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rrwick / Unicycler

hybrid assembly pipeline for bacterial genomes
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Is "--isolate" option of SPAdes applied to all k-mer sizes? #290

Open ilnamkang opened 2 years ago

ilnamkang commented 2 years ago

Hi,

It seems that the "--isolate" option is used for SPAdes assembly step of Unicycler v0.5.0.

I'd like to know whether or not the "--isolate" option is applied to all k-mer sizes, because this option appears only for the 1st k-mer size in the log file.

In other words, does SPAdes run with the "--restart-from" option inherit the "--isolate" option from the previous run?

I looked into the SPAdes repository, but couldn't find clear explanation on this issue.

I attach below an edited version of my Unicycler log file.

------- spades.py -o output_dir/spades_assembly -k 27 --threads 32 --isolate -1 Illumina.trim.1.fq.gz -2 Illumina.trim.2.fq.gz -m 1024

spades.py -o output_dir/spades_assembly -k 27,53 --threads 32 --restart-from k27 -m 1024

spades.py -o output_dir/spades_assembly -k 27,53,71 --threads 32 --restart-from k53 -m 1024

spades.py -o output_dir/spades_assembly -k 27,53,71,87 --threads 32 --restart-from k71 -m 1024

spades.py -o output_dir/spades_assembly -k 27,53,71,87,99 --threads 32 --restart-from k87 -m 1024 -------

bplants10 commented 2 years ago

I've noticed that the new version does this too, except my assemblies are getting hung up on the k87 phase, and getting to this point takes ~8h and does not continue., compared to the ~2h before. I ran an old assembly with the new version and the speed was greatly reduced in the new version, taking more time. Selecting the K-mer size appeared to relatively quick in the previous version. Is this a SPAdes issue?

safrye commented 2 years ago

Same problem here with version 0.5.0 with an error after K87 but only for some of the runs. 24/24 runs with Illumnia V3 kit data gave no problem but 8/23 runs with Illumina V2 kit data stopped with an error.

ilnamkang commented 2 years ago

(1) I'm not sure whether the two comments above are related to my original question, because my Unicycler run has been finished without any errors. The Unicycler log I posted was a just part of the whole log file.

(2) Regarding my original question, I confirmed with my test run that SPAdes run with the "--restart-from" option inherits the "--isolate" option from the previous run.