Copying @vsatheesh's message from slack and #16 (comment) to a separate Issue, since this is unrelated to the SNPeff PR.
After adding these two lines to the slurm script, the pipeline completed successfully.
# Unset conflicting Singularity environment variables
unset SINGULARITYENV_TMPDIR
unset SINGULARITYENV_NXF_DEBUG
[9a/4915ee] process > DNA_VARIANT_CALLING:FastqTo... [100%] 27 of 27 ✔
[42/490b61] process > DNA_VARIANT_CALLING:MarkIll... [100%] 27 of 27 ✔
[e2/5c9a78] process > DNA_VARIANT_CALLING:SamToFa... [100%] 27 of 27 ✔
[18/a33d64] process > DNA_VARIANT_CALLING:bwamem2... [100%] 1 of 1 ✔
[d8/d501c2] process > DNA_VARIANT_CALLING:bwamem2... [100%] 27 of 27 ✔
[53/1155e9] process > DNA_VARIANT_CALLING:CreateS... [100%] 1 of 1 ✔
[f8/969de5] process > DNA_VARIANT_CALLING:samtool... [100%] 1 of 1 ✔
[0f/a92e33] process > DNA_VARIANT_CALLING:MergeBa... [100%] 27 of 27 ✔
[1c/6ebcc7] process > DNA_VARIANT_CALLING:MarkDup... [100%] 27 of 27 ✔
[86/d10967] process > DNA_VARIANT_CALLING:SortAnd... [100%] 27 of 27 ✔
[2d/7fd6ba] process > DNA_VARIANT_CALLING:bedtool... [100%] 1 of 1 ✔
[ae/f93ecc] process > DNA_VARIANT_CALLING:gatk_Ha... [100%] 10 of 10 ✔
[02/d68957] process > DNA_VARIANT_CALLING:merge_vcf [100%] 1 of 1 ✔
[b5/0f8110] process > DNA_VARIANT_CALLING:vcftool... [100%] 1 of 1 ✔
[39/b07f21] process > DNA_VARIANT_CALLING:SortVcf... [100%] 1 of 1 ✔
[be/9ac910] process > DNA_VARIANT_CALLING:calc_DP... [100%] 1 of 1 ✔
[19/d72b93] process > DNA_VARIANT_CALLING:Variant... [100%] 1 of 1 ✔
[17/563fc9] process > DNA_VARIANT_CALLING:keep_on... [100%] 1 of 1 ✔
Completed at: 13-Jun-2024 00:22:28
Duration : 35m 53s
CPU hours : 2.4
Succeeded : 209
There has been an update of the server and I will have to check the pipeline again.
Copying @vsatheesh's message from slack and #16 (comment) to a separate Issue, since this is unrelated to the SNPeff PR.