Open Mxrcon opened 2 years ago
removing the file with this command worked:
rm -f ‘/data/mariliaconceicao/Davi/mtbseq-nf-master/work/conda/env-9bc281415c98bcad7a1079004336496d/opt/gatk-3.8/GenomeAnalysisTK.jar
Hmm, interesting.
Could you please outline, how exactly I can reproduce this on my end?
In any case, the following line gives a hint
cp: cannot create regular file ‘/data/mariliaconceicao/Davi/mtbseq-nf-master/work/conda/env-9bc281415c98bcad7a1079004336496d/opt/gatk-3.8/GenomeAnalysisTK.jar’: File exists
The problem is that gatk-register
process, used in each of the MTBSEQ modules, copies the jar to the location where the MTBseq
code is installed, which in case of conda
is .../work/conda/env...
NOTE: This problem will likely only occur in case of conda
since it makes persistent change to the filesystem. When using docker
, as soon as the container is shut down, it removes all changes.
There are a few possible solutions
gatk-register
command offers a -force
(or similar) option to forcefully overwrite the jar in case it exists.../work/conda/ENV_FOR_MTBSEQ...
to force conda
to recreate another env.conda
profile as discussed here https://stackoverflow.com/questions/22009364/is-there-a-try-catch-command-in-bashcopy_gatk38_jar
and modify the scripts to use something like ${params.copy_gatk38_jar ? (gatk-register ...) : ""}
What do you think?
Hmm, interesting.
Could you please outline, how exactly I can reproduce this on my end?
I just cloned the latest version, and then wrote this command: nextflow run main.nf -profile conda -params-file params/params.yml
with a fresh copy of the pipeline and some genomes. not sure if the can be reproduced so easily.
In that case, I think we can just track this as an issue but in case you run across this one again - please try out the suggestions here https://github.com/mtb-bioinformatics/mtbseq-nf/issues/54#issuecomment-975910260
i think that the best option would be 4, to introduce code to check the situation, in multi threading executions i think that a force script or instruct env removal would generate new issues. I'll work on this solution soon.
Hey, while I've been testing the latest version, i found this error: I'm providing a gatk jar as requested, and using a fresh conda env.
I'll test some solutions and reply here if i found anything new.
Kindly, Davi