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Hi I am trying to run command on local Ubuntu serv...
# denovotranscript
l
Hi I am trying to run command on local Ubuntu server using Singularity and hitting a persistent error before any processes launch. 
~/software/nextflow run "$PIPELINE" \
--work-dir "$WORKDIR" \
--input "$BASE/src/CP_primary_files.csv" \
--outdir "$BASE/results/plurivora_denovo" \
--skip_fastp \
--skip_fastqc \
--assemblers trinity_no_norm \
--extra_trinity_args "--SS_lib_type RF --jaccard_clip" \
--busco_lineage 'stramenopiles_odb10' \
-profile singularity \
-resume \
2>&1 | tee "$LOG"
Every run completes with 
succeededCount=0; failedCount=0
 — no processes ever start. When I had SORTMERNA, it always shows 
work-dir=null
.I downloaded the earlier version of NextFlow (25.04.4) with pipeline version (v1.2.1) to try and manage this and have tried a variety of tiny fixes. From this script, I am getting the issue of ERROR ~ Cannot invoke “java.nio.file.Path.getFileSystem()” because “path” is null -- Check script ‘/home/c838579834/software/nfcore_denovotranscript/subworkflows/nf-core/utils_nfcore_pipeline/main.nf’ at line: 82 or see ‘.nextflow.log’ file for more details [- ] NFCORE_DENOVOTRANSCRIPTDENOVOTRANSCRIPTCAT_FASTQ - [- ] NFCORE_DENOVOTRANSCRIPTDENOVOTRANSCRIPTTRINITY_NO_NORM - [- ] NFCORE_DENOVOTRANSCRIPTDENOVOTRANSCRIPTCAT_CAT - [- ] NFCORE_DENOVOTRANSCRIPTDENOVOTRANSCRIPTEVIGENE_TR2AACDS - [- ] NFCORE_DENOVOTRANSCRIPTDENOVOTRANSCRIPTTX2GENE - [- ] NFCORE_DENOVOTRANSCRIPTDENOVOTRANSCRIPTBUSCO_BUSCO - [- ] NFCORE_DENOVOTRANSCRIPTDENOVOTRANSCRIPTRNAQUAST - [- ] NFCORE_DENOVOTRANSCRIPTDENOVOTRANSCRIPTTRANSRATE - [- ] NFCORE_DENOVOTRANSCRIPTDENOVOTRANSCRIPTSALMON_INDEX - [- ] NFCORE_DENOVOTRANSCRIPTDENOVOTRANSCRIPTSALMON_QUANT - [- ] NFCORE_DENOVOTRANSCRIPTDENOVOTRANSCRIPTMULTIQC - Pulling Singularity image depot.galaxyproject.org/singularity/ubuntu:20.04 [cache /home/c838579834/singularity_cache/depot.galaxyproject.org-singularity-ubuntu-20.04.img] ERROR ~ Cannot invoke “java.nio.file.Path.getFileSystem()” because “path” is null Thoughts? Thanks.
a
Hi Iheger, I think you will need to try using just one dash for setting the work directory: 
-w
or 
-work-dir
. Please let me know if that works
l
That did not fix the “null” issue; thank you for the idea!
a
Ah, I see. Could you please share the .nextflow.log file so I can get a better idea of what might be happening?
l
I started getting this and so I adjusted the memory in the config file and I am still getting the same error:
Copy code
Jul-02 10:09:07.577 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE (CP_P_T1_7); work-dir=/home/(removed intentionally)
  error [nextflow.exception.ProcessFailedException]: Process `NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE (CP_P_T1_7)` terminated with an error exit status (134)
Jul-02 10:09:07.577 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE (CP_P_T1_7); work-dir=/home/c838579834/rnaseq/CP2/09/2f7d64eaed243cb82f34dd3f05b1c5
  error [nextflow.exception.ProcessFailedException]: Process `NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE (CP_P_T1_7)` terminated with an error exit status (134)
Jul-02 10:09:07.588 [TaskFinalizer-7] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE (CP_P_T1_7)'

Caused by:
  Process `NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE (CP_P_T1_7)` terminated with an error exit status (134)


Command executed:

  stringtie \
      CP_P_T1_7.markdup.sorted.bam \
      --rf \
      -G Cytospora-plurivora-v1.0.a1.6709ad7990b4b-evm.genes-KARE80.filtered.gtf \
      -o CP_P_T1_7.transcripts.gtf \
      -A CP_P_T1_7.gene.abundance.txt \
      -C CP_P_T1_7.coverage.gtf \
      -b CP_P_T1_7.ballgown \
      -p 1 \
      -M 0.25 -m 300

Command exit status:
  134

Command output:
  (empty)

Command error:
  *** buffer overflow detected ***: terminated
  .command.sh: line 11:    41 Aborted                 (core dumped) stringtie CP_P_T1_7.markdup.sorted.bam --rf -G Cytospora-plurivora-v1.0.a1.6709ad7990b4b-evm.genes-KARE80.filtered.gtf -o CP_P_T1_7.tr
anscripts.gtf -A CP_P_T1_7.gene.abundance.txt -C CP_P_T1_7.coverage.gtf -b CP_P_T1_7.ballgown -p 1 -M 0.25 -m 300
m
can you test it first with just using 
-profile singularity,test
and without inputs and other modification, to test your overall setup?
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