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brentp / somalier

fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"
MIT License
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Occasional access errors with http file pointers: Read block operation failed with error 2 after 0 of 4 bytes #9

Open avilella opened 5 years ago

avilella commented 5 years ago 
# /home/avilella/somalier/somalier -t 1 /home/avilella/CEGX_Run704/CEGX_Run704.CEGX_Run704-12345678.input.list -f /home/avilella/Genomes/Homo_sapiens/NCBI/GRCh38Decoy/GRCh38Decoy.fa -s /home/avilella/Annotations/somalier/GRCh38/GRCh38.AF.0p50.vcf.gz -o /home/avilella/CEGX
_Run704//CEGX_Run704.CEGX_Run704-12345678.input

Any ideas what these may be? Would they affect the results?

avilella@avilellaM710t:~/CEGX_Run701$ [somalier] checked reference for 10000 sites
[somalier] checked reference for 20000 sites
[somalier] checked reference for 30000 sites
[somalier] checked reference for 40000 sites
[somalier] sites:48666 threads:1
[somalier] spawning sample:0
[E::bgzf_read] Read block operation failed with error 2 after 0 of 4 bytes
[hts-nim] error in bam.query:-2
[E::bgzf_read] Read block operation failed with error 2 after 0 of 4 bytes
[hts-nim] error in bam.query:-2
[E::bgzf_read] Read block operation failed with error 2 after 0 of 4 bytes
[hts-nim] error in bam.query:-2
[E::bgzf_read] Read block operation failed with error 3 after 0 of 4 bytes
[hts-nim] error in bam.query:-2
[E::bgzf_read] Read block operation failed with error 2 after 0 of 4 bytes
[hts-nim] error in bam.query:-2
[E::bgzf_read] Read block operation failed with error 2 after 0 of 4 bytes
[hts-nim] error in bam.query:-2
[E::bgzf_read] Read block operation failed with error 2 after 0 of 4 bytes
[hts-nim] error in bam.query:-2
brentp commented 5 years ago

I've seen this before with http(s), I guess it's an intermittent network error or something with htslib. It wont affect the results noticeably.

brentp commented 5 years ago

hi, I think these errors are gone with htslib 1.9 and newer. Do you see them using that version?

svural commented 3 years ago

I get this error for a sample, i run. I am using the static binary from lates release. It is effecting the result. The relatedness is produces as -nan whereas it should be 1.

brentp commented 3 years ago

if this is still happening, it might be a corrupt bam/cram. does samtools quickcheck $bam pass?