The bioBakery help forum

"ERROR: Unable to write file" when '--bypass-trim' is used

I have problems with the trimmomatic part of the internal kneaddata pipeline, because It doesn’t trim the adapters of my sequences (fastqc reports the same % of nextera in pre and post reads), so I’m trying the --bypass-trim option on previously trimmed reads. The problem is that now I’m getting the following error:

Bypass trimming                                                                                                                                                                                               
Total reads after trimming path_to_file.....  16644446.0
Total reads after trimming path_to_file ...... 16644446.0
ERROR: Unable to write file: reformatted_identifiers14xejcfc_decompressed_eh21s7c4_ERR1855538_trimmed_1

The file reformatted_identifiers14xejcfc_decompressed_eh21s7c4_ERR1855538_trimmed_1 already exist, because was produced by previous steps of the kneaddata pipeline, so i’m not sure if it fails because want to write a file with the same name again or something else.

I tried with multiple files and it’s always the same problem (besides the name of the temp file of course), so I’m pretty sure that this only happens when --bypass-trim is used.

I’m using kneaddata v0.10.0