ShortStack on mRNA data?

[meerveld96]

Hi Mike,

I got the following error and the ShortStack 4.0.3 stopped running:

Traceback (most recent call last): File "/lustre/BIF/nobackup/ruite093/miniconda3/envs/ShortStack4.0.3/bin/ShortTracks", line 282, in if last_pos < chr_sizes[last_chr]: KeyError: 'foobarbaz'

Candidates examined: 0it [00:00, ?it/s] Traceback (most recent call last): File "/lustre/BIF/nobackup/ruite093/miniconda3/envs/ShortStack4.0.3/bin/ShortStack", line 3619, in mir_qdata = mirna(args, merged_bam, fai, pmir_bedfile, read_count) File "/lustre/BIF/nobackup/ruite093/miniconda3/envs/ShortStack4.0.3/bin/ShortStack", line 2261, in mirna dn_q_bedlines, dn_locus_bedlines = zip(*denovo_mloci1) ValueError: not enough values to unpack (expected 2, got 0)

I'm wondering how this could happen, is there a maximum amount of sequences of input of ShortStack? I feed forward and reversed messenger RNA fq.gz files with a total size around 450 Gigabytes. I did ran ShortStack on the BAM files, gives the same problem. I ran also ShortStack on small RNAs in another experiment, this ran fluently.

Thanks,

Best regards, Stefan