Open BEFH opened 1 year ago
Can you check your input for position 28101822, please? It's 400 bp to the variants you reported. Just to see if there's a variant with this position.
There's no variant there. There are variants at 28101821 and 28101823, but not 28101822. Also, the bad record is actually between 28101479 and 28101482 in the output file. There's nothing between those in the input file either.
Hi, is there any solution to this? I'm also getting the same error,
[W::bcf_record_check] Bad BCF record at 10542449: Invalid CONTIG id -1
at the Finalization step, while phasing rare variants in our cohort (phasing the common ones was fine). I haven't tested much yet, but any help would be appreciated (happy to provide more info if needed).
Thanks, Yiorgos
Hi all,
I pushed a new commit on a new branch "contig". It should solve this issue: https://github.com/odelaneau/shapeit5/tree/contig
I produced two new static binaries you can find at this folder: https://www.dropbox.com/scl/fo/0gpiermhrtf7nz20pgao0/h?rlkey=ddpz9f4nhox1j77y923z4rhi3&dl=0
Can you please try to re-run phase_rare?. If that does not work, please rerun phase_common as well for the scaffolded region, and then phase_rare again?
Let me know if it solves the issue.
Simone
Dear Simone,
I got the new binary and phasing was then complete without errors! Thanks a lot for providing the update. FYI, I didn't re-phase the common ones as I managed without (but will likely repeat all soon).
Kind regards, Yiorgos
This is great news, and I will retest shortly.
On Wed, Jul 26, 2023 at 12:37 PM Yiorgos Kalantzis @.***> wrote:
Dear Simone,
I got the new binary and phasing was then complete without errors! Thanks a lot for providing the update. FYI, I didn't re-phase the common ones as I managed without (but will likely repeat all soon).
Kind regards, Yiorgos
— Reply to this email directly, view it on GitHub https://github.com/odelaneau/shapeit5/issues/34#issuecomment-1652155644, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAZ2Z2ELAO63B6PJMRQDBA3XSFBVDANCNFSM6AAAAAAYWCE54M . You are receiving this because you authored the thread.Message ID: @.***>
Great news! I've been testing the changes and have not had any issues. I did not have to use the new phase_common; the new phase_rare was good enough.
I used the static binaries rather than recompiling.
phase_rare
is failing while attempting to index the output, with errors like the following printed to stderr across all chunks:Upon trying to index the output bcf myself, it's clear the file is malformed, with the same error happening. Looking in the output, I have isolate the place in the file where it first errors (truncated from ~ 36k samples):
This was obtained by running
bcftools view [output_file].bcf | less -S
, searching for28101
and scrolling down until I saw the error.Looking at the input file, there are no variants in between:
This was obtained by running
bcftools view -r chr22:28101479-28101482 [input_file].bcf > dagnostic.vcf
The full command for
phase_rare
was as follows:I got the following log (the HTSlib error was printed to stderr):