Slow process

[YiweiNiu]

Hi,

Thank you for developing this useful tool.

Recently, I tested telomerecat using several WGS samples (~30X) on a CentOS server.

I found that it didn't end even after ~24h and the output was empty. This has been reported before: issue 13, but the issue was closed without a solution.

Here is the command I used.

# conda
conda activate telomerecat

# run
time telomerecat bam2length \
  --output $outdir/telomerecat_length.csv \
  -N 100 \
  -v 2 \
  -p 2 \
  $bam

Here is the log message.

telomerecat bam2length has started. Start Time: 2022-04-11 09:46:42
-------------------------------------------------------------------

DEBUG: Starting telbam generation for 1 inputs
DEBUG: Inline execution of telbam generation, 2 threads per process
 Collecting meta-data for all samples | 2022-04-11 10:47:33
    - HG00315.final.bam | 2022-04-11 10:47:33

I previously thought it was because of the parameter -N 100. I also tested it with the default setting (-N 10), but it did not work.

Thanks in advance.

Bests, Yiwei