Error running get_kmers.py

[Johannes Nicolaus Wibisana]

Hi all,

I just got access to slurm HPC, but I got the following error, for several different job IDs:

Traceback (most recent call last):
  File "/usr/local/bin/get_kmers.py", line 265, in <module>
    idx_path)
  File "/usr/local/bin/get_kmers.py", line 97, in __init__
    self.chrom, self.start, self.end = self.get_region()
  File "/usr/local/bin/get_kmers.py", line 130, in get_region
    job_id))
ValueError: 596 Job id is larger than available indices

when running get_kmers.py. 

Best regards,

Nico

[Delva Leão]

Hi Nico,

This just means you attributed an array that was too long in the --array option. 

For making kmers and aligning them, the array length should match the number of lines in chrsize_index.tsv

For the other steps --array should be equal to the number of scaffolds or chromosomes you have in the input genome.

Best,

Delva

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Delva Leão

Biotechnologist, MSc.