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zajakin / sRNAflow

sRNAflow – a tool for analysis of small RNA-seq data
GNU General Public License v3.0
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Time of execution #1

Open Anto9393 opened 5 months ago

Anto9393 commented 5 months ago

Hi,

First of all, congratulations on this amazing tool!

I've tried running the Docker with 6 FASTQ files divided into 2 groups, without environment. However, it seems to stop at the end of the quality control step. How long does the entire execution typically take? If there's an issue, is it possible to see it in the prompt?

At the end of the qc It seems to stop, after the pc fans start working again, and after they stop but there were not more files in the fólder.

Thanks for your response.

Best regards,

amarinderthind commented 1 month ago

I tested and observed the same thing.

zajakin commented 1 month ago

Hi,

sorry for the late reply. When You writes your issues, You probably decide at first run that the process is finished when the BLAST stage is started. If you have not uploaded the BLAST database (via SETUP -> Create/Update local BLAST db, which can take several days), the BLAST stage is performed on remote servers. This has minimal resource usage, but can take one to two days depending on the selected subset size. In my experience, working with local databases is much faster. Steps such as metagenome generation can also be time and resource-consuming, depending on the number of identified species.

I hope that all works finished same time ago and You obtained all the results.

amarinderthind commented 2 weeks ago

Thanks for your reply. wondering, instead of using setup option, if i download blast separtely at specified location. it will work? right (via SETUP -> Create/Update local BLAST db, which can take several days)