SECAPR issue
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14 months ago

Hello everyone,

I am using the pipeline SECAPR to align an Hyb-Seq dataset. At the second step of the pipeline, a script is supposed to trim the samples using trimmomatic, and it consistently fails. I know I can use trimmomatic alone, but I wish to be consistent in the use of the pipeline.

The error given is:

('Sample', '_2_', 'not found in control file. Skipped.')
***SECAPR-ERROR: No FASTQ files were found. Check if correct path is provided for --input flag and if all FASTQ files are unzipped


The pipeline does not find the samples in the directory designated in the index file. I have checked multiples times, and the samples are indeed in the right format, properly labelled, in this directory.

Has anyone experienced the same issue? Is the control file quoted is the same than the index file?

SECAPR reads trimmomatic pipeline alignement • 271 views