Error running gem with biowulf slurm executor: genome sequence file not found at directory

on an interactive node, running champagne with the biowulf profile (uses slurm executor for each process)

nextflow run main.nf -profile test_mm10,biowulf -resume

ERROR ~ Error executing process > 'CALL_PEAKS:GEM (CTCF_ChIP_MEF_p20_1)'

Caused by:
  Process `CALL_PEAKS:GEM (CTCF_ChIP_MEF_p20_1)` terminated with an error exit status (255)

Command executed:

  java -Xmx30g -jar $GEMJAR \
    --t 12 \
    --d Read_Distribution_default.txt \
    --g mm10.fa.sizes \
    --genome chr17.fa ref.fa chr9.fa chr13.fa chr19.fa chr8.fa chr12.fa chr7.fa chr14.fa chr6.fa chr5.fa chr_rDNA.fa chr15.fa splitRef.py chr4.fa chr3.fa chrY.fa chr10.fa chr16.fa chr2.fa chrX.fa chr18.fa chr1.fa chrom.sizes chr11.fa chrM.fa \
    --expt CTCF_ChIP_MEF_p20_1.TagAlign.bed \
    --ctrl WCE_p20.TagAlign.bed \
    --out CTCF_ChIP_MEF_p20_1 \
    --k_min 6 \
    --k_max 13 \
    --outNP \
    --nrf

Command exit status:
  255

Command output:

  ============================ Round 0 ============================

  Running with 12 threads ...

  100   /2353272    23.7s
  1000  /2353272    2.1m
  10000 /2353272    2.6m
  1000000   /2353272    6.7m
  2000000   /2353272    6.7m
  2353272   /2353272    6.7m

  Scaling condition , IP/Control = 0.84

  ---------------------------
  Events discovered
  Significant:  61550
  Insignificant:    537
  Filtered: 3

  Total 10723 homotypic events (within 501bp of other events).

  Finish binding event prediction: 6.7m

  Refine read distribution from 2000 binding events.

  ============================ Round 1 ============================

  Running with 12 threads ...

  100   /2353272    2.3s
  1000  /2353272    3.3s
  10000 /2353272    4.3s
  1000000   /2353272    1.7m
  2000000   /2353272    3.3m
  2353272   /2353272    3.9m
  ---------------------------
  Events discovered
  Significant:  63921
  Insignificant:    1135
  Filtered: 0

  Total 4650 homotypic events (within 545bp of other events).

  Finish binding event prediction: 4.0m

  Refine read distribution from 2000 binding events.

  Loading genome sequences ...

Command error:
  WARNING: While bind mounting '/gpfs:/gpfs': destination is already in the mount point list

  chr11.fa genome sequence file is not found at directory chr17.fa.

Work dir:
  /gpfs/gsfs12/users/sovacoolkl/champagne_mm10/work/57/bfcb8c6762e41a5131e578f84294fe

CCBR / CHAMPAGNE

Error running gem with biowulf slurm executor: genome sequence file not found at directory #78