHHHHHHHGGHHHGHGHHHGGGGFHHHHHHHHGHHHHHHHHHHHHHGGHGGHHHHHHFHGGHHHHFHGHHEHHHHHHHGHHHHHD@FGGHHHHHFFFHHGGHGH?DHHHHHGHGHEGG/@?ADGFGGFFFFAFFFFFFFFFFFFFFFFFFFFFFFAAFFFFFFDFFFFFFFF;D9BFFFFFFFFFFFFFFFFFEFFFBBFFF0BFFFBBFF0EFFFFFFFA	SA:Z:gi|251831106|ref|NC_012920.1|,16490,+,80M171S,60,1;	MD:Z:72A98	RG:Z:picard_ARRG.bam	NM:i:1	AS:i:166	XS:i:0
-M01368:8:000000000-A3GHV:1:1102:7765:18353	99	gi|251831106|ref|NC_012920.1|	1	60	119S132M	=	1	236	CTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTC	CCDCCCCCCBCFGGGGGGGGGGGGGGGHHHHHHDHHHHHHHHHHHGGGGGHHGHGHHHGHHHHHHFHHHHGHHHHHHGHGHHHGHHHHHGGGGHHHHHHHHHHHHHHHHHHHHHHGGHGGHHHHHHHGFFHHHHHGHHHHHHHHHHHGHHHHHGCFGGHGHFHHGHGHGHHHHGGFHHHHGGGHGBFGCC=BFFFFFFFF-@DFFFFFFFFFFFFFFFFFFFFFFAFFAEF.::FBFBFFE-A9:BFFFF0	SA:Z:gi|251831106|ref|NC_012920.1|,16451,+,119M132S,60,1;	MD:Z:72A59	RG:Z:picard_ARRG.bam	NM:i:1	AS:i:127	XS:i:0
-M01368:8:000000000-A3GHV:1:1103:10405:17879	99	gi|251831106|ref|NC_012920.1|	1	60	80S171M	=	1	228	GTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACG	CBCCCFCCCCCFGGGGGGGGGGHHHHHHHHHHHHGHHHGHHHHHHHHHHHGGGGGGHHHHHHHHHHHHHHHHHHHHGGHGGHHHGHHGHHGHHHHHHHHHCGGFHHHHGHHHHHGCFGGHHGHHHHHHGFHHHGHHHHHHHGHGHGFF/CC?ADAFGFFFFFFFFFFFFFFDFFFFFFFFAFFFFFFFFFFFEDFFFFFFFFFFAFFFFFFFFFFFFFFFFFFFFFFBBFBFBFFFFFFFFFFFFFFFFF?	SA:Z:gi|251831106|ref|NC_012920.1|,16490,+,80M171S,60,1;	MD:Z:72A98	RG:Z:picard_ARRG.bam	NM:i:1	AS:i:166	XS:i:0
********
*SNIP *
********
+M01368:8:000000000-A3GHV:1:1108:16350:22621	2131	gi|251831106|ref|NC_012920.1|	16520	60	50M201H	=	1	-16569	CATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATG	/FFE;/FFFFFFFAF99.EB;.DEDA;EFEFFFFFBFGF0FFB;.?BB:0	SA:Z:gi|251831106|ref|NC_012920.1|,1,-,50S201M,60,1;	MD:Z:6G43	RG:Z:id-1	NM:i:1	AS:i:45	XS:i:0
+M01368:8:000000000-A3GHV:1:1111:9655:13916	2195	gi|251831106|ref|NC_012920.1|	16520	60	50M201H	=	1	-16569	CATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATG	:FBEF;0FFFFFFFBFFFFFEADEFBFFFFFFGGGFGFFBBB/F.GGFC9	SA:Z:gi|251831106|ref|NC_012920.1|,1,-,50S201M,60,3;	MD:Z:6G43	RG:Z:id-1	NM:i:1	AS:i:45	XS:i:0
+M01368:8:000000000-A3GHV:1:1108:21791:23272	2131	gi|251831106|ref|NC_012920.1|	16522	60	48M203H	=	1	-16569	TAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATG	/.FFFFFBBFBFBFFFEFEEFFFDFFFFFFFB//BBEFFB/.AABBFF	SA:Z:gi|251831106|ref|NC_012920.1|,1,-,48S203M,60,1;	MD:Z:4G43	RG:Z:id-1	NM:i:1	AS:i:43	XS:i:0
+M01368:8:000000000-A3GHV:1:1111:8665:25542	2195	gi|251831106|ref|NC_012920.1|	16522	60	48M203H	=	1	-16569	TAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATG	/EFB:BFFBB/AB.DDA:;.;.FDD?B/F/FFFFBFB;FBB?EGFGGG	SA:Z:gi|251831106|ref|NC_012920.1|,1,-,48S203M,60,2;	MD:Z:4G43	RG:Z:id-1	NM:i:1	AS:i:43	XS:i:0
+M01368:8:000000000-A3GHV:1:1106:23625:4236	2195	gi|251831106|ref|NC_012920.1|	16524	60	46M205H	=	1	-16569	AAACCTAAATAGCCCACCCGTTCCCCTTAAATAAGACATCACGATG	;/:/9/B;/./:@9-9..A9AAFFBFBBFFFB/BB:B:/:.DGFC;	SA:Z:gi|251831106|ref|NC_012920.1|,1,-,46S205M,60,1;	MD:Z:2G14A28	RG:Z:id-1	NM:i:2	AS:i:38	XS:i:0
