-[nf-core/clipseq] Pipeline completed with errors- Error executing process > 'dedup (PTBP1iCLIP_siCtrl_repl2_s)' Caused by: Process

dedup (PTBP1iCLIP_siCtrl_repl2_s)

terminated with an error exit status (1) Command executed: umi_tools \ dedup \ --umi-separator=":" \ -I PTBP1iCLIP_siCtrl_repl2_s.Aligned.sortedByCoord.out.bam \ -S PTBP1iCLIP_siCtrl_repl2_s.dedup.bam \ --output-stats=PTBP1iCLIP_siCtrl_repl2_s \ --log=PTBP1iCLIP_siCtrl_repl2_s.log samtools index -@ 12 PTBP1iCLIP_siCtrl_repl2_s.dedup.bam Command exit status: 1 Command output: (empty) Command error: INFO: Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred INFO: Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred OverflowError: cannot convert float infinity to integer Exception ignored in: 'umi_tools._dedup_umi.edit_distance' OverflowError: cannot convert float infinity to integer OverflowError: cannot convert float infinity to integer Exception ignored in: 'umi_tools._dedup_umi.edit_distance' OverflowError: cannot convert float infinity to integer Traceback (most recent call last): File "/opt/conda/envs/nf-core-clipseq-1.0.0/bin/umi_tools", line 11, in <module> sys.exit(main()) File "/opt/conda/envs/nf-core-clipseq-1.0.0/lib/python3.7/site-packages/umi_tools/umi_tools.py", line 61, in main module.main(sys.argv) File "/opt/conda/envs/nf-core-clipseq-1.0.0/lib/python3.7/site-packages/umi_tools/dedup.py", line 331, in main threshold=options.threshold) File "/opt/conda/envs/nf-core-clipseq-1.0.0/lib/python3.7/site-packages/umi_tools/network.py", line 419, in call clusters = self.UMIClusterer(counts, threshold) File "/opt/conda/envs/nf-core-clipseq-1.0.0/lib/python3.7/site-packages/umi_tools/network.py", line 369, in call min(len_umis), max(len_umis))) AssertionError: not all umis are the same length(!): 17 - 18

Hi! This can happen if the delimiter in the FASTQ header is incorrectly specified. The default is

:

but some demultiplexing tools use

_

Thanks ! Here's the beginning :

Ok - it doesn’t look like there are any UMIs in the header - either because they weren’t used, or because they haven’t been moved there in the demultiplexing, so that’s why the process is failing

Ho ok. I'm not sure what was done actually. It's the ERR605258.fastq that was mentioned in the paper.

Yes, if you’ve downloaded the raw data from SRA then you will need to move the UMI to the header

Ok thanks a lot . I'll try to change the part for the UMI and see if it can resume from here.