Trim_galore with gnu parallel
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Entering edit mode
7 months ago
francesca3 ▴ 50

Hi, I'm trying to paralize trim_galore. I followed what was written here How to speed up trimming using trim galorer, but I continue to get an error. Here, there is my code

folder_genUnit=/pathtomyfolder
output_folder=/pathtomyfolder
export folder_genUnit output_folder
parallel --plus 'trim_galore {...}.gz  --phred33 --q 20 --fastqc --illumina -o $output_folder' ::: $folder_genUnit/*.gz

This is the error I get

Multicore support not enabled. Proceeding with single-core trimming.
Path to Cutadapt set as: 'cutadapt' (default)
Cutadapt seems to be working fine (tested command 'cutadapt --version')
Cutadapt version: 2.6
single-core operation.
Output will be written into the directory:  /mypath/
gzip: /mypath/01_1_S4_R1_001.gz: No such file or  directory
Input file '/mypath/AFSC/01_1_S4_R1_001.gz' seems to be completely empty. Consider respecifying!

So, it says that the folder is empy but it is not true (in fact, it reports also the file that it should use) I'm running it in PBS mode, I don't know if it can make any difference.

Thanks a lot, Francesca

parallel trim_galore RNA-Seq trim fastq • 338 views
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can you verify that ls /mypath/AFSC/01_1_S4_R1_001.gz is working? ( post the output of it here)

and you have not accidentally overwritten your input files while testing the cmdline or such?

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the result is this one

/mypath/AFSC/01_tot_S5_R1_001.fastq.gz

I noticed that also with loop says the same thing. So I don't think it is a parallel problem.

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Entering edit mode

the folder is really called 'mypath/' ??? hard to believe ;-)

moreover I also notice that both

gzip: /mypath/01_1_S4_R1_001.gz: No such file or directory

Input file '/mypath/AFSC/01_1_S4_R1_001.gz' se

are mentioned, so either one of them is likely not correct

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