Variable 'length' referenced before assignment

[fkollingiv]

Hello,

I'm working my way through the early steps of the pipeline and can't get past the rageMatch.py script. I am receiving the following error: UnboundLocalError: local variable 'length' referenced before assignment

Here is the command: python ~/rageseq-master/rageMatch.py -q ../Dartmouth-RAGESeq-Nanopoe-LSK110-8242021/fastq_pass/rage.fastq.gz -o ./ -b transformed-bc.tsv --length 200 -t 10 -f 250 -n 1

Any help is greatly appreciated.

[fkollingiv]

I probably should have included the error as well:

Traceback (most recent call last):
File "/dartfs-hpc/rc/home/j/f00331j/rageseq-master/rageMatch.py", line 129, in
main()
File "/dartfs-hpc/rc/home/j/f00331j/rageseq-master/rageMatch.py", line 79, in main
do_batch(args, fq_list, bcs, out)
File "/dartfs-hpc/rc/home/j/f00331j/rageseq-master/rageMatch.py", line 95, in do_batch
k = re.search(bc[2], fq[1][:length])
UnboundLocalError: local variable 'length' referenced before assignment

[Psy-Fer]

Hello,

Please do a git clone to the the small bug fix I just did on rageMatch.py to fix this issue.
Sorry about that. Our internal version of these scripts has been totally re-written, so I didn't catch this bug.

Cheers,
James