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Published 20 hours ago • verified publisher icon brentp

panic:gzip: invalid header

Open gaom001 opened this issue 2 years ago • 8 comments

I used singullarity to run smoove, but met below info and the job was killed. Do you konw the reason? something wrong with bam header? how to fix this? Thanks in advance.

singularity exec \
smoove_latest.sif smoove call \
-x \
--name smoove.sv.vcf\
--exclude /smoove/exclude.b37.bed \
--fasta /homo_sapiens/GRCh37d5/genome/gr37.fasta \
-p 1 \
--outdir smoove/output \
--genotype \
N01_01_WG01.bam

Output: [smoove] 2022/05/04 00:07:40 starting with version 0.2.6 panic: gzip: invalid header

goroutine 1 [running]: github.com/brentp/smoove/lumpy.check(...) /home/brentp/go/go/src/github.com/brentp/smoove/lumpy/lumpy.go:54 github.com/brentp/smoove/lumpy.lumpy_filter_cmd(0x7ffc9f88e482, 0x2d, 0x7ffc9f88e4fe, 0x24, 0x7ffc9f88e4b8, 0x37, 0x0, 0x0, 0x0, 0x0, ...) /home/brentp/go/go/src/github.com/brentp/smoove/lumpy/lumpy.go:83 +0x105b github.com/brentp/smoove/lumpy.Lumpy(0x7ffc9f88e453, 0x2e, 0x7ffc9f88e4b8, 0x37, 0x7ffc9f88e4fe, 0x24, 0xc000126f00, 0x2, 0x2, 0xc000099360, ...) /home/brentp/go/go/src/github.com/brentp/smoove/lumpy/lumpy.go:119 +0x12b github.com/brentp/smoove/lumpy.Main() /home/brentp/go/go/src/github.com/brentp/smoove/lumpy/lumpy.go:335 +0x261 main.main() /home/brentp/go/go/src/github.com/brentp/smoove/cmd/smoove/smoove.go:121 +0x1ce

gaom001 avatar May 04 '22 04:05 gaom001

can you run samtools quickcheck N01_01_WG01.bam ? and also make sure that directory is mounted for singularity access. and that the index is available.

brentp avatar May 04 '22 08:05 brentp

Yes, I have done bind and mount for singularity.
When I typed samtools quickcheck N01_01_WG01.bam, it did not show any output. I think this is due to the samtools version. Let me clone a new to check.

gaom001 avatar May 04 '22 13:05 gaom001

1.15.1 version samtools stii does not show any output after run the above command.

gaom001 avatar May 04 '22 14:05 gaom001

I print out the header of my bam:

