Comments (8)
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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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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I think I need to use the .bam
i create for pilon to also check coverage. Sigh.
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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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Did a version of pilon or something else change in the background?
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@andersgs No - Still pilon 1.22
from March this year.
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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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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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Related Issues (20)
- Pilon memory config error
- [shovill] Assembly failed - spades.fasta has zero contigs! HOT 1
- Resulting contig is way longer than expected
- Spades finished abnormally, OS return value: 21
- Error
- Error 256 HOT 2
- Confusing min ram requirements
- Failed to download resource "velvet"
- Coverage information for contigs assembled by Megahit
- Shovil tool on genome assembly of staph MRSA has 5632 error
- Harishk illumina sequence
- Hsrish
- Error 256 HOT 3
- GFA files in skesa
- what fastq filetype are available to use shovill ?
- Running shovill 1.1.0 and passing the option `'--plasmid'` to spades HOT 2
- [shovill] Can't see adapter file: /usr/local/db/trimmomatic.fa
- Illegal division by zero at /usr/local/bin/shovill line 162.
- Does Shovill support bash for running multiple fastq input files
- is it going to be compatible with SPAdes v4.0
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