getKmers.py generates empty *.gz files

[Rotem]

Hi,

I just run getKmers.py, no errors were reported and the stdout looked like "Created all sequences for chr1:1-30584173" for each chromosome and scaffold. When I tried to run bowtie, turned out there was nothing to align because all kmer files generated by getKmers.py were empty.

Could you please help me to figure this out?

Best,

Rotem

[Mehran Karimzadeh]

Hello Rotem,

Please provide more details: Python version and package versions you are using, the command you run, etc.

Also, did it work on the test data and not on your own data? If so, please provide a reproducible example.

Thanks,

Mehran

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[Katherine Domb]

Thanks for your reply,

I used Python 2.7.18 on Ubuntu 16.04

Cloned umap with git clone 2 months ago, how do I check the version?

I created and run a shell script to run get_kmers.py:

for i in $(eval echo {1..444}); do echo python get_kmers.py --job_id $i /umap/umap/mpoly/chrsize.tsv /umap/umap/mpoly/kmers/k150 /umap/umap/mpoly/chr /umap/umap/mpoly/chrsize_index.tsv; done > run_getKmers.sh

Seems like it didn't work on the test data, because no new files were generated there?

[Pooran Dewari]

Hi Katherine,

Just wondering if you managed to make it work. I am facing the same problem; fails with the test data.

thanks