I am trying to run the nfcore methylseq pipeline as I've done previously with the same type of .fastq.gz files in the past. The issue I am facing is that I am now on a different computer and I've had to set up all the packages and such by myself and I really don't have a clear idea of what I've managed to do - but I am alone and I have no one to provide support on this at my university.
This is the error log that I'm obtaining after running the pipeline, specifically for cutadapt:
AUTO-DETECTING ADAPTER TYPE =========================== Attempting to auto-detect adapter type from the first 1 million sequences of the first file (>> PN0341_0002_S2_L001_R1_001.fastq.gz <<) Found perfect matches for the following adapter sequences: Adapter type Count Sequence Sequences analysed Percentage Illumina 434 AGATCGGAAGAGC 1000000 0.04 smallRNA 0 TGGAATTCTCGG 1000000 0.00 Nextera 0 CTGTCTCTTATA 1000000 0.00 Using Illumina adapter for trimming (count: 434). Second best hit was smallRNA (count: 0) Writing report to 'PN0341_0002_S2_L001_R1_001.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: PN0341_0002_S2_L001_R1_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.4 Python version: could not detect Number of cores used for trimming: 4 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 Running FastQC on the data once trimming has completed Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.4). Setting -j 4 Writing final adapter and quality trimmed output to PN0341_0002_S2_L001_R1_001_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file PN0341_0002_S2_L001_R1_001.fastq.gz <<< This is cutadapt 3.4 with Python 3.8.8 Command line parameters: -j 4 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC PN0341_0002_S2_L001_R1_001.fastq.gz Run "cutadapt --help" to see command-line options. See https://cutadapt.readthedocs.io/ for full documentation. cutadapt: error: [Errno 2] No such file or directory Cutadapt terminated with exit signal: '512'. Terminating Trim Galore run, please check error message(s) to get an idea what went wrong...
I have no other error messages so I literally have no idea of what could've gone wrong.
What I do know is:
a) the file is definitely being read because the way that the nf-core pipeline works is that I provide an input path and the pipeline reads the .fastq.gz files with the corresponding naming convention. This is the right file, right name and it is in the specified directory, so I think (I might be wrong) that the error must be a matter of some outdated parameter, but I cannot figure out which.
TrimGalore version is 0.6.6 and cutadapt version is 3.4