Comments (5)
Yeah, the script that converted old docker command to singularity script went wrong. I fixed it manually so now hopefully it works.
I don't use singularities internally, so the scripts with singularities are more likely to have errors.
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For dockers, the makeSomaticScripts.py
script/command is working quite well. In the next month or two, I'll probably extend a "docker or singularities" options to that, and retire those legacy .sh scripts.
from somaticseq.
Hi,
thanks for the fix!!
it seems to be ok now. I will wait for the run to complete and if ok I will close the issue
Best
from somaticseq.
Hi,
I am still getting an error with VarScan2 (see below). I should mention that I modified your code to run with Slurm directives.
Anyway, I was able to find some similar reports. It seems that this error may be related to concurrent 'use' of singularity cache (apptainer/singularity#4555).
Is this a problem you have seem before or others have reported ?
Unable to handle docker://djordjeklisic/sbg-varscan2:v1 uri: unable to build: conveyor failed to get: no descriptor found for reference "bf0727087446514ec77d99f7a40fbb43316dcb95f2f516fda6ceedde28f308fd"
Thanks
from somaticseq.
Hi,
according to the singularity blog, this problem can be solved by building the .sif once, before going into any parallel processing. Then 'referring' to it as needed for parallel computations.
Nevertheless, what I do not understand is why I am having this issue only with VarScan2 and not then other callers.
Anyway, right now, if I rerun the varScan2 scripts that fail, eventually they complete without errors.
Thanks!
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Related Issues (20)
- Special setting for b37? HOT 14
- Question about simulating somatic mutations HOT 7
- Pretrained Classifier HOT 3
- Docker issue with latest version HOT 1
- SEQC2: Some high confidence SNVs and INDELs in VCF are outside of regions defined by High-Confidence_Regions_v1.2.bed HOT 2
- Somaticseq makeSomaticScripts.py running and output issues HOT 8
- Slow RNA variant calling HOT 8
- Question for the paper on establishing the reference call set HOT 3
- Where are the 10x Genomics single-cell copy number variation (CNV) analysis results? HOT 7
- Ground Truths required for training HOT 1
- somaticseq failing for same command it had previously successfully run HOT 11
- Applying internal filters to outputs before running SomaticSeq HOT 1
- Dockerized alignment workflow does not work with multiple input files HOT 5
- Error when running makeSomaticScripts with multiple threads HOT 3
- Output allele of the normal sample HOT 2
- UnboundLocalError: cannot access local variable 'normal_name' where it is not associated with a value HOT 10
- how to obtain all variants where the "FILTER" column is not labeled as "PASS" HOT 1
- Are multi-nucleotide and complex variants ignored? HOT 2
- Error when running FFPE training data from SEQ2C HOT 5
- AI consensus calling error on WGS samples HOT 9
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