+M01368:8:000000000-A3GHV:1:1103:25465:20010	2211	gi|251831106|ref|NC_012920.1|	16525	60	45M206H	=	1	-16406	AACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATG	AAABBFFFFFDFGGGGGGGGGGHHHHHHGHHHGFHHHHHHHGGGG	SA:Z:gi|251831106|ref|NC_012920.1|,1,+,45S120M86S,60,2;	MD:Z:1G43	RG:Z:id-1	NM:i:1	AS:i:43	XS:i:0
+M01368:8:000000000-A3GHV:1:1105:7169:17145	2147	gi|251831106|ref|NC_012920.1|	16525	60	45M206H	=	1	-16275	AACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATG	CCCCCFFFFFFFGGGGGGGGGGHHHHHHHHHHHBHHHHHHHGGHG	SA:Z:gi|251831106|ref|NC_012920.1|,1,+,45S206M,60,1;	MD:Z:1G43	RG:Z:id-1	NM:i:1	AS:i:43	XS:i:0
+M01368:8:000000000-A3GHV:1:1108:7626:10048	2211	gi|251831106|ref|NC_012920.1|	16525	60	45M206H	=	1	-16388	AACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATG	BCCDDFFFFFFFGGGGGGGGGGHHHHHHHHHHHHHHHHHHHGGGG	SA:Z:gi|251831106|ref|NC_012920.1|,1,+,45S138M68S,60,1;	MD:Z:1G43	RG:Z:id-1	NM:i:1	AS:i:43	XS:i:0
+M01368:8:000000000-A3GHV:1:1114:16639:15258	2147	gi|251831106|ref|NC_012920.1|	16527	60	43M208H	=	1	-16287	CCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATG	11>>ABFFFFFFGGCGC1BBF1GHHHBHHHHGFHGH1A100AA	SA:Z:gi|251831106|ref|NC_012920.1|,1,+,43S208M,60,4;	MD:Z:43	RG:Z:id-1	NM:i:0	AS:i:43	XS:i:0
+M01368:8:000000000-A3GHV:1:1103:17657:20856	2195	gi|251831106|ref|NC_012920.1|	16527	60	5H43M203H	=	1	-16569	CCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATG	FFEFFF?FEFFFFEAA.;AAFFF:0FB0FFBFFFB:A9A90FF	SA:Z:gi|251831106|ref|NC_012920.1|,1,-,48S203M,60,2;	MD:Z:43	RG:Z:id-1	NM:i:0	AS:i:43	XS:i:0
+M01368:8:000000000-A3GHV:1:1103:25465:20010	2131	gi|251831106|ref|NC_012920.1|	16527	60	88H43M120H	=	1	-16569	CCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATG	HFHHHGAFA<.HFGHGGGGGHGGDDGHHHHFHFHGGFC?HGHH	SA:Z:gi|251831106|ref|NC_012920.1|,1,-,131S120M,60,2;	MD:Z:43	RG:Z:id-1	NM:i:0	AS:i:43	XS:i:0
+M01368:8:000000000-A3GHV:1:1106:15481:16176	2131	gi|251831106|ref|NC_012920.1|	16527	60	5H43M203H	=	1	-16569	CCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATG	FFFFFB.FEFAA:EFFE:.;AFBB;FFFFFFFGFF/FEDFGGG	SA:Z:gi|251831106|ref|NC_012920.1|,1,-,48S203M,60,1;	MD:Z:43	RG:Z:id-1	NM:i:0	AS:i:43	XS:i:0
+M01368:8:000000000-A3GHV:1:1107:24817:14233	2195	gi|251831106|ref|NC_012920.1|	16527	60	5H43M203H	=	1	-16569	CCTAAATAGCCCACACTTTCCCCTTAAATAAGACATCACGATG	FB;BF:A/.A.9///;.DAFFFBBFFBB9BB/;BFFA:.BFFF	SA:Z:gi|251831106|ref|NC_012920.1|,1,-,48S203M,60,2;	MD:Z:16G26	RG:Z:id-1	NM:i:1	AS:i:38	XS:i:0
+M01368:8:000000000-A3GHV:1:1107:24830:14440	2195	gi|251831106|ref|NC_012920.1|	16527	60	5H43M203H	=	1	-16569	CCTAACTAGCCCACACGTTCCCCTTAAATAAGACATCACGATG	FFFB:.;/A.9.BAEDA.?FA//;/FFFFFFFFGFC:.ABB9B	SA:Z:gi|251831106|ref|NC_012920.1|,1,-,48S203M,60,1;	MD:Z:5A37	RG:Z:id-1	NM:i:1	AS:i:38	XS:i:0
+M01368:8:000000000-A3GHV:1:1108:7626:10048	2131	gi|251831106|ref|NC_012920.1|	16527	60	70H43M138H	=	1	-16569	CCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATG	GFHHHHHHGGGHGGHGGGGGGHHHFGGGGHHGFHHHF<GGHHH	SA:Z:gi|251831106|ref|NC_012920.1|,1,-,113S138M,60,1;	MD:Z:43	RG:Z:id-1	NM:i:0	AS:i:43	XS:i:0
