Open redincla opened 2 years ago
what aligner generated those bam files?
Hi again,
I've used bwa-mem So this could be an error from the alignment step?
On Mon, Feb 21, 2022 at 11:38 AM Brent Pedersen @.***> wrote:
what aligner generated those bam files?
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Hi, see the linked issue above. It's an invalid date that can't be parsed by biogo/hts (and therefore by smoove).
Maybe you can check the date
command on the host machine where bwa mem was run?
Hi Brent,
Thanks a lot for the comment. I've thus added an extra step to fix all DT fields from the bam header using 'accepted' biogo/hts DT formats, and it now runs to the next step and generates disc.bam/bam.cso/bam.orig.bam and split.bam/split.bam.orig.bam outputs. But I get the following.
singularity run /dcsrsoft/singularity/containers/smoove-0.2.7.sif smoove call \
--outdir ./ --exclude /data/exclude.cnvnator_100bp.GRCh38.20170403.bed \ --name GVA_VZV_01 --fasta /data/Homo_sapiens_assembly38.fasta \ -p 1 --genotype GVA_VZV_01.bam WARNING: group: unknown groupid 124638 [smoove] 2022/02/22 08:47:09 starting with version 0.2.7 [smoove] 2022/02/22 08:47:09 calculating bam stats for 1 bams [smoove]: ([E]lumpy-filter) 2022/02/22 08:47:09 /bin/bash: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8) [smoove] 2022/02/22 08:47:50 done calculating bam stats [smoove]:([E]lumpy-filter) 2022/02/22 09:26:06 [lumpy_filter] extracted splits and discordants from 648546193 total aligned reads [smoove]:2022/02/22 09:26:10 finished process: lumpy-filter (set -eu; lumpy_filter -f /scratch) in user-time:15m44.996517s system-time:4m50.279452s bash: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8) 2022/02/22 09:26:52 couldn't get region from line
Last error message couldn't get region from line seems to fail to proceed to the next genotyping step, as I have no *genotyped.vcf.gz output. Any idea on how I could fix this?
Thanks a ton, and sorry for bothering again,
Claire
On Mon, Feb 21, 2022 at 12:34 PM Brent Pedersen @.***> wrote:
Hi, see the linked issue above. It's an invalid date that can't be parsed by biogo/hts (and therefore by smoove). Maybe you can check the date command on the host machine where bwa mem was run?
— Reply to this email directly, view it on GitHub https://github.com/brentp/smoove/issues/189#issuecomment-1046782724, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACKLJZREXKL3ENMR3TDXGPDU4IPNTANCNFSM5O6FKQTA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.
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Hi, I don't know why this is happening, but you can get around it by using the --noextrafilters
flag to smoove call.
For some reason, it's getting empty lines in some bed output. if you can share a quantized.bed.gz file from a failed run, that might help to understand what's happening.
Thanks a ton! I figured that the exclusion bed file I used was corrupted (in case it's helpful for others). Now everything runs smoothly. Have a great day,
Claire
On Wed, Feb 23, 2022 at 12:18 PM Brent Pedersen @.***> wrote:
Hi, I don't know why this is happening, but you can get around it by using the --noextrafilters flag to smoove call.
For some reason, it's getting empty lines in some bed output. if you can share a quantized.bed.gz file from a failed run, that might help to understand what's happening.
— Reply to this email directly, view it on GitHub https://github.com/brentp/smoove/issues/189#issuecomment-1048678664, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACKLJZQ3UBADVS3QTOOULI3U4S663ANCNFSM5O6FKQTA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.
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Hi,
I'm having a weird parsing time issue when running smoove call on individual WGS cram (same on converted bam) samples (running it on population cohort):
Any idea how to fix this? It does create 2 files: GVA_VZV_01.disc.bam.tmp.bam and GVA_VZV_01.split.bam.tmp.bam But I guess these are truncated.
Thanks a lot for your help,
Claire