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XPRESSyourself / XPRESSpipe

An alignment and analysis pipeline for Ribosome Profiling and RNA-seq data
https://xpresspipe.readthedocs.io/en/latest/
GNU General Public License v3.0
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Trimming seg fault #19

Closed j-berg closed 5 years ago

j-berg commented 5 years ago

When I run the pipeline, it breaks during trimming with this error:

sh: line 1: 51633 Segmentation fault: 11  fastp --thread 12 -i /Users/jordan/Desktop/mpci_rp/MPCI_120m_RNA.fastq -o /Users/jordan/Desktop/mpci_out/trimmed_fastq/trimmed_MPCI_120m_RNA.fastq --trim_poly_x -l 17 -q 28 -j /Users/jordan/Desktop/mpci_out/trimmed_fastq/MPCI_120m_RNAfastp.json -h /Users/jordan/Desktop/mpci_out/trimmed_fastq/MPCI_120m_RNAfastp.html >> /Users/jordan/Desktop/mpci_out/mpci.log 2>&1
j-berg commented 5 years ago

Issue arises when polyX adaptor trimming essentially throws out all reads due to low quality.