Open marina-yurieva opened 1 year ago
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
Problem
I had the GLIB issue before. Now, with the updated pipeline, when I run main.nf, I get this error: