laibinhuang

Thank you, yes please! I am getting these same errors when I am using my own existing conda package. For example: rule Diting: input: reads=expand('/home/lbhuang/Moore/results_test/Ditingreads/{IDS}_{READ}.fastq.gz', IDS=file_ids.id, READ=file_ids.read), contig=expand('/home/lbhuang/Moore/results_test/Ditingcontigs/{IDS}.fa',IDS= file_ids.id) output:...

This is the command: snakemake -kpr -s Snakefile_Test --profile /home/lbhuang/ref/farm-hpc/ fastqc thank you the snakefile_test is: ##### SETUP ##### ## DEFINE WORKDIR ## WORKDIR=workflow.basedir+'/' # Gather files to be processed....

Thanks, I checked in my cluster config file: I have only one of them. I run the same one month ago, and there was no problem. __default__: account: jorgelmrgrp partition:...

Yes, here it is! Thank you, Laibin Run started Thu Mar 7 11:56:21 2024 in coassembly mode SqueezeMeta v1.6.3, September 2023 - (c) J. Tamames, F. Puente-Sánchez CNB-CSIC, Madrid, SPAIN...

the version is: SqueezeMeta v1.6.3 I am rerunning it: -binners "maxbin, metabat, concoct" it doesn't work. On Fri, Mar 8, 2024 at 10:37 AM Fernando Puente-Sánchez < ***@***.***> wrote: >...

I removed it for a new run: using Snakemake I will get it to you once I have it Thank you for your help! Laibin, On Fri, Mar 8, 2024...

The only issue here in the snakemake is out of memory, but when I am running in the without snakemake, it doesn't have problems. below is the snakemake code: file_ids...

they stop at the taxonomy step due to memory issues; I am trying not to use Snakemake (do multiple samples together). I will let you know. Thank you, Laibin On...

Dear Javier, ANy suggestion for this parts, I provide my own contigs in a folder for this, but it doesn't work: p: -r not specified; omitting directory '/home/lbhuang/Moore/results_2021/contig/' Renaming contigs...

Meanwhile, How can I assign an output dir for the result, when I use -o, but it still create a new output-dir that different from mine. Thank you