+M01368:8:000000000-A3GHV:1:1114:14540:5315	2131	gi|251831106|ref|NC_012920.1|	16527	60	5H43M203H	=	1	-16569	CCTAAATAGCCCCCACGTTCCCCTTAAATAAGACATCACGATG	09BFBB:--A=-.A;FEBFFFFFFFFFFFFFFFC//?AA0EFF	SA:Z:gi|251831106|ref|NC_012920.1|,1,-,48S203M,60,1;	MD:Z:12A30	RG:Z:id-1	NM:i:1	AS:i:38	XS:i:0
+M01368:8:000000000-A3GHV:1:1109:19224:11655	2147	gi|251831106|ref|NC_012920.1|	16530	60	40M211H	=	1	-16346	AAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATG	BBB@A4FFFBBBGGGGGGGGGGHHHHHHHHFHHHHGFGHG	SA:Z:gi|251831106|ref|NC_012920.1|,1,+,40S186M25S,60,2;	MD:Z:40	RG:Z:id-1	NM:i:0	AS:i:40	XS:i:0
+M01368:8:000000000-A3GHV:1:1109:19224:11655	2195	gi|251831106|ref|NC_012920.1|	16530	60	26H40M185H	=	1	-16569	AAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATG	FFFEFFD.A:..D.GGAGFBFFFGGFGFFBB:C9.ABGFE	SA:Z:gi|251831106|ref|NC_012920.1|,1,-,66S185M,60,1;	MD:Z:40	RG:Z:id-1	NM:i:0	AS:i:40	XS:i:0
+M01368:8:000000000-A3GHV:1:1101:5446:12248	2131	gi|251831106|ref|NC_012920.1|	16532	60	38M213H	=	1	-16569	ATAGCCCACACGTTCCCCTTAAATAAGACATCACGATG	FFFEFFFFFEFFFFFFBFFFFFFFFFFBFFFFFFFFFG	SA:Z:gi|251831106|ref|NC_012920.1|,1,-,38S213M,60,1;	MD:Z:38	RG:Z:id-1	NM:i:0	AS:i:38	XS:i:0
+M01368:8:000000000-A3GHV:1:1102:21788:11027	2147	gi|251831106|ref|NC_012920.1|	16535	60	35M216H	=	1	-16323	GCCCACACGTTCCCCTTAAATAAGACATCACGATG	ABCCBCCBBFFFGGGGGGGGGGGHGHHHHHHGGHG	SA:Z:gi|251831106|ref|NC_012920.1|,1,+,35S213M3S,60,1;	MD:Z:35	RG:Z:id-1	NM:i:0	AS:i:35	XS:i:0
+M01368:8:000000000-A3GHV:1:1110:12808:18367	2211	gi|251831106|ref|NC_012920.1|	16535	60	35M216H	=	1	-16323	GCCCACACGTTCCCCTTAAATAAGACATCACGATG	ABCCCCDDDFFFGGGGGGGGGGHHHHHHHHHGGGG	SA:Z:gi|251831106|ref|NC_012920.1|,1,+,35S213M3S,60,2;	MD:Z:35	RG:Z:id-1	NM:i:0	AS:i:35	XS:i:0
+M01368:8:000000000-A3GHV:1:1110:16559:7507	2211	gi|251831106|ref|NC_012920.1|	16535	60	35M216H	=	1	-16285	GCCCACACGTTCCCCTTAAATAAGACATCACGATG	>AABBCCCCFFFGGGGGGGGGGHHHHHHHHHGGHG	SA:Z:gi|251831106|ref|NC_012920.1|,1,+,35S216M,60,1;	MD:Z:35	RG:Z:id-1	NM:i:0	AS:i:35	XS:i:0
+M01368:8:000000000-A3GHV:1:1111:14287:20817	2147	gi|251831106|ref|NC_012920.1|	16535	60	35M216H	=	1	-16286	GCCAACACGTTCCCCTTAAATAAGACATCACGATG	>>A3>AAAACFFFGFGFGGGGGHGHHHHHHHGGGG	SA:Z:gi|251831106|ref|NC_012920.1|,1,+,35S216M,60,4;	MD:Z:3C31	RG:Z:id-1	NM:i:1	AS:i:31	XS:i:0
+M01368:8:000000000-A3GHV:1:1102:21788:11027	2195	gi|251831106|ref|NC_012920.1|	16535	60	3H35M213H	=	1	-16569	GCCCACACGTTCCCCTTAAATAAGACATCACGATG	.D../A.FEDABA0B0FFFFFFFFFFFFF9BFFB0	SA:Z:gi|251831106|ref|NC_012920.1|,1,-,38S213M,60,1;	MD:Z:35	RG:Z:id-1	NM:i:0	AS:i:35	XS:i:0
+M01368:8:000000000-A3GHV:1:1110:12808:18367	2131	gi|251831106|ref|NC_012920.1|	16535	60	3H35M213H	=	1	-16569	GCCCACACGTTCCCCTTAAATAAGACATCACGATG	FFFFF?FA..9BFFBFBBFFFFFFBFFFFEFFFBG	SA:Z:gi|251831106|ref|NC_012920.1|,1,-,38S213M,60,1;	MD:Z:35	RG:Z:id-1	NM:i:0	AS:i:35	XS:i:0

