#C0493FQQZ3P Hi, I am running nf-core

rnasplice

(see code below) but always the pipeline fails (see below)? Can someone please help me how to fix this issue?

module use --append /projects/omics_share/meta/modules/
module load nextflow
module load singularity

nextflow run /projects/lab/toufim/nfcore_rnasplice/1_0_4/rnasplice \
--input /flashscratch/toufim/23_pal_003004_rnasplice/23_Palucka_003_004_samplesheet.csv \
--contrasts /flashscratch/toufim/23_pal_003004_rnasplice/23_Palucka_003_004_Contrastsheet.csv \
--outdir /flashscratch/toufim/23_pal_003004_rnasplice/ \
--fasta /projects/lab/toufim/GENCODE/GRCh38.p14_Release_47/GRCh38.primary_assembly.genome.fa \
--gtf /projects/lab/toufim/GENCODE/GRCh38.p14_Release_47/gencode.v47.primary_assembly.annotation.gtf \
--aligner star \
--save_reference \
--gencode \
--gtf_extra_attributes gene_id \
--rmats_read_len 150 \
-profile jax -resume

Log output:

Plus 32 more processes waiting for tasks…
WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition
ERROR ~ Error executing process > 'NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:GENERATE_EVENTS_IOE'

Caused by:
  java.io.IOException: Failed to create Singularity cache directory: /fastscratch/singularity_cache_nfcore -- Make sure a file with the same name does not exist and you have write permission



 -- Check '.nextflow.log' file for details
-[nf-core/rnasplice] Pipeline completed with errors-



[-        ] NFC…ARE_GENOME:GTF_GENE_FILTER -
[-        ] NFC…OME:MAKE_TRANSCRIPTS_FASTA -
[-        ] NFC…ENOME:CUSTOM_GETCHROMSIZES -
[-        ] NFC…GENOME:STAR_GENOMEGENERATE -
[-        ] NFC…REPARE_GENOME:SALMON_INDEX -
[-        ] NFC…UT_CHECK:SAMPLESHEET_CHECK -
[-        ] NFC…_CHECK:CONTRASTSHEET_CHECK -
[-        ] NFC…SPLICE:RNASPLICE:CAT_FASTQ -
[-        ] NFC…UMITOOLS_TRIMGALORE:FASTQC -
[-        ] NFC…OOLS_TRIMGALORE:TRIMGALORE -
[-        ] NFC…LICE:ALIGN_STAR:STAR_ALIGN -
[-        ] NFC…ATS_SAMTOOLS:SAMTOOLS_SORT -
[-        ] NFC…TS_SAMTOOLS:SAMTOOLS_INDEX -
[-        ] NFC…TS_SAMTOOLS:SAMTOOLS_STATS -
[-        ] NFC…SAMTOOLS:SAMTOOLS_FLAGSTAT -
[-        ] NFC…SAMTOOLS:SAMTOOLS_IDXSTATS -
[-        ] NFC…XSEQ_DEU:DEXSEQ_ANNOTATION -
[-        ] NFC…CE:DEXSEQ_DEU:DEXSEQ_COUNT -
[-        ] NFC…ICE:DEXSEQ_DEU:DEXSEQ_EXON -
[-        ] NFC…GER_DEU:SUBREAD_FLATTENGTF -
Plus 32 more processes waiting for tasks…
WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition
ERROR ~ Error executing process > 'NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:GENERATE_EVENTS_IOE'

Caused by:
  java.io.IOException: Failed to create Singularity cache directory: /fastscratch/singularity_cache_nfcore -- Make sure a file with the same name does not exist and you have write permission

I think

java.io.IOException: Failed to create Singularity cache directory: /fastscratch/singularity_cache_nfcore -- Make sure a file with the same name does not exist and you have write permission

is pretty descriptive -- just do what it says. (The

Make sure a file with the same name does not exist

is there because the pipeline wants to write to a directory of that name, which cannot be created if a file already exists. I consider that unlikely, it seems more probably that you don't have write permissions.) Since I suspect that the Singularity cache directory was set to that location in the

jax

profile, I would discuss this with your sysadmins -- either they need to give you write permissions or have the profile changed.)

@Thomas Danhorn thank you for the response. Yes, it was about the Singularity cache directory. It is now fixed, and I could submit the run again.