Vardict error.

[lindenb]

Hi , I got the following error: (I added -set x ; set -e ; set -o pipefail to view the output of callers/vardict I also set my $sample=""; line 32 of "var2vcf_valid.pl" )

(...)
rule prepare_caller:
    input: /SCRATCH-BIRD/users/lindenbaum-p/work/NEXTFLOW/20210312.varCA/BAMS/CM_Br334_C02_p20_run3.sorted.rename
d.bam, /SCRATCH-BIRD/users/lindenbaum-p/work/NEXTFLOW/20210312.varCA/20210312.ATAC/peaks/CM_Br334_C02_p20_run3.so
rted/peaks.bed, /LAB-DATA/BiRD/resources/species/human/cng.fr/hs37d5/hs37d5_all_chr.fasta, callers/vardict
    output: /SCRATCH-BIRD/users/lindenbaum-p/work/NEXTFLOW/20210312.varCA/20210312.ATAC/callers/CM_Br334_C02_p20_
run3.sorted/vardict
    jobid: 0
    wildcards: sample=CM_Br334_C02_p20_run3.sorted, caller=vardict

+ set -e
+ bgzip
+ vardict-java -G /LAB-DATA/BiRD/resources/species/human/cng.fr/hs37d5/hs37d5_all_chr.fasta -N CM_Br334_C01_p32_r
un4.sorted -b /SCRATCH-BIRD/users/lindenbaum-p/work/NEXTFLOW/20210312.varCA/BAMS/CM_Br334_C01_p32_run4.sorted.ren
amed.bam -v -c 1 -S 2 -E 3 /SCRATCH-BIRD/users/lindenbaum-p/work/NEXTFLOW/20210312.varCA/20210312.ATAC/peaks/CM_B
r334_C01_p32_run4.sorted/peaks.bed -VS SILENT
+ var2vcf_valid.pl
+ teststrandbias.R
/LAB-DATA/BiRD/users/lindenbaum-p/notebook/2021/20210312.varCA/varCA/.snakemake/conda/2501cca1/lib/R/bin/R: line 
238: /LAB-DATA/BiRD/users/lindenbaum-p/notebook/2021/20210312.varCA/varCA/.snakemake/conda/2501cca1/lib/R/etc/ldp
aths: No such file or directory

[aryarm]

Hi @lindenb, This sounds like it might be related to issue #20? We are actively looking for ways to deal with that issue. It looks like there is already a potential fix written within the conda-forge/r-base-feedstock repository, but it hasn't been merged in yet. In most cases it should go away if you delete the conda environment and then allow Snakemake to recreate it automatically upon a subsequent execution:

rm -r .snakemake/conda/2501cca1