[E::bwa_set_rg] the read group line contained literal <tab> characters -- replace with escaped tabs: \t
Traceback (most recent call last):
File "/path/bin/bwa-meth-0.10/bwameth.py", line 601, in <module>
main(sys.argv[1:])
File "/path/bin/bwa-meth-0.10/bwameth.py", line 586, in main
set_as_failed=args.set_as_failed)
File "/path/bwa-meth-0.10/bwameth.py", line 259, in bwa_mem
as_bam(cmd, fa, prefix, calmd, set_as_failed)
File "/path/bin/bwa-meth-0.10/bwameth.py", line 293, in as_bam
raise Exception("bad or empty fastqs")
Exception: bad or empty
When using bwameth with bwa >=0.7.16 and not specifying
--read-group
, I'm getting the error already reported inhttps://github.com/brentp/bwa-meth/issues/44#issuecomment-334573644
i.e.:
This is due to the following change in bwa:
https://github.com/lh3/bwa/pull/84