Annotating VCF at BLAT ED

[shivUSF]

I am currently running this pipeline on multiple samples, most of them run fine with few problem with cravat we just fixed.
Have seen for some of the samples at the Annotate BLAT ED step the annotate.ED.py file is throwing this specific error " Failed to fetch sequence in chrM:-38-62" is there something recently changed in the the genome library ?

#----
02:22:50 : INFO : Processing VCF Positions
02:22:52 : INFO : Running samtools faidx
[W::fai_get_val] Reference chrM:-38-62 not found in file, returning empty sequence
[faidx] Failed to fetch sequence in chrM:-38-62
Traceback (most recent call last):
File "/usr/local/src/ctat-mutations/src/annotate_ED.py", line 165, in
main()
File "/usr/local/src/ctat-mutations/src/annotate_ED.py", line 84, in main
subprocess.check_call(cmd, shell=True)
File "/opt/conda/lib/python3.7/subprocess.py", line 347, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'samtools faidx /tmp/ctat_mutation_out/220300000234-C08/cromwell-executions/ctat_mutations/f4a8e00f-b9cb-4e26-980d-553b0b05bef1/call-AnnotateVariants/annotate_variants_wf/64c9af0a-1ef2-4aeb-80ff-784b9e355e59/call-annotate_blat_ED/inputs/817306935/ref_genome.fa --region-file /tmp/ctat_mutation_out/220300000234-C08/cromwell-executions/ctat_mutations/f4a8e00f-b9cb-4e26-980d-553b0b05bef1/call-AnnotateVariants/annotate_variants_wf/64c9af0a-1ef2-4aeb-80ff-784b9e355e59/call-annotate_blat_ED/tmp.87e3a9a4/positions.fa > /tmp/ctat_mutation_out/220300000234-C08/cromwell-executions/ctat_mutations/f4a8e00f-b9cb-4e26-980d-553b0b05bef1/call-AnnotateVariants/annotate_variants_wf/64c9af0a-1ef2-4aeb-80ff-784b9e355e59/call-annotate_blat_ED/tmp.87e3a9a4/faidx_output.fa' returned non-zero exit status 1.

------

Shivani

[brianjohnhaas]

Hi, I think you hit an edge case that we haven't encountered. I can look further into this and patch the code, as it shouldn't be trying to extract sequence from a negative coordinate value... ~b

…

On Tue, Dec 13, 2022 at 5:28 PM shivUSF ***@***.***> wrote: I am currently running this pipeline on multiple samples, most of them run fine with few problem with cravat we just fixed. Have seen for some of the samples at the Annotate BLAT ED step the annotate.ED.py file is throwing this specific error " Failed to fetch sequence in chrM:-38-62" is there something recently changed in the the genome library ? #---- 02:22:50 : INFO : Processing VCF Positions 02:22:52 : INFO : Running samtools faidx [W::fai_get_val] Reference chrM:-38-62 not found in file, returning empty sequence [faidx] Failed to fetch sequence in chrM:-38-62 Traceback (most recent call last): File "/usr/local/src/ctat-mutations/src/annotate_ED.py", line 165, in main() File "/usr/local/src/ctat-mutations/src/annotate_ED.py", line 84, in main subprocess.check_call(cmd, shell=True) File "/opt/conda/lib/python3.7/subprocess.py", line 347, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command 'samtools faidx /tmp/ctat_mutation_out/220300000234-C08/cromwell-executions/ctat_mutations/f4a8e00f-b9cb-4e26-980d-553b0b05bef1/call-AnnotateVariants/annotate_variants_wf/64c9af0a-1ef2-4aeb-80ff-784b9e355e59/call-annotate_blat_ED/inputs/817306935/ref_genome.fa --region-file /tmp/ctat_mutation_out/220300000234-C08/cromwell-executions/ctat_mutations/f4a8e00f-b9cb-4e26-980d-553b0b05bef1/call-AnnotateVariants/annotate_variants_wf/64c9af0a-1ef2-4aeb-80ff-784b9e355e59/call-annotate_blat_ED/tmp.87e3a9a4/positions.fa > /tmp/ctat_mutation_out/220300000234-C08/cromwell-executions/ctat_mutations/f4a8e00f-b9cb-4e26-980d-553b0b05bef1/call-AnnotateVariants/annotate_variants_wf/64c9af0a-1ef2-4aeb-80ff-784b9e355e59/call-annotate_blat_ED/tmp.87e3a9a4/faidx_output.fa' returned non-zero exit status 1. ------ Shivani — Reply to this email directly, view it on GitHub <#123>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZRKX2P2GASE2YADBGUB4DWND2AHANCNFSM6AAAAAAS5XVLAY> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

-- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>

[shivUSF]

Ohh ! in that case do you need me to share any file to test?
I can share file for two of the samples have the same issue.
Thank you once again.

[brianjohnhaas]

I think I can just patch the code w/o needing to run your sample. Remind me - do you use docker or singularity? If so, I can cut another image. Otherwise, the just now updated devel branch should work for you here, and pick up where it left off.

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On Tue, Dec 13, 2022 at 5:54 PM shivUSF ***@***.***> wrote: Ohh ! in that case do you need me to share any file to test? I can share file for two of the samples have the same issue. Thank you once again. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: ***@***.***>

-- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas

[shivUSF]

I am using singularity for the run.

[brianjohnhaas]

Here's a new singularity image for you to try: https://data.broadinstitute.org/Trinity/CTAT_SINGULARITY/CTAT_MUTATIONS/dev/ It should pick up where it left off on the couple you had issues with. Let me know if it gives you any trouble. best, ~brian

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On Tue, Dec 13, 2022 at 10:07 PM shivUSF ***@***.***> wrote: I am using singularity for the run. — Reply to this email directly, view it on GitHub <#123 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZRKX7GR3WG7WUT6BKGWGLWNE2XNANCNFSM6AAAAAAS5XVLAY> . You are receiving this because you commented.Message ID: ***@***.***>

-- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>

[shivUSF]

Thanks Brian! The samples are currently running, will let you know the results once its done.

[shivUSF]

Hey Brian,
It worked for all the samples, thank you once again for your help!

[brianjohnhaas]

Excellent! Great to hear. thanks!! ~b

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On Wed, Dec 21, 2022 at 11:19 AM shivUSF ***@***.***> wrote: Hey Brian, It worked for all the samples, thank you once again for your help! — Reply to this email directly, view it on GitHub <#123 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZRKX276FDLR7GRS6AEPS3WOMUZ5ANCNFSM6AAAAAAS5XVLAY> . You are receiving this because you commented.Message ID: ***@***.***>

-- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>