gravatar for olechnwin

3 hours ago by

Hi All,

I'm hoping someone can help me. I'm running trim_galore in a pipeline to automate trimming multiple fastq files. It works for some paired fastq files but then failed with "Unable to create directory <directory_name> File exists". This is the code I ran trim_galore:

trim_galore -q 20 --length 20 --illumina -o trim --paired  fastq_pair1 fastq_pair2 --fastqc --fastqc_args '--outdir fastqc_rslt'

Example of fastq_pair1 is

../fastq/D9_20-0658_563R2/D9_20-0658_563R2_S68_L002_R1_001.sub.fastq.gz

and fastq_pair2 is

../fastq/D9_20-0658_563R2/D9_20-0658_563R2_S68_L002_R1_001.sub.fastq.gz

It supposed to run trim_galore for each pair and put them in trim directory. trim_galore works for other pairs but will fail for some and generates "Unable to create directory trim/ File exists" error. I should add that if I ran the same code to process the same fastq files, trim_galore will fail for different pairs.

I'm puzzled. I already checked that the filenames are unique and trimmed file D9_20-0658_563R2_S68_L002_R1_001 is not yet in the trim directory.

Anyone has any idea how to fix this? Trim_galore version is 0.6.6

Thanks in advance for your help.

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modified 2 hours ago

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3 hours ago
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olechnwin30



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