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alekseyzimin / masurca

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Polca.sh short read output. #155

Open LeebanY opened 4 years ago

LeebanY commented 4 years ago

Dear @alekseyzimin,

First of all, thanks for the cool pipeline, it's been great using it to assemble some genomes. I had a question about the output file for the polishing tool, polca. The polca.sh script works perfectly fine, but the output is unintuitive; instead of getting contigs of the same length (or longer, as expected) as my input genome file, I'm getting very short contigs as output(100 bp). I'm not sure if this is the desired output (if so, would I reassemble using the output 'corrected contigs'?), or am I missing something?

Here is my script:

polca=/shelf/apps/user/conda/envs/masurcaENV/bin/polca.sh genome=genome.ctg.fasta error_corrected=pe.cor.fa

$polca -a $genome -r $error_corrected -t 16 -m 5G

Thanks for the help! Leeban

alekseyzimin commented 4 years ago

Hello, Something is going wrong. Do you have "bwa mem" available on the path? Can you send me the output of "ls -lth" on the working directory?

--Aleksey

On Mon, Feb 3, 2020 at 11:57 AM LeebanY notifications@github.com wrote:

Dear @alekseyzimin https://github.com/alekseyzimin,

First of all, thanks for the cool pipeline, it's been great using it to assemble some genomes. I had a question about the output file for the polishing tool, polca. The polca.sh script works perfectly fine, but the output is unintuitive; instead of getting contigs of the same length (or longer, as expected) as my input genome file, I'm getting very short contigs as output(100 bp). I'm not sure if this is the desired output (if so, would I reassemble using the output 'corrected contigs'?), or am I missing something?

Here is my script:

polca=/shelf/apps/user/conda/envs/masurcaENV/bin/polca.sh genome=genome.ctg.fasta error_corrected=pe.cor.fa

$polca -a $genome -r $error_corrected -t 16 -m 5G

Thanks for the help! Leeban

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/alekseyzimin/masurca/issues/155?email_source=notifications&email_token=AGPXGHIFSUB6XKR4P2VCLELRBBEGVA5CNFSM4KPISWOKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4IKU3TKQ, or unsubscribe https://github.com/notifications/unsubscribe-auth/AGPXGHLKV5OFC534RB3Y56TRBBEGVANCNFSM4KPISWOA .

-- Dr. Alexey V. Zimin Associate Research Scientist Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA (301)-437-6260 website http://ccb.jhu.edu/people/alekseyz/ blog http://masurca.blogspot.com