-
In the `feature_hic_scaffolding` branch many processes are requesting >20 cpus when using the Uppmax profile. This causes an error and nextflow exits the pipeline.
This happened with FASTK_FASTK (r…
-
Hello,
I am running the pipeline version v4.3.4 on a slurm cluster.
The first steps work fine (windowmasker, minimap, chunk_stats, busco and cov_stats).
I get an error for the diamond steps.
Here…
-
Hi @marieBvr ,
I met same issues with #1 , I also continue the install piplines, but the size of taxonomy.tmp.sqlite not changed. can you help me resolve it?
Sincerely yours,
Nailou
PS: Th…
-
### Description of the bug
1. In your configuration script setup_db.nf, the line 131, wget is used to retrive mmseqs_vrefseq.tar.gz, but it is not getting into the system, i tried it manually but, …
-
Hi all,
I am attempting to build an up-to-date Centrifuge nt index on a machine with 40 cores and 196 GB of RAM. Your example for building nt suggests using 16 threads and a bmax of 1342177280, wh…
-
Dear Shenwei,
Thank you very much for providing a good tool, I am trying to adjust the output table as desired according to KMCP format.
- Currently I use search with all the databases you provide…
-
Thank you very much for your powerful tools!
I ran into the following error while running the make_kreport.py script.
python make_kreport.py -i P1_S7_L001_R_kraken2.txt -t nt_ktaxonomy -o P1
…
-
Hey I am having some problems running diamond.
I run this command for db creation:
diamond makedb -p 40 --in /home/blast_db/nr.fasta --taxonmap /home/blast_db/nr.acc2taxid.txt --taxonnodes ../…
-
I am using the following code to run kraken2 with the standard 67GB database:
kraken2 --db /data/coffmanm/tools/krakenBig --threads 10 --confidence 0.05 --output krakenOut/${base}.output.txt --re…
-
## Expected Behavior
Taxonomy database created based on a `seqdb` created from UniProt sequences
## Current Behavior
Program crashed with `core dumped` error and reports `Error: createbintaxo…