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Comments (8)

tseemann avatar tseemann commented on September 25, 2024

That's a feature!

I've never seen a 31 kbp contig with coverage 0.00017 - what the hell is going on?

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kwongj avatar kwongj commented on September 25, 2024

It sounds like a sensible feature, but I don't believe the actual coverage reported by spades in their contig names. Removing these removes >99% of the assembly!

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tseemann avatar tseemann commented on September 25, 2024

I think I need to use the .bam i create for pilon to also check coverage. Sigh.

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tseemann avatar tseemann commented on September 25, 2024

I just ran shovill and I did not get the same result as you?

% shovill --R1 ERR036060_1.fastq.gz --R2 ERR036060_2.fastq.gz --outdir shovill

Removing low coverage contig (< 2 x): NODE_249_length_236_cov_1.12707_pilon

Final assembly in: shovill/contigs.fa
It contains 439 (min=76) contigs totalling 2143049 bp.

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andersgs avatar andersgs commented on September 25, 2024

Did a version of pilon or something else change in the background?

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tseemann avatar tseemann commented on September 25, 2024

@andersgs No - Still pilon 1.22 from March this year.

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tseemann avatar tseemann commented on September 25, 2024

We also need to decipher the warnings.log file in spades.

=== Error correction and assembling warnings:
 * 0:00:07.339    96M / 8G    WARN    General                 (kmer_coverage_model.cpp   : 367)   Failed to determine erroneous kmer threshold. Threshold set to: 21
 * 0:00:09.585    96M / 8G    WARN    General                 (simplification.cpp        : 569)   The determined erroneous connection coverage threshold may be determined improperly
 * 0:00:06.018    88M / 8G    WARN    General                 (kmer_coverage_model.cpp   : 219)   Too many erroneous kmers, the estimates might be unreliable
 * 0:00:06.025    88M / 8G    WARN    General                 (kmer_coverage_model.cpp   : 328)   Valley value was estimated improperly, reset to 1
 * 0:00:06.025    88M / 8G    WARN    General                 (kmer_coverage_model.cpp   : 367)   Failed to determine erroneous kmer threshold. Threshold set to: 1
 * 0:00:10.306    88M / 8G    WARN    General                 (pair_info_count.cpp       : 319)   Unable to estimate insert size for paired library #0
 * 0:00:10.306    88M / 8G    WARN    General                 (pair_info_count.cpp       : 325)   None of paired reads aligned properly. Please, check orientation of your read pairs.
 * 0:00:10.306    88M / 8G    WARN    General                 (repeat_resolving.cpp      :  62)   Insert size was not estimated for any of the paired libraries, repeat resolution module will not run.
======= Warnings saved to 

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tseemann avatar tseemann commented on September 25, 2024

Turns out @kwongj was used fixed kmers 31...121. THe problem is that the reads are only 75bp and from older technology with higher error rate.

Solution is to let Shovill dynamically choose kmers.

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