error when running pipeline project
i have an error when i run the project antarctique on the last release using the custom python script to add the blank filters
see there
/media/superdisk/edna/working/antarctique/snakemake_rapidrun_swarmthe error codes gives this
Traceback (most recent call last):
File "/media/superdisk/edna/working/antarctique/snakemake_rapidrun_swarm/.snakemake/conda/23ff45b8/bin/cutadapt", line 10, in <module>
File "/media/superdisk/edna/working/antarctique/snakemake_rapidrun_swarm/.snakemake/conda/23ff45b8/lib/python3.8/site-packages/cutadapt/__main__.py", line 845, in main_cli
File "/media/superdisk/edna/working/antarctique/snakemake_rapidrun_swarm/.snakemake/conda/23ff45b8/lib/python3.8/site-packages/cutadapt/__main__.py", line 899, in main
File "/media/superdisk/edna/working/antarctique/snakemake_rapidrun_swarm/.snakemake/conda/23ff45b8/lib/python3.8/site-packages/cutadapt/__main__.py", line 437, in open_output_files
File "/media/superdisk/edna/working/antarctique/snakemake_rapidrun_swarm/.snakemake/conda/23ff45b8/lib/python3.8/site-packages/cutadapt/__main__.py", line 504, in open_demultiplex_out
File "/media/superdisk/edna/working/antarctique/snakemake_rapidrun_swarm/.snakemake/conda/23ff45b8/lib/python3.8/site-packages/cutadapt/utils.py", line 167, in xopen
File "/media/superdisk/edna/working/antarctique/snakemake_rapidrun_swarm/.snakemake/conda/23ff45b8/lib/python3.8/site-packages/xopen/__init__.py", line 615, in xopen
OSError: [Errno 24] Too many open files: 'results/intermediates/03_demultiplex_tag/Blank/vert/blank_vert_201019_NB501850_A_L1-4_AIMI-274_253.fastq'
Traceback (most recent call last):
File "/media/superdisk/edna/working/antarctique/snakemake_rapidrun_swarm/.snakemake/conda/23ff45b8/bin/cutadapt", line 10, in <module>
File "/media/superdisk/edna/working/antarctique/snakemake_rapidrun_swarm/.snakemake/conda/23ff45b8/lib/python3.8/site-packages/cutadapt/__main__.py", line 845, in main_cli
File "/media/superdisk/edna/working/antarctique/snakemake_rapidrun_swarm/.snakemake/conda/23ff45b8/lib/python3.8/site-packages/cutadapt/__main__.py", line 899, in main
File "/media/superdisk/edna/working/antarctique/snakemake_rapidrun_swarm/.snakemake/conda/23ff45b8/lib/python3.8/site-packages/cutadapt/__main__.py", line 437, in open_output_files
File "/media/superdisk/edna/working/antarctique/snakemake_rapidrun_swarm/.snakemake/conda/23ff45b8/lib/python3.8/site-packages/cutadapt/__main__.py", line 504, in open_demultiplex_out
File "/media/superdisk/edna/working/antarctique/snakemake_rapidrun_swarm/.snakemake/conda/23ff45b8/lib/python3.8/site-packages/cutadapt/utils.py", line 167, in xopen
File "/media/superdisk/edna/working/antarctique/snakemake_rapidrun_swarm/.snakemake/conda/23ff45b8/lib/python3.8/site-packages/xopen/__init__.py", line 615, in xopen
OSError: [Errno 24] Too many open files: 'results/intermediates/03_demultiplex_tag/Blank/vert/blank_vert_201104_NB501850_A_L1-4_AIMI-270_254.fastq'
[Fri Feb 26 19:27:58 2021]
Error in rule demultiplex_tag:
jobid: 33750
output: results/intermediates/03_demultiplex_tag/flags/201019_NB501850_A_L1-4_AIMI-274_demultiplex_tag.done
log: logs/intermediates/03_demultiplex_tag/201019_NB501850_A_L1-4_AIMI-274.log (check log file(s) for error message)
conda-env: /media/superdisk/edna/working/antarctique/snakemake_rapidrun_swarm/.snakemake/conda/23ff45b8
shell:
cutadapt -m 20 --revcomp -O 8 --discard-untrimmed -g file:results/intermediates/01_settings/barcodes/201019_NB501850_A_L1-4_AIMI-274.fasta results/intermediates/02_merge_fastq/201019_NB501850_A_L1-4_AIMI-274.fastq -o {name}.fastq > logs/intermediates/03_demultiplex_tag/201019_NB501850_A_L1-4_AIMI-274.log
wait
bash scripts/cp_duplicated_barcode.sh results/intermediates/01_settings/barcodes/201019_NB501850_A_L1-4_AIMI-274_duplicated.csv
wait
bash scripts/check_missing_files.sh results/intermediates/01_settings/barcodes/201019_NB501850_A_L1-4_AIMI-274.fasta >> logs/intermediates/03_demultiplex_tag/201019_NB501850_A_L1-4_AIMI-274.log
wait
touch results/intermediates/03_demultiplex_tag/flags/201019_NB501850_A_L1-4_AIMI-274_demultiplex_tag.done
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
[Fri Feb 26 19:27:58 2021]
Error in rule demultiplex_tag:
jobid: 33746
output: results/intermediates/03_demultiplex_tag/flags/201104_NB501850_A_L1-4_AIMI-270_demultiplex_tag.done
log: logs/intermediates/03_demultiplex_tag/201104_NB501850_A_L1-4_AIMI-270.log (check log file(s) for error message)
conda-env: /media/superdisk/edna/working/antarctique/snakemake_rapidrun_swarm/.snakemake/conda/23ff45b8
shell:
cutadapt -m 20 --revcomp -O 8 --discard-untrimmed -g file:results/intermediates/01_settings/barcodes/201104_NB501850_A_L1-4_AIMI-270.fasta results/intermediates/02_merge_fastq/201104_NB501850_A_L1-4_AIMI-270.fastq -o {name}.fastq > logs/intermediates/03_demultiplex_tag/201104_NB501850_A_L1-4_AIMI-270.log
wait
bash scripts/cp_duplicated_barcode.sh results/intermediates/01_settings/barcodes/201104_NB501850_A_L1-4_AIMI-270_duplicated.csv
wait
bash scripts/check_missing_files.sh results/intermediates/01_settings/barcodes/201104_NB501850_A_L1-4_AIMI-270.fasta >> logs/intermediates/03_demultiplex_tag/201104_NB501850_A_L1-4_AIMI-270.log
wait
touch results/intermediates/03_demultiplex_tag/flags/201104_NB501850_A_L1-4_AIMI-270_demultiplex_tag.done
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)