lpryszcz
commented
5 years ago It's been dealt with through e-mail. The reason was not unique FASTA headers. Putting here for reference. There are two possible explanations:
- Your contigs are very short - Redundans skips contigs shorter than 200 nt (--minLength 200).
- Your contigs have non-unique names - you can check with
grep -m50 ">" genome.fasta
Hi everyone,
I am pretty new to Redundans and I am trying to perform the “Redundancy Reduction” step on a very heterozygous insect genome.
For that, I used the following command line:
redundans.py --verbose --noscaffolding --nogapclosing --fasta genome.fasta --identity 0.95 --overlap 0.66 --minLength 500 --threads 7 --outdir outdir --log genome.log
Please not that I used the "--noscaffolding" and "--nogapclosing" parameters, as I’m only interested in the Redundancy Reduction step of the pipeline.
After some hours of run I got the following message:
“[WARNING] Nothing reduced”
My “.log” file looks like this:
fname contigs bases GC [%] contigs>1kb bases>1kb N50 N90 Ns longest
genome.fasta 30 48147108 28.249 30 48147108 7306273 3975295 226300 13637223 contigs.fa 30 48147108 28.249 30 48147108 7306273 3975295 226300 13637223 contigs.reduced.fa 12 47642345 28.255 12 47642345 7306273 3975295 226300 13637223 scaffolds.reduced.fa 12 47642345 28.255 12 47642345 7306273 3975295 226300 13637223
What is very weird is that my genome has 17,817 scaffolds, but it seems that Redundans analyzed only 30 of them.
When I run the command grep -c ">" contigs.fa it returns to me “17817”, so it seems that the program is loading all contigs into the pipeline.
So, what I guess is that redundans is working, but it’s not processing the entire fasta file and thus the assembly unchanged (as less than 1% of the contigs were reported in the “.log” file).
Any ideas of what is happening?
Thank you all for the help, Dani.