@HD	VN:1.6	SO:coordinate
@SQ	SN:1	LN:249250621	M5:1b22b98cdeb4a9304cb5d48026a85128	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fasta	SP:HUMAN
@SQ	SN:2	LN:243199373	M5:a0d9851da00400dec1098a9255ac712e	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fasta	SP:HUMAN
@SQ	SN:3	LN:198022430	M5:fdfd811849cc2fadebc929bb925902e5	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fasta	SP:HUMAN
@SQ	SN:4	LN:191154276	M5:23dccd106897542ad87d2765d28a19a1	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fasta	SP:HUMAN
@SQ	SN:5	LN:180915260	M5:0740173db9ffd264d728f32784845cd7	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fasta	SP:HUMAN
@SQ	SN:6	LN:171115067	M5:1d3a93a248d92a729ee764823acbbc6b	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fasta	SP:HUMAN
@SQ	SN:7	LN:159138663	M5:618366e953d6aaad97dbe4777c29375e	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fasta	SP:HUMAN
@SQ	SN:8	LN:146364022	M5:96f514a9929e410c6651697bded59aec	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fasta	SP:HUMAN
@SQ	SN:9	LN:141213431	M5:3e273117f15e0a400f01055d9f393768	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fasta	SP:HUMAN
@SQ	SN:10	LN:135534747	M5:988c28e000e84c26d552359af1ea2e1d	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fasta	SP:HUMAN
@SQ	SN:11	LN:135006516	M5:98c59049a2df285c76ffb1c6db8f8b96	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fasta	SP:HUMAN
@SQ	SN:12	LN:133851895	M5:51851ac0e1a115847ad36449b0015864	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fasta	SP:HUMAN
@SQ	SN:13	LN:115169878	M5:283f8d7892baa81b510a015719ca7b0b	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fasta	SP:HUMAN
@SQ	SN:14	LN:107349540	M5:98f3cae32b2a2e9524bc19813927542e	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fasta	SP:HUMAN
@SQ	SN:15	LN:102531392	M5:e5645a794a8238215b2cd77acb95a078	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fasta	SP:HUMAN
@SQ	SN:16	LN:90354753	M5:fc9b1a7b42b97a864f56b348b06095e6	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fasta	SP:HUMAN
@SQ	SN:17	LN:81195210	M5:351f64d4f4f9ddd45b35336ad97aa6de	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fasta	SP:HUMAN
@SQ	SN:18	LN:78077248	M5:b15d4b2d29dde9d3e4f93d1d0f2cbc9c	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fasta	SP:HUMAN
@SQ	SN:19	LN:59128983	M5:1aacd71f30db8e561810913e0b72636d	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fasta	SP:HUMAN
@SQ	SN:20	LN:63025520	M5:0dec9660ec1efaaf33281c0d5ea2560f	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fasta	SP:HUMAN
@SQ	SN:21	LN:48129895	M5:2979a6085bfe28e3ad6f552f361ed74d	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fasta	SP:HUMAN
@SQ	SN:22	LN:51304566	M5:a718acaa6135fdca8357d5bfe94211dd	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fasta	SP:HUMAN
@SQ	SN:X	LN:155270560	M5:7e0e2e580297b7764e31dbc80c2540dd	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fasta	SP:HUMAN
@SQ	SN:Y	LN:59373566	M5:1fa3474750af0948bdf97d5a0ee52e51	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fasta	SP:HUMAN
@SQ	SN:MT	LN:16569	M5:c68f52674c9fb33aef52dcf399755519	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fasta	SP:HUMAN
@SQ	SN:GL000207.1	LN:4262	M5:f3814841f1939d3ca19072d9e89f3fd7	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fasta	SP:HUMAN
@SQ	SN:GL000226.1	LN:15008	M5:1c1b2cd1fccbc0a99b6a447fa24d1504	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fastaSP:HUMAN
@SQ	SN:GL000229.1	LN:19913	M5:d0f40ec87de311d8e715b52e4c7062e1	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fastaSP:HUMAN