bgruening · 2023-09-26T16:40:58Z

:( still failing

gallardoalba added 4 commits June 6, 2023 20:46

Add_files

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Update files

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gallardoalba marked this pull request as ready for review September 1, 2023 10:16

Update files

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gallardoalba force-pushed the Update_piccard branch from b059603 to 3b59324 Compare September 1, 2023 13:22

gallardoalba added 3 commits September 1, 2023 16:30

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gallardoalba requested a review from bgruening September 1, 2023 15:51

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tools/picard/picard_AddOrReplaceReadGroups.xml Outdated Show resolved Hide resolved

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bgruening added 2 commits September 5, 2023 12:57

remove r-base as it is part of picard

9cb35ed

https://github.com/bioconda/bioconda-recipes/blob/master/recipes/picard/meta.yaml#L21 I hope that helps the solver and fixes 4 of our 5 problems. The 5th problem is a simsize of BAM files, you should not use simsize here, just diff.

is 447 not working?

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bgruening closed this Sep 5, 2023

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gallardoalba added 3 commits September 5, 2023 15:22

Update test

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Merge branch 'Update_piccard' of github.com:gallardoalba/tools-iuc in…

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…to Update_piccard

Update tests

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Update tools/picard/picard_macros.xml

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bgruening changed the title ~~Picard update v.3.0.0~~ Picard update v.3.1.0 Sep 7, 2023

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Merge branch 'Update_piccard' of github.com:gallardoalba/tools-iuc in…

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Update_test

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Picard update v.3.1.0 #5348

Picard update v.3.1.0 #5348

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Picard update v.3.1.0 #5348

Picard update v.3.1.0 #5348

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