/usr/bin/env: ‘python2’: No such file or directory

[marina-yurieva]

Problem

I had the GLIB issue before. Now, with the updated pipeline, when I run main.nf, I get this error:

xecutor >  slurm (80)
[0a/49436e] process > fastqc (d5w-114-col-13-rep1)   [100%] 15 of 15 ✔
[46/c60d80] process > trimmomatic (cis-117-col-25... [100%] 15 of 15 ✔
[3c/1a2f6b] process > fastqc_trimmed (cis-117-col... [100%] 15 of 15 ✔
[fd/5a0e7e] process > star (cis-117-col-25-rep1)     [100%] 15 of 15 ✔
[34/9e91c3] process > stringtie (cis-117-col-25-r... [100%] 15 of 15 ✔
[2e/0e97a9] process > prep_de                        [100%] 1 of 1, failed: 1 ✘
[88/e12ecf] process > stringtie_merge (1)            [100%] 1 of 1 ✔
[-        ] process > rmats                          -
[f5/21b75d] process > multiqc (1)                    [100%] 1 of 1 ✔
[db/f8fcb5] process > collect_tool_versions_env1     [100%] 1 of 1 ✔
[ef/8ba6d4] process > collect_tool_versions_env2     [100%] 1 of 1 ✔
-[splicing-pipelines-nf] Pipeline completed with errors-
-[splicing-pipelines-nf] Cleanup: Working directory was not cleared from intermediate files due to pipeline errors. You can re-use them with -resume option. 
 -
WARN: Failed to render execution report -- see the log file for details
WARN: Failed to render execution timeline -- see the log file for details
Error executing process > 'prep_de'

Caused by:
  Process `prep_de` terminated with an error exit status (127)

Command executed:
 echo "d5w-114-col-08-rep2
  d5w-114-col-08-rep3
  cis-117-col-18-rep1
  ccr-134-col-04-rep2
  cis-117-col-25-rep2
  cis-117-col-18-rep3
  ccr-134-col-04-rep1
  d5w-114-col-13-rep3
  ccr-134-col-04-rep3
  d5w-114-col-08-rep1
  d5w-114-col-13-rep2
  cis-117-col-18-rep2
  cis-117-col-25-rep3
  d5w-114-col-13-rep1
  cis-117-col-25-rep1" > samples.txt
      echo "d5w-114-col-08-rep2_for_DGE.gtf
  d5w-114-col-08-rep3_for_DGE.gtf
  cis-117-col-18-rep1_for_DGE.gtf
  ccr-134-col-04-rep2_for_DGE.gtf
  cis-117-col-25-rep2_for_DGE.gtf
  cis-117-col-18-rep3_for_DGE.gtf
  ccr-134-col-04-rep1_for_DGE.gtf
  d5w-114-col-13-rep3_for_DGE.gtf
  ccr-134-col-04-rep3_for_DGE.gtf
  d5w-114-col-08-rep1_for_DGE.gtf
  d5w-114-col-13-rep2_for_DGE.gtf
  cis-117-col-18-rep2_for_DGE.gtf
  cis-117-col-25-rep3_for_DGE.gtf
  d5w-114-col-13-rep1_for_DGE.gtf
  cis-117-col-25-rep1_for_DGE.gtf" > gtfs.txt
      paste -d ' ' samples.txt gtfs.txt > sample_lst.txt
prepDE.py -i sample_lst.txt  -l 150               -g tnbc_splicing_project_2023-01-16_01-17-23_gene_count_matrix.csv -t tnbc_splicing_project_2023-01-16_01-17-23_transcript_count_matrix.csv
  
      # save .command.* logs
      task_hash=`basename ${PWD} | cut -c1-6`; mkdir command-logs-$task_hash ; cp .command.*{err,log,sh} command-logs-$task_hash

Command exit status:
  127

Command output:
  (empty)

Command error:
  /usr/bin/env: ‘python2’: No such file or directory