Trim_galore error: quality_trim_index()

Question

[bekahlee54]

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)[0].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?

[Devon Ryan]

My guess is that cutadapt doesn't work in python 2.6 (that's incredibly outdated anyway). Use python 2.7.

[Eric Lim]

Cutadapt's doc indicates it supports 2.6. I just tested with Python 2.6.9 and everything worked. OP used 2.6.6. Unsure if that's the culprit.

[Devon Ryan]

Perhaps it's cython then. This function exists twice in the cutadapt code, once with 4 arguments and once with 3, so it's picking up the wrong one for some reason. A likely simpler solution would be for cutadapt to only define the function once.

[Eric Lim]

OP should just install cutadapt via miniconda/bioconda and be done with it.

[Marcel M]

Thanks, I’ve removed the 3-argument version now. This would not fix the problem the OP has, though since the underlying problem is that the extension module (which contains the 4-argument version of the function) could not be loaded. This points to a version mismatch or some other installation problem.

[bekahlee54]

Updating the python version solved the problem.