I am running trim-galore on a computing cluster and would like to remove adapters from my sequences. I downloaded and installed the cutadapt package for this task.
The following is the line of code I'm using for trimming:
./trim_galore -q 30 --illumina -o /work/bekhorn/Trimmed/ --gzip --paired --path_to_cutadapt /work/bekhorn/bin/cutadapt SRR1518485_1.fastq SRR1518485_2.fastq
Cutadapt appears to start working, however, I get error messages and the program terminates with no written output.
Here are the lines printed to the screen:
"No quality encoding type selected. Assuming that the data provided uses Sanger encoded Phred scores (default) Path to Cutadapt set as: '/work/bekhorn/bin/cutadapt' (user defined) 1.11 Cutadapt seems to be working fine (tested command '/work/bekhorn/bin/cutadapt --version') Writing report to '/global/a/work/bekhorn/Trimmed/SRR1518485_1.fastq_trimming_report.txt' SUMMARISING RUN PARAMETERS Input filename: SRR1518485_1.fastq Trimming mode: paired-end Trim Galore version: 0.4.2 Cutadapt version: 1.11 Quality Phred score cutoff: 30 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) 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 Writing final adapter and quality trimmed output to SRR1518485_1_trimmed.fq.gz Now performing quality (cutoff 30) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGArom file SRR1518485_1.fastq. This is cutadapt 1.11 with Python 2.6.6 Command line parameters: -f fastq -e 0.1 -q 30 -O 1 -a AGATCGGAAGAGC SRR1518485_1.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Traceback (most recent call last): File "/work/bekhorn/bin/cutadapt", line 5, in <module> pkg_resources.run_script('cutadapt==1.11', u'cutadapt') File "/usr/lib/python2.6/site-packages/pkg_resources.py", line 461, in run_script self.require(requires).run_script(script_name, ns) File "/usr/lib/python2.6/site-packages/pkg_resources.py", line 1194, in run_script execfile(script_filename, namespace, namespace) File "/gwork/bekhorn/lib64/python2.6/site-packages/cutadapt-1.11-py2.6-linux-x86_64.egg/EGG-INFO/scripts/cutadapt", 10, in <module> cutadapt.main() File "/work/bekhorn/lib64/python2.6/site-packages/cutadapt-1.11-py2.6-linux-x86_64.egg/cutadapt/scripts/cutadapt.pyne 702, in main stats = process_single_reads(reader, modifiers, filters) File "/work/bekhorn/lib64/python2.6/site-packages/cutadapt-1.11-py2.6-linux-x86_64.egg/cutadapt/scripts/cutadapt.pyne 115, in process_single_reads read = modifier(read) File "/work/bekhorn/lib64/python2.6/site-packages/cutadapt-1.11-py2.6-linux-x86_64.egg/cutadapt/modifiers.py", line in __call__ start, stop = quality_trim_index(read.qualities, self.cutoff_front, self.cutoff_back, self.base) TypeError: quality_trim_index() takes at most 3 arguments (4 given) Cutadapt terminated with exit signal: '256'. Terminating Trim Galore run, please check error message(s) to get an idea what went wrong..."
Has anyone else experienced this same problem or know what I am doing wrong?