I have a paired collection of paired-end fastqsanger.gz files which I am trying to run through TrimGalore! using the default settings. However, after running for several hours, one of the jobs hits the following error: Fatal error: Exit code 141 ()
Multicore support not enabled. Proceeding with single-core trimming. Path to Cutadapt set as: 'cutadapt' (default) Cutadapt seems to be working fine (tested command 'cutadapt --version') Cutadapt version: 2.3 single-core operation. Output will be written into the directory: /corral4/main/jobs/040/441/40441407/working/ AUTO-DETECTING ADAPTER TYPE =========================== Attempting to auto-detect adapter type from the first 1 million sequences of the first file (>> input_1.fastq.gz <<) Found perfect matches for the following adapter sequences: Adapter type Count Sequence Sequences analysed Percentage Illumina 8075 AGATCGGAAGAGC 1000000 0.81 Nextera 1493 CTGTCTCTTATA 1000000 0.15 smallRNA 11 TGGAATTCTCGG 1000000 0.00 Using Illumina adapter for trimming (count: 8075). Second best hit was Nextera (count: 1493) Writing report to '/corral4/main/jobs/040/441/40441407/working/input_1.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: input_1.fastq.gz Trimming mode: paired-end Trim Galore version: 0.6.3 Cutadapt version: 2.3 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 2.3). Setting -j 1 Writing final adapter and quality trimmed output to input_1_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file input_1.fastq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed gzip: short write
It’s not obvious to me where the error is coming from. Any insight is appreciated.