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brentp / smoove

structural variant calling and genotyping with existing tools, but, smoothly.
Apache License 2.0
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panic:gzip: invalid header #198

Open gaom001 opened 2 years ago

gaom001 commented 2 years ago

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

brentp commented 2 years ago

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.

gaom001 commented 2 years ago

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 commented 2 years ago

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

gaom001 commented 2 years ago

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
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@SQ SN:7    LN:159138663    M5:618366e953d6aaad97dbe4777c29375e UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fasta   SP:HUMAN
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@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
james-guevara commented 2 years ago

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
brentp commented 2 years ago

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

goleft samplename $bam

where goleft should be in your singularity image for smoove.

gaom001 commented 2 years ago

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

brentp commented 2 years ago

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