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Hi,
I am running 20 paired-end RNA-seq samples since yesterday (more than 24 hours over) and only 7 samples have been completed (others are still running) on 16 GB RAM computer.
Any way to make it …
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I could have sworn I'd previously opened an issue here with an idea for a benchmark but now I can't find it. There was a discussion of some algorithms that are hard/impossible to do in a vectorized wa…
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I tried to align whole genome reads (hg19) generated from pbsim using GraphAligner.
However, the program crashed when building minimizer seeder from the graph.
This is the error message that I got:…
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Hi
Is mmseqs deterministic? When running linclust on a large FASTA file of proteins, one would expect to get very similar clusters when rerunning the same command on the same fasta file (with defau…
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Hi there,
I'm having issues running trinity in separate stages. My cluster has a time limit to 3 days so i have to run the script in separate stages. However, i have selected --no_distributed_trini…
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I am using sourmash to compare some custom kmer sets. I've used `sourmash compare` successfully, but in scaling up, I hit memory issues. To fix this, I tried `sourmash scripts pairwise`, which is much…
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Hi, when plotting the kmer_freq, it reported errors like this:
```
"23-09-13 23:23:33 [INFO] Plot k15_q200_f2.kmer_freq.pdf
Traceback (most recent call last):
File "~/.conda/envs/SubPhaser/bin…
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Here's the command I used:
liftoff \
-g GCF_910596095.1_fThuMac1.1_genomic.gff \
-o ./lift.gff \
-dir ./intermediate_files \
-a 0.7 \
-s 0.7 \
-flank 0.1 \
-exclude_partial \
-copi…
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Anton reported that it crashes with:
```
unexpected problem: repart bucket
unexpected problem: repart bucket
unexpected problem: repart bucket
````
I'll investigate someday.
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I have had kraken2 standard installed for a couple of years and have used it with no issues. I would like to add fungal identification to my analysis, so I would like to replace the standard kraken2 …