Christopher E. Laumer

Singularity error: "destination must be an absolute path"

1

Hello, Just writing to report that I'm still having trouble getting the most recent version of Finder to work as documented on an HPC cluster via singularity. The run_finder job,...

cds_predict error

5

Hello there, I'm trying to use FINDER for the first time, on a Drosophila de novo assembly with locally stored RNA-seq data. Many parts of the pipeline seem to have...

Merging Salsa beds from multiple experiments

3

Hi Eoghan et al, After sorting out my python env issues, I've managed to successfully run Pore-C-Snakemake through to its salsa bed outputs, and it seemed to work beautifully in...

local_pairwise_align_ssw giving unpredictable AlignmentError

1

Hi skbio devs, I'm seeing what I think of as odd behavior from the alignments.local_pairwise_align_ssw function. I've written a script which takes an unaligned, multisequence fasta file and uses this...

TransPi on HPC failing to pull singularity image

3

Hi there, I've been trying to use TransPi (love the concept and the benchmarking in the paper looks great!) to re-assemble some older public datasets. Running on an interactive slurm...

Floating point exception in break10x

11

Hi there, I'm running break10x on my cluster as follows: /nfs/research1/marioni/claumer/Scaff10X/src/break10x -nodes 40 -gap 100 -reads 5 -score 20 -cover 50 -ratio 15 /nfs/research1/marioni/claumer/DalyG_HiFi/Scaff10x/DalyG_HiFi_q10_redbean_all.ctg.fa /nfs/research1/marioni/claumer/DalyG_HiFi/fwdrev_all/Scaff10x/DalyG_10x_R1.fastq /nfs/research1/marioni/claumer/DalyG_HiFi/fwdrev_all/Scaff10x/DalyG_10x_R2.fastq DalyG_wtdbg2_break10x DalyG_wtdbg2_break10x_breakpoints I've installed...

Variable positions for group labels

1

Hello, I was wondering if there is a way to draw taxon labels on a tree (as you did with the rectangular boxes in the tutorial on this subject), but...