Originally posted by fkrueger
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Please help! (Trim Galore of RRBS data)
Hi!
I want to use Trim Galore to precess RRBS data before working with bismark.
System win7 ultimate, 64bit
However, I get the following error message:
Traceback (most recent call last):
File "F:\RRBSCML\cutadapt\scripts\cutadapt.py", line 71, in <module> from cutadapt import seqio, __version__
ImportError: cannot import name seqio
What am I doing wrong?
Thanks for help!!
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Hi magisterh,
The error you are seeing is caused by Cutadapt not being able to find required packages under Windows. I would suggest to either contact Marcel Martin directly (the developer of Cutadapt), or follow BB's suggestion to use his suite of tools.
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trim galore and cutadapt software errors
hi...
this is the error i am getting while running the Trim galore and cutadapt... what is the exactly this error, and how can solve this problem ????
cutadapt/_align.c:8:22: fatal error: pyconfig.h: No such file or directory
#include "pyconfig.h"
^
compilation terminated.
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
----------------------------------------
Cleaning up...
Command /usr/bin/python -c "import setuptools, tokenize;__file__='/tmp/pip_build_manman/cutadapt/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-V_zM1D-record/install-record.txt --single-version-externally-managed --compile failed with error code 1 in /tmp/pip_build_manman/cutadapt
Storing debug log for failure in /home/manman/.pip/pip.log
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Originally posted by JQL View PostHi
I try to run trim galore but received an error message (pasted below). It says "cutadapt ... failed at /usr/local/bin/trim_galore line 420". Anyone knows what it means?
thanks
###############################
$ No quality encoding type selected. Assuming that the data provided uses Sanger encoded Phred scores (default)
SUMMARISING RUN PARAMETERS
==========================
Input filename: Sample_C1.R1.fastq.gz
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'GATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGCCGTCTTCTGCTTG'
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 20 bp
Minimum required sequence length before a sequence gets removed: 20 bp
Running FastQC on the data once trimming has completed
Running FastQC with the following extra arguments: '--outdir ./'
Output file will be GZIP compressed
Writing final adapter and quality trimmed output to Sample_C1.R1_trimmed.fq
>>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'GATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGCCGTCTTCTGCTTG' from file Sample_C1.R1.fastq.gz <<<
open3: exec of cutadapt -f fastq -e 0.1 -q 20 -O 20 -a GATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGCCGTCTTCTGCTTG Sample_C1.R1.fastq.gz failed at /usr/local/bin/trim_galore line 420
RUN STATISTICS FOR INPUT FILE: Sample_C1.R1.fastq.gz
=============================================
0 sequences processed in total
Illegal division by zero at /usr/local/bin/trim_galore line 506.
^C
[3]- Exit 255 trim_galore --fastqc_args "--outdir ./" -a GATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGCCGTCTTCTGCTTG -s 20 Sample_C1.R1.fastq.gz
i am also getting the same error ... please can tell me how did you try to solve this problem ????
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Hi everyone, does anyone know how to fix this trim galore/cutadapt error:
SUMMARISING RUN PARAMETERS
==========================
Input filename: paired
Trimming mode: single-end
Trim Galore version: 0.3.7
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC'
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length before a sequence gets removed: 20 bp
Writing final adapter and quality trimmed output to paired_trimmed.fq
>>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file paired <<<
'import site' failed; use -v for traceback
Traceback (most recent call last):
File "/jhpce/shared/community/compiler/gcc/4.4.7/python/3.4.0/lib/python3.4/encodings/__init__.py", line 31, in <module>
import codecs
File "/jhpce/shared/community/compiler/gcc/4.4.7/python/3.4.0/lib/python3.4/codecs.py", line 88
*, _is_text_encoding=None):
^
SyntaxError: invalid syntax
Cutadapt terminated with exit signal: '256'.
Terminating Trim Galore run, please check error message(s) to get an idea what went wrong...
Yet codecs is part of my available python modules!
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Hi Varenka,
not quite sure what is going wrong exactly but you need to get Cutadapt up and running before using Trim Galore. If you enter
Code:$ cutadapt
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