@SQ	SN:GL000231.1	LN:27386	M5:ba8882ce3a1efa2080e5d29b956568a4	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fastaSP:HUMAN
@SQ	SN:GL000210.1	LN:27682	M5:851106a74238044126131ce2a8e5847c	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fastaSP:HUMAN
@SQ	SN:GL000239.1	LN:33824	M5:99795f15702caec4fa1c4e15f8a29c07	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fastaSP:HUMAN
@SQ	SN:GL000235.1	LN:34474	M5:118a25ca210cfbcdfb6c2ebb249f9680	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fastaSP:HUMAN
@SQ	SN:GL000201.1	LN:36148	M5:dfb7e7ec60ffdcb85cb359ea28454ee9	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fastaSP:HUMAN
@SQ	SN:GL000247.1	LN:36422	M5:7de00226bb7df1c57276ca6baabafd15	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fastaSP:HUMAN
@SQ	SN:GL000245.1	LN:36651	M5:89bc61960f37d94abf0df2d481ada0ec	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fastaSP:HUMAN
@SQ	SN:GL000197.1	LN:37175	M5:6f5efdd36643a9b8c8ccad6f2f1edc7b	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fastaSP:HUMAN
@SQ	SN:GL000203.1	LN:37498	M5:96358c325fe0e70bee73436e8bb14dbd	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fastaSP:HUMAN
@SQ	SN:GL000246.1	LN:38154	M5:e4afcd31912af9d9c2546acf1cb23af2	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fastaSP:HUMAN
@SQ	SN:GL000249.1	LN:38502	M5:1d78abec37c15fe29a275eb08d5af236	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fastaSP:HUMAN
@SQ	SN:GL000196.1	LN:38914	M5:d92206d1bb4c3b4019c43c0875c06dc0	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fastaSP:HUMAN
@SQ	SN:GL000248.1	LN:39786	M5:5a8e43bec9be36c7b49c84d585107776	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fastaSP:HUMAN
@SQ	SN:GL000244.1	LN:39929	M5:0996b4475f353ca98bacb756ac479140	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fastaSP:HUMAN
@SQ	SN:GL000238.1	LN:39939	M5:131b1efc3270cc838686b54e7c34b17b	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fastaSP:HUMAN
@SQ	SN:GL000202.1	LN:40103	M5:06cbf126247d89664a4faebad130fe9c	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fastaSP:HUMAN
@SQ	SN:GL000234.1	LN:40531	M5:93f998536b61a56fd0ff47322a911d4b	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fastaSP:HUMAN
@SQ	SN:GL000232.1	LN:40652	M5:3e06b6741061ad93a8587531307057d8	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fastaSP:HUMAN
@SQ	SN:GL000206.1	LN:41001	M5:43f69e423533e948bfae5ce1d45bd3f1	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fastaSP:HUMAN
@SQ	SN:GL000240.1	LN:41933	M5:445a86173da9f237d7bcf41c6cb8cc62	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fastaSP:HUMAN
@SQ	SN:GL000236.1	LN:41934	M5:fdcd739913efa1fdc64b6c0cd7016779	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fastaSP:HUMAN
@SQ	SN:GL000241.1	LN:42152	M5:ef4258cdc5a45c206cea8fc3e1d858cf	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fastaSP:HUMAN
@SQ	SN:GL000243.1	LN:43341	M5:cc34279a7e353136741c9fce79bc4396	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fastaSP:HUMAN
@SQ	SN:GL000242.1	LN:43523	M5:2f8694fc47576bc81b5fe9e7de0ba49e	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fastaSP:HUMAN
@SQ	SN:GL000230.1	LN:43691	M5:b4eb71ee878d3706246b7c1dbef69299	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fastaSP:HUMAN
@SQ	SN:GL000237.1	LN:45867	M5:e0c82e7751df73f4f6d0ed30cdc853c0	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fastaSP:HUMAN
@SQ	SN:GL000233.1	LN:45941	M5:7fed60298a8d62ff808b74b6ce820001	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fastaSP:HUMAN
@SQ	SN:GL000204.1	LN:81310	M5:efc49c871536fa8d79cb0a06fa739722	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fastaSP:HUMAN
