"No reads contained in input file(s)."

[kevinmuret]

Hi,

I'm working with fseq2 with murine data.
When I run fseq2, it works on a part of my .bed file (MT, X, Y, ....) and leaves out the "numerical" chromosomes (1 --> 18).
When I sub-select chromosomes 1 to 18, this is what it shows me:

PROGRAM: fseq2.0.3 callpeak
F-Seq Version 2.0.3
#1: Read in files and calculate parameters
/env/products/f-seq2/2.0.3/lib/python3.8/site-packages/fseq2/fseq2.py:57: FutureWarning: Dropping of nuisance columns in DataFrame reductions (with 'numeric_only=None') is deprecated; in a future version this will raise TypeError. Select only valid columns before calling the reduction.
bed['end_new'] = (bed[['end', 'strand']]).max(axis=1)
Error: No reads contained in input file(s).

Note that my file contains 12868084 lines and its format (bed) seems classic:
18 90600554 90600572 N1:1:HCGMLBGX5:3:23603:4197:5544/2 34 +
18 90600563 90600620 N1:1:HCGMLBGX5:2:13301:23722:11856/2 32 +
18 90600609 90600642 N1:1:HCGMLBGX5:3:23603:4197:5544/1 34 -
18 90600693 90600728 N1:1:HCGMLBGX5:2:13301:23722:11856/1 32 -
...

Do you have any idea what's going on?

Thanks !

[kevinmuret]

Update : if I change numerical chromosomes : 1 -> chr1 : it works !

[nsamzhao]

Yes, chromosomes should come with "chr". We will make this error more explicit! Thanks, Kevin.