Problem calling Fastqc in Trim Galore?

[MDeBiasse]

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.

[fkrueger]

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

[MDeBiasse]

Oh my goodness, silly mistake. Changing the path did fix the problem. Thank you very much Felix!