@SQ	SN:GL000198.1	LN:90085	M5:868e7784040da90d900d2d1b667a1383	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fastaSP:HUMAN
@SQ	SN:GL000208.1	LN:92689	M5:aa81be49bf3fe63a79bdc6a6f279abf6	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fastaSP:HUMAN
@SQ	SN:GL000191.1	LN:106433	M5:d75b436f50a8214ee9c2a51d30b2c2cc	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fastaSP:HUMAN
@SQ	SN:GL000227.1	LN:128374	M5:a4aead23f8053f2655e468bcc6ecdceb	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fastaSP:HUMAN
@SQ	SN:GL000228.1	LN:129120	M5:c5a17c97e2c1a0b6a9cc5a6b064b714f	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fastaSP:HUMAN
@SQ	SN:GL000214.1	LN:137718	M5:46c2032c37f2ed899eb41c0473319a69	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fastaSP:HUMAN
@SQ	SN:GL000221.1	LN:155397	M5:3238fb74ea87ae857f9c7508d315babb	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fastaSP:HUMAN
@SQ	SN:GL000209.1	LN:159169	M5:f40598e2a5a6b26e84a3775e0d1e2c81	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fastaSP:HUMAN
@SQ	SN:GL000218.1	LN:161147	M5:1d708b54644c26c7e01c2dad5426d38c	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fastaSP:HUMAN
@SQ	SN:GL000220.1	LN:161802	M5:fc35de963c57bf7648429e6454f1c9db	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fastaSP:HUMAN
@SQ	SN:GL000213.1	LN:164239	M5:9d424fdcc98866650b58f004080a992a	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fastaSP:HUMAN
@SQ	SN:GL000211.1	LN:166566	M5:7daaa45c66b288847b9b32b964e623d3	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fastaSP:HUMAN
@SQ	SN:GL000199.1	LN:169874	M5:569af3b73522fab4b40995ae4944e78e	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fastaSP:HUMAN
@SQ	SN:GL000217.1	LN:172149	M5:6d243e18dea1945fb7f2517615b8f52e	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fastaSP:HUMAN
@SQ	SN:GL000216.1	LN:172294	M5:642a232d91c486ac339263820aef7fe0	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fastaSP:HUMAN
@SQ	SN:GL000215.1	LN:172545	M5:5eb3b418480ae67a997957c909375a73	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fastaSP:HUMAN
@SQ	SN:GL000205.1	LN:174588	M5:d22441398d99caf673e9afb9a1908ec5	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fastaSP:HUMAN
@SQ	SN:GL000219.1	LN:179198	M5:f977edd13bac459cb2ed4a5457dba1b3	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fastaSP:HUMAN
@SQ	SN:GL000224.1	LN:179693	M5:d5b2fc04f6b41b212a4198a07f450e20	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fastaSP:HUMAN
@SQ	SN:GL000223.1	LN:180455	M5:399dfa03bf32022ab52a846f7ca35b30	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fastaSP:HUMAN
@SQ	SN:GL000195.1	LN:182896	M5:5d9ec007868d517e73543b005ba48535	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fastaSP:HUMAN
@SQ	SN:GL000212.1	LN:186858	M5:563531689f3dbd691331fd6c5730a88b	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fastaSP:HUMAN
@SQ	SN:GL000222.1	LN:186861	M5:6fe9abac455169f50470f5a6b01d0f59	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fastaSP:HUMAN
@SQ	SN:GL000200.1	LN:187035	M5:75e4c8d17cd4addf3917d1703cacaf25	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fastaSP:HUMAN
@SQ	SN:GL000193.1	LN:189789	M5:dbb6e8ece0b5de29da56601613007c2a	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fastaSP:HUMAN
@SQ	SN:GL000194.1	LN:191469	M5:6ac8f815bf8e845bb3031b73f812c012	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fastaSP:HUMAN
@SQ	SN:GL000225.1	LN:211173	M5:63945c3e6962f28ffd469719a747e73c	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fastaSP:HUMAN
