TrimGalore error : Cutadapt terminated with exit signal: '512'.

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5.9 years ago

lovishpuri • 0

Hi, I'm getting this error while trying to remove adapters and contaminants using Trim_Galore. Please help.

> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file
> /home//samples/chronic pancreatitis/SRR5020215.fastq <<<
>
  sh: 1: Syntax error: "(" unexpected
> 
> 
> Cutadapt terminated with exit signal: '512'. Terminating Trim Galore
> run, please check error message(s) to get an idea what went wrong...

cutadapt trim_galore adapter_trimming • 3.1k views

ADD COMMENT • link updated 5.9 years ago by Pierre Lindenbaum 161k • written 5.9 years ago by lovishpuri • 0

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what was the command line ?

ADD REPLY • link 5.9 years ago by Pierre Lindenbaum 161k

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`/home//samples/chronic pancreatitis`

did you edit user name here? By any chance, are these files from SRA dump?

ADD REPLY • link 5.9 years ago by cpad0112 21k

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/home//samples/chronic pancreatitis

The error may be due to the space in the folder name. As a rule of thumb, avoid spaces altogether in file and folder names - while many programs deals with them just fine, some don't. If you do use spaces, escape the space (/home//samples/chronic\ pancreatitis) or use single quotes ('/home//samples/chronic pancreatitis').

ADD REPLY • link 5.9 years ago by h.mon 35k

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