Abdoallah Sharaf

icon indicating a website link https://abdosha.wixsite.com/asharaf icon indicating an email [email protected]

icon location SequAna - Sequencing Analysis Core Facility, University of Konstanz icon location Presently, I'm a senior bioinformatician at SequAna - Sequencing Analysis Core Facility, University of Konstanz

Results 9 comments of Abdoallah Sharaf

error with end-to-end

thanks @apcamargo , here is the mmseq2 log file. [mmseqs2.log](https://github.com/apcamargo/genomad/files/13402781/mmseqs2.log)

error with end-to-end

Hello @apcamargo, i tried several `--splits` and still have the same error. any thoughts?

tmp/3407079133035171875/tmp_hsp1/941510883324284880/blastp.sh: line 99: 13762 Killed

Hi @zzsunday, i'm facing the same error. did you manage to figure out the solution?

Issue with --download-library nt

@SenyuanGu , i didn't figured out but i download the indexed database from https://benlangmead.github.io/aws-indexes/k2 , and it works

Issue with --download-library nt

Hi @KeyLllll, in the https://benlangmead.github.io/aws-indexes/k2 page a table for each database and the corresponding URL.

Issue with --download-library nt

You should first download the NCBI taxonomy using: kraken2-build --download-taxonomy --db $DBNAME

Issue with --download-library nt

i didn't remember encountering this problem but I had already changed a line in rsync file according to: https://github.com/DerrickWood/kraken2/issues/508 Cheers

smudgeplot.py hetmers not producing kmerpairs_text.smu (.trim.ktab only)

Hi @KamilSJaron , @gemmacol , @vincianem , I’m encountering the same issue. Have you been able to figure it out? Cheers, Abdo

smudgeplot.py hetmers not producing kmerpairs_text.smu (.trim.ktab only)

> [@abdo3a](https://github.com/abdo3a) and [@vincianem](https://github.com/vincianem) does either of you have a dataset that generates this error that is public / or not too giant to share? It would be good to...