Chromosome not always identified if read depth is low

[dfornika]

For some samples, we see an output like this in the logs:

  2023-11-08 11:29:25.807 | INFO     | plassembler:run:700 - More than one contig was assembled with Flye.
  2023-11-08 11:29:25.807 | INFO     | plassembler:run:701 - Extracting Chromosome.
  2023-11-08 11:29:25.881 | INFO     | plassembler:end_plassembler:117 - Plassembler has finished
  2023-11-08 11:29:25.882 | INFO     | plassembler:end_plassembler:118 - Elapsed time: 254.34 seconds
  2023-11-08 11:29:25.882 | ERROR    | plassembler:run:727 - No chromosome was idenfitied. please check your -c or --chromosome parameter, it may be too high.
  Likely, there was insufficient long read depth to assemble a chromosome. Increasing sequencing depth is recommended.

The samtools faidx index of that flye assembly looks like this:

contig_1        909291  10      60      61
contig_2        1960722 924466  60      61
contig_3        1794423 2917877 60      61
contig_4        500997  4742218 60      61
contig_6        60401   5251575 60      61
contig_7        171600  5312993 60      61
contig_8        101747  5487463 60      61

Since this crashes the pipeline for all samples, and the focus of the pipeline is to generate plasmid assemblies, we should make that chromosome assembly an optional output.

[dfornika]

This issue can be mitigated by choosing a lower value for plassembler's --chromosome flag (mapped to this pipeline's --chromosome_length) flag. We've implemented a lower default in #2. I'll leave this open because it doesn't completely address the issue.