Error in step A: read group line contained literal <tab>

[sanderdebacker]

When running the process_reseq_1.0.py script, the following error occurs:

Line : 677 - Error in step A (bwa-mem): [E::bwa_set_rg] the read group line contained literal <tab> characters -- replace with escaped tabs: \t

Does anyone know whatever causes this error and how to resolve it?

[guiguimartin]

Maybe this is linked to a new version of BWA installed. Which version have you installed? On our computer we use: bwa/0.7.15 and it works fine.

[sanderdebacker]

Solution that worked for me (with bwa-0.7.17).

Replace line 657 in the /utilsSR/utilsSR.py script to:
rg_tag = '@RG"\\t"ID:'+ACC_ID+'"\\t"SM:'+ACC_ID+'"\\t"LB:'+ACC_ID+'"\\t"PU:whatever"\\t"PL:ILLUMINA'

Original:
rg_tag = '@RG"\t"ID:'+ACC_ID+'"\t"SM:'+ACC_ID+'"\t"LB:'+ACC_ID+'"\t"PU:whatever"\t"PL:ILLUMINA'