trim galore and cutadapt software errors

Question

[nikhilvgbt]

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

[GouthamAtla]

How did you install them? Are you facing errors while installing them?

[nikhilvgbt]

Yes, I have a problem in installing the cutadapt software itself.

[nikhilvgbt]

hi..

@Devon Ryan...

please tell me that

can I use this file as a reference genome for Tophat since they have mentioned that word as Variant ??

please check the link given bellow:

ftp://ftp.ncbi.nlm.nih.gov/sra/reports/Assembly/GRCh37-HG19_Broad_variant/Homo_sapiens_assembly19.fasta

[Devon Ryan]

This should be a new question, but there's no reason you shouldn't be able to use that. Just keep in mind that the annotation file you might get from elsewhere may or may not match it.

[nikhilvgbt]

thanks Ryan:

but one thing I didn't understand what is the deference between the UCSC fasta file as a reference and this file... as a reference file will be better...and what about the Variant they have mentioned in root directory ???

[Devon Ryan]

"Difference", not "deference".

It's unclear exactly what the differences are. At least the b37 reference from Broad has a slightly different sequence and possibly some different contigs in some cases. You'd have to either ask someone from the Broad (they have documentation about this somewhere) or just look yourself by comparing the sequences. In any case, unless you're calling variants on the same samples, then you might as well just use either the UCSC or Ensembl references.

Answer 1

[Devon Ryan]

sudo apt-get install python-dev

or whatever the equivalent is on your system.

[nikhilvgbt]

Thanks Devon;

I get one more error while running the trim_galore command. Could you please help me with it?

My error:

perl trim_galore --paired --phred333 --q 20 --a AGATCGGAAGAGC -stringency 5 -e 0.1 --t --r1 35 --r2 35 SRR364313_1.fastq SRR364313_2.fastq
No quality encoding type selected. Assuming that the data provided uses Sanger encoded Phred scores (default)

Writing report to '--paired_trimming_report.txt'

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 <<<
open3: exec of cutadapt -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC --paired failed at trim_galore line 507.

[Devon Ryan]

Is cutadapt in your PATH? That is, if you simply type cutadapt from the command line then what is returned?

[nikhilvgbt]

cutadapt: command not found

[Devon Ryan]

So it needs to be added to your PATH then. Here's one (of many) sites explaining how to change the PATH: http://www.cyberciti.biz/faq/unix-linux-adding-path/

[nikhilvgbt]

trim_galore --paired --phred333 --q 20 --a AGATCGGAAGAGC - stringency 5 --e 0.1 --t --r1 35 --r2 35 SRR364313_1.fastq SRR364313_2.fastq

Please check the command which I have given above. Whether it's correct or not? Still I am not able to run the trim galore software. Could you please help me.

[Devon Ryan]

I assume that --phred333 should be --phred33, though I expect that that's the default. Anyway, when saying "not able to run" something, it's a good idea to give the error message you receive. Otherwise, it's impossible to help you.

[nikhilvgbt]

Thank you so much sir

Now the program is running.

This is the correct command which I used

trim_galore --paired --phred33 -q 20 -a AGATCGGAAGAGC --stringency 5 -e 0.1 --retain_unpaired --trim1 -r1 35 -r2 35 SRR364314_1.fastq SRR364314_2.fastq

[nikhilvgbt]

and how to define path in the trim galore for cutadapt

[Felix Krueger]

Open Trim Galore in a text editor and edit the path to the Cutadapt executable where it says:

# change these paths if needed:
my $path_to_cutadapt = 'cutadapt';

[nikhilvgbt]

my $path_to_cutadapt = 'cutadapt';

in this command 'cutadapt' will be replaced with the path of the cutadapt folder .. right or path of the python script inside the the folder???

[Devon Ryan]

The path of the executable. The alternative is to simply add the directory to your PATH variable, as detailed in the link I gave.