Fontconfig error in the newest gatk docker image
Answered
Hi
I just tried 4.2.6.0 docker image for germline CNV workflow and came across this error message in the logs.
08:57:35.253 DEBUG ScriptExecutor - --contig_ploidy_prior_table=/home/GATK_CNV/contig_priors.tsv
08:57:35.253 DEBUG ScriptExecutor - --output_model_path=/home/GATK_CNV/DCP/CP_CNV-model
Fontconfig error: No writable cache directories
Fontconfig error: No writable cache directories
Fontconfig error: No writable cache directories
Fontconfig error: No writable cache directories
08:57:50.682 INFO cohort_determine_ploidy_and_depth - THEANO_FLAGS environment variable has been set to: device=cpu,floatX=float64,optimizer=fast_run,compute_test_value=ignore,openmp=true,blas.ldflags=-lmkl_rt,openmp_elemwise_minsize=10,base_compiledir=/home/GATK_CNV/tmp
Fontconfig error messages were not a part of 4.2.5.0 and earlier.
Did something change in the docker image configuration?
Regards.
-
Hi SkyWarrior,
Thanks for updating us about this. Is it a fatal error?
We're having a hard time determining what would have caused this. It would be helpful to see the command and full program log for the tool where this occurred. Is this DetermineGermlineContigPloidy?
Thanks for your help.
Best,
Genevieve
Please sign in to leave a comment.
1 comment