search

sjroth / ARTDeco

MIT License
15 stars 7 forks source link

issue with ValueError: invalid literal for int() with base 10: b'' #23

Closed haonanduanmu closed 1 month ago

haonanduanmu commented 3 months ago

Hi,

I'm using ARTDeco and coming across a question about "ValueError: invalid literal for int() with base 10: b''.

My code is

ARTDeco -home-dir ARTDeco_dir/ -bam-files-dir bam_file/ -gtf-file dmel_flybase.gtf -chrom-sizes-file genome.chrom.sizes

and there are 80 bam files which were sorted. the problem is

multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/public1/home/scfa2661/anaconda3/envs/ARTDeco/lib/python3.9/multiprocessing/pool.py", line 125, in worker result = (True, func(*args, *kwds)) File "/public1/home/scfa2661/anaconda3/envs/ARTDeco/lib/python3.9/multiprocessing/pool.py", line 48, in mapstar return list(map(args)) File "/public1/home/scfa2661/anaconda3/envs/ARTDeco/lib/python3.9/site-packages/ARTDeco-0.4-py3.9.egg/ARTDeco/misc.py", line 364, in count_reads return int(output.strip()) ValueError: invalid literal for int() with base 10: b'' """

I have no idea about this bug, maybe the bam files have some wrong? Could you help me? Thank u!

sjroth commented 3 months ago

Hi,

Can you please show all of your stdout rather than just the error?

Sam

haonanduanmu commented 3 months ago

Here is the picture of all stdout

1709864267572

sjroth commented 3 months ago

This appears to be an issue with one of your BAM files. One of them is likely not properly formatted.

haonanduanmu commented 3 months ago

Is there any method to find this un-formatted bam file? I have tried 'samtools quickcheck' to find this uncorrect file, but it showed that all ok.

sjroth commented 3 months ago

Try running "samtools view -c" with whatever other necessary keywords to count the number of reads for each sample. Parsing the output of this command is where the error is occurring.

sjroth commented 1 month ago

Inactive for now so closing.