SUMMARISING RUN PARAMETERS
==========================
Input filename: /Volumes/web/metacarcinus/Salmo_Calig/analyses/20190806_TrimGalore/Sealice_F1_S20_L002_R1_001_val_1.fq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4_dev
Cutadapt version: 1.16
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; default (inconclusive auto-detection))
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
All Read 1 sequences will be trimmed by 7 bp from their 5' end to avoid poor qualities or biases
All Read 2 sequences will be trimmed by 7 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications)
All Read 1 sequences will be trimmed by 7 bp from their 3' end to avoid poor qualities or biases
All Read 2 sequences will be trimmed by 7 bp from their 3' end to avoid poor qualities or biases
Output file will be GZIP compressed


This is cutadapt 1.16 with Python 3.6.8
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /Volumes/web/metacarcinus/Salmo_Calig/analyses/20190806_TrimGalore/Sealice_F1_S20_L002_R1_001_val_1.fq.gz
Running on 1 core
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Traceback (most recent call last):
  File "/anaconda3/bin/cutadapt", line 11, in <module>
    load_entry_point('cutadapt==1.16', 'console_scripts', 'cutadapt')()
  File "/anaconda3/lib/python3.6/site-packages/cutadapt/__main__.py", line 747, in main
    stats = runner.run()
  File "/anaconda3/lib/python3.6/site-packages/cutadapt/pipeline.py", line 174, in run
    (n, total1_bp, total2_bp) = self.process_reads()
  File "/anaconda3/lib/python3.6/site-packages/cutadapt/pipeline.py", line 216, in process_reads
    for read in self._reader:
  File "src/cutadapt/_seqio.pyx", line 201, in __iter__ (src/cutadapt/_seqio.c:5386)
  File "/anaconda3/lib/python3.6/gzip.py", line 289, in read1
    return self._buffer.read1(size)
  File "/anaconda3/lib/python3.6/_compression.py", line 68, in readinto
    data = self.read(len(byte_view))
  File "/anaconda3/lib/python3.6/gzip.py", line 469, in read
    buf = self._fp.read(io.DEFAULT_BUFFER_SIZE)
  File "/anaconda3/lib/python3.6/gzip.py", line 91, in read
    self.file.read(size-self._length+read)
OSError: [Errno 5] Input/output error