@SQ	SN:GL000192.1	LN:547496	M5:325ba9e808f669dfeee210fdd7b470ac	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fastaSP:HUMAN
@SQ	SN:NC_007605	LN:171823	M5:6743bd63b3ff2b5b8985d8933c53290a	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fastaSP:HUMAN
@SQ	SN:hs37d5	LN:35477943	M5:5b6a4b3a81a2d3c134b7d14bf6ad39f1	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fastaSP:HUMAN
@RG	ID:1	CN:institute	SM:N01_01_WG01	PU:1	PL:ILLUMINA	PM:ILLUMINA-NOVASEQ-6000
@PG	PN:bwa-mem2	ID:bwa-mem2	VN:2.0	CL:/opt/wtsi-cgp/bin/bwa-mem2 mem -v 1 -R @RG\tID:1\tSM:XPRO_0608_N_IGO_08822_OX_3 -t 32 /igo/work/nabors/tools/bwamem2/ref/gr37.fasta /igo/staging/stats/naborsd_workspace/PPG/MICHELLE_0481/tmpMap_XPRO_0608_N_IGO_08822_OX_3/split/1/pairedfq1.0.fastq.gz /igo/staging/stats/naborsd_workspace/PPG/MICHELLE_0481/tmpMap_XPRO_0608_N_IGO_08822_OX_3/split/1/pairedfq2.0.fastq.gz
@PG	PN:samtools	ID:samtools	VN:1.11	PP:bwa-mem2	CL:/opt/wtsi-cgp/bin/samtools fixmate -m --output-fmt bam,level=0 -@ 32 - -
@PG	PN:samtools	ID:samtools.1	VN:1.11	PP:samtools	CL:/opt/wtsi-cgp/bin/samtools sort -m 2G --output-fmt bam,level=0 -T /igo/staging/stats/naborsd_workspace/PPG/MICHELLE_0481/tmpMap_XPRO_0608_N_IGO_08822_OX_3/bamsort.1_tmp -@ 32 -
@PG	PN:samtools	ID:samtools.2	VN:1.11	PP:samtools.1	CL:/opt/wtsi-cgp/bin/samtools calmd --output-fmt bam,level=1 -Q -@ 32 - /igo/work/nabors/tools/bwamem2/ref/gr37.fasta
@PG	PN:samtools	ID:samtools.3	VN:1.11	PP:samtools.2	CL:/opt/wtsi-cgp/bin/samtools merge -u -@ 32 - /igo/staging/stats/naborsd_workspace/PPG/MICHELLE_0481/tmpMap_XPRO_0608_N_IGO_08822_OX_3/sorted/1_pairedfq1.0.fastq.gz_sorted.bam
@PG	PN:samtools	ID:samtools.4	VN:1.11	PP:samtools.3	CL:/opt/wtsi-cgp/bin/samtools markdup --mode t --output-fmt bam,level=0 -S --include-fails -T /igo/staging/stats/naborsd_workspace/PPG/MICHELLE_0481/tmpMap_XPRO_0608_N_IGO_08822_OX_3/strmdup -@ 32 -f /igo/staging/stats/naborsd_workspace/PPG/MICHELLE_0481/XPRO_0608_N_IGO_08822_OX_3.bam.met - -
@PG	PN:samtools	ID:samtools.5	VN:1.11	PP:samtools.4	CL:/opt/wtsi-cgp/bin/samtools view -T /igo/work/nabors/tools/bwamem2/ref/gr37.fasta --output-fmt bam -@ 32 -
@PG	PN:samtools	ID:samtools.6	VN:1.11	PP:samtools.5	CL:/usr/local/bin/samtools merge -s 97cad87f-111e-4289-adc2-142c1f270359 -@1 - /work/isabl/data/experiments/55/50/155550/data/IID_H209389_N01_01_WG01_26ff01922c2b9cd6_XPRO_0608_N_IGO_08822_OX_3.bam
@PG	PN:samtools	ID:samtools.7	VN:1.11	PP:samtools.6	CL:/usr/local/bin/samtools view -H -@1
@PG	ID:samtools.8	PN:samtools	PP:samtools.7	VN:1.11	CL:/usr/local/bin/samtools reheader /work/isabl/tmp/isablbot/2022/02/08/tmpsxqzwkl7 /work/isabl/data/experiments/55/50/155550/data/IID_H209389_N01_01_WG01_26ff01922c2b9cd6_XPRO_0608_N_IGO_08822_OX_3.bam
@PG	ID:samtools.9	PN:samtools	PP:samtools.8	VN:1.15.1	CL:./samtools view -H /work/isabl/data/analyses/20/71/472071/IID_H209389_N01_01_WG01.bam

gaom001 avatar May 04 '22 14:05 gaom001

Should there be a space before SP on these lines?

@SQ	SN:hs37d5	LN:35477943	M5:5b6a4b3a81a2d3c134b7d14bf6ad39f1	UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fastaSP:HUMAN

james-guevara avatar May 04 '22 18:05 james-guevara

Hi, I don't see the problem. Can you run:

goleft samplename $bam

where goleft should be in your singularity image for smoove.

brentp avatar May 09 '22 08:05 brentp

When I run the command, the output is the sample ID

gaom001 avatar May 11 '22 16:05 gaom001

so this might mean that you don't have any split or discordant reads in the $bam or that coverage is low?

brentp avatar May 12 '22 06:05 brentp