"Error: unhandled exception: invalid bgzf file [ValueError]" on an S3 bam file that samtools-1.9 can view.

Question

"Error: unhandled exception: invalid bgzf file [ValueError]" on an S3 bam file that samtools-1.9 can view.

splichte opened this issue 5 years ago · comments

Here is my command history:

ubuntu $ ./mosdepth pref http://s3.amazonaws.com/1000genomes/phase3/data/NA21103/alignment/NA21103.chrom11.ILLUMINA.bwa.GIH.low_coverage.20120522.bam
[E::knet_seek] SEEK_END is not supported for HTTP. Offset is unchanged
../../../../root/.nimble/pkgs/hts-0.2.8/hts/bam.nim(297) open
Error: unhandled exception: invalid bgzf file [ValueError]

ubuntu $ samtools view http://s3.amazonaws.com/1000genomes/phase3/data/NA21103/alignment/NA21103.chrom11.ILLUMINA.bwa.GIH.low_coverage.20120522.bam >/dev/null

samtools is built with htslib-1.9. mosdepth can read this file just OK if I copy it from S3 first. I put this issue on hts-nim since it seems like it is in bam.nim and has nothing to do with mosdepth itself.

I'm happy to attempt a fix if you have any idea what might be going on. Thanks!

splichte commented 5 years ago

thanks!

Brent Pedersen · Answer 1 · Tue Sep 03 2019 08:39:53 GMT+0800 (China Standard Time)

thank you. i just pushed a fix for this.

Brent Pedersen · Answer 2 · Tue Sep 03 2019 08:41:16 GMT+0800 (China Standard Time)

thanks for reporting. not sure how I haven't seen this before, but good to get it resolved.

splichte · Answer 3 · Wed Sep 11 2019 08:32:09 GMT+0800 (China Standard Time)

would you be able to push a new release for hts-nim with this fix included? thanks!

…

On Mon, Sep 2, 2019 at 8:41 PM Brent Pedersen ***@***.***> wrote: thanks for reporting. not sure how I haven't seen this before, but good to get it resolved. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#48?email_source=notifications&email_token=AAX55I5I4GBCCH7JOPX6LOTQHWXC5A5CNFSM4ITA3CS2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD5WWTHQ#issuecomment-527264158>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAX55IYAMHMKWKP4E7CEUOLQHWXC5ANCNFSM4ITA3CSQ> .

Brent Pedersen · Answer 4 · Wed Sep 11 2019 10:03:38 GMT+0800 (China Standard Time)

yes. just tagged v0.2.21.

splichte · Answer 5 · Wed Sep 11 2019 12:25:31 GMT+0800 (China Standard Time)

wonderful, thank you for the speedy response as always!

…

On Tuesday, September 10, 2019, Brent Pedersen ***@***.***> wrote: yes. just tagged v0.2.21. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#48?email_source=notifications&email_token=AAX55IYBW7JO3PMODIZHGJTQJBGXXA5CNFSM4ITA3CS2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6NANRY#issuecomment-530187975>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAX55IZVIDIHXFFSF2HIJVTQJBGXXANCNFSM4ITA3CSQ> .