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TrinityCTAT / ctat-mutations

Mutation detection using GATK4 best practices and latest RNA editing filters resources. Works with both Hg38 and Hg19
https://github.com/TrinityCTAT/ctat-mutations
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Annotating VCF at BLAT ED #123

Open shivUSF opened 1 year ago

shivUSF commented 1 year ago

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 ?

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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.

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Shivani

brianjohnhaas commented 1 year ago

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

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

shivUSF commented 1 year ago

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 commented 1 year ago

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.

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.

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

shivUSF commented 1 year ago

I am using singularity for the run.

brianjohnhaas commented 1 year ago

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

On Tue, Dec 13, 2022 at 10:07 PM shivUSF @.***> wrote:

I am using singularity for the run.

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shivUSF commented 1 year ago

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

shivUSF commented 1 year ago

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

brianjohnhaas commented 1 year ago

Excellent! Great to hear. thanks!!

~b

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!

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