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Old 07-05-2014, 04:25 PM   #1
MDeBiasse
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Location: Baton Rouge, LA

Join Date: Jul 2014
Posts: 2
Default Problem calling Fastqc in Trim Galore?

Hello,
When running Trim Galore, my .trimmed.fq file is blank and I get an error message. I suspect it is because Fastqc is not installed correctly (?). The output is pasted below. Thank you for any advice!

############
No quality encoding type selected. Assuming that the data provided uses Sanger encoded Phred scores (default)

Writing report to 'file2.fastq_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: file2.fastq
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 file2_trimmed.fq


>>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file file2.fastq <<<
sh: /~Programs/cutadapt: is a directory

RUN STATISTICS FOR INPUT FILE: file2.fastq
=============================================
0 sequences processed in total
Illegal division by zero at trim_galore.pl line 565.
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Old 07-05-2014, 10:26 PM   #2
fkrueger
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It appears that you have specified the path to Cutadapt as the directory and not the executable. Appending cutadapt to the end of the path should fix that problem.

Cheers, Felix
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Old 07-06-2014, 04:17 AM   #3
MDeBiasse
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Oh my goodness, silly mistake. Changing the path did fix the problem. Thank you very much Felix!
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