"Something went wrong with the generated fasta file" error message with bacterial genreads wrapper

[bhanugandham]

When I run the bacterial genreads wrapper script I get the following error message:

$python bacterial_genreads_wrapper.py -r Escherichia_coli.fa -i 40 -g 3 -k 0.25 -c 40
Using default sequencing error model.
Using default gc-bias model.
found index ../reproducePaper/varcall_evaluation/representative_genomes_for_nanopore_illumina_hybrid_assemblies/Escherichia_coli.fa.fai
reading NC_000913.3...
2.428 (sec)
--------------------------------
generating mutated fasta...
[----------]
Read sampling completed in 259 (sec)
Something went wrong with the generated fasta file.

These are the output files created:

-rw-r--r--  1 bgandham  1594166068  6206365 Oct 19 12:12 bacterium_0_1.fasta
-rw-r--r--  1 bgandham  1594166068        0 Oct 19 12:12 neat_temporary_fasta_file.fa

[cjfields]

@bhanugandham just checking, was this on the genreads_overhaul branch?

[bhanugandham]

@cjfields yes it was on the genreads_overhaul branch

[joshfactorial]

@bhanugandham Okay, I have isolated the problem and was able to reproduce your error. It has to do with how genreads is processing the index file. A temporary solution is to move, delete, or simply rename the index temporarily (or copy the reference to a new folder without the index) and run it again. I need to fix how genreads interprets the chromosome name based on the index, as that seems to be what is causing the problem.

[joshfactorial]

(base) joshfactorial@DESKTOP-JLLVC5E:~$ python neat-genreads/bacterial_genreads_wrapper.py -r ecoli.fa -g 1 -i 2
Using default sequencing error model.
Using default gc-bias model.
found index ecoli.fa.fai
reading Chromosome...
2.597 (sec)
--------------------------------
generating mutated fasta...
[----------]
Read sampling completed in 272 (sec)
Something went wrong with the generated fasta file.

Then I did:

(base) joshfactorial@DESKTOP-JLLVC5E:~$ mv ecoli.fa.fai ecoli.fa.fai.backup

which gets us past that error:

(base) joshfactorial@DESKTOP-JLLVC5E:~$ python neat-genreads/bacterial_genreads_wrapper.py -r ecoli.fa -g 1 -i 2
Using default sequencing error model.
Using default gc-bias model.
Index not found, creating one...
0.030 (sec)
reading Chromosome dna_rm:chromosome chromosome:ASM584v2:Chromosome:1:4641652:1 REF...
2.567 (sec)
--------------------------------
generating mutated fasta...
[----------]
Read sampling completed in 283 (sec)
Using default sequencing error model.
Using default gc-bias model.
Index not found, creating one...
0.036 (sec)
reading Chromosome dna_rm:chromosome chromosome:ASM584v2:Chromosome:1:4641652:1 REF...
2.845 (sec) ...