Gemma Collins comments

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                                            Gemma Collins

Out of Memory but the job seemed already finished

Hi all, I have the OOM issue with slurm also. Running earlGreyLibConstruct with 250G mem and 32 CPUS using apptainer with slurm. Large and highly repetitive genome, so expecting it...

Out of Memory but the job seemed already finished

Hi Toby, I have checked the two things you suggest and indeed it seems that TEstrainer finished and the issue is further down the pipeline. AXX_polished_unitigs-families.fa.strained = 45581630 AXX_polished_unitigs-families.fa.nonsatellite.classified =...

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

Hi Kamil, I tried your suggestion: `Histex -G Fastk_Table > kmer.hist` Then plotted kmer.hist with genomescope. The model didn't fit well, but as far as I can tell it looks...

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

I have re-created the issue this time with a single slurm script and here provide the two files you asked for as well as the script and the log files...

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

Here are the hidden files as a google drive link: https://drive.google.com/drive/folders/12keGxYN5jkY8t--Rksq_sZ3FrcXXnDuj?usp=sharing

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

I did not find the solution yet and have been meaning to get back to this topic..

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

Hi Kamil & Gene, Thanks for looking into it again. Ah good question. I was following some advice from your email 21/11/24 "You might want to consider to use homopolymer...

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

Hi Kamil, removing the `-c `option from fastk solved it. I now have the `.smu` file. Thanks!