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Hi,
I am trying to get the taxonomy of several contigs present in a multi-fasta file, but I'm having some issues with the `easy-taxonomy` command, as it is has not completed the assignment of about …
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I ran spades.py on my reads to have a plant genome assemby which has an estimated size of 600M. I am providng a memory of 998G but it was stuck at subclustering hamming graph for 2 days. I have Nanopo…
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Hi,
This is my first time using PIPITS. I had no issue with the tutorial on mock samples but during pipits_process for my actual samples, I run into this issue: Error: None zero returncode: classif…
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Hi,
I am interested in using long and short reads to assemble a transcriptome with RNA-Bloom2.
I had a few questions regarding pre-processing of reads before using RNA-Bloom2.
I am loosely fo…
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Hi,
Not sure if it's a spades specific issue but I was running the same command on two linux computer due to memory issue and oberved a huge difference of speed despite having more memory/cores on th…
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Hi,
I have two questions about the usage of PanGenie:
1. The paper of PanGenie says that the constructed graph is a directed acyclic graph. Can PanGenie also be used on non-directed acyclic graph…
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**#This following is the params.txt**
Command line: ./../SPAdes-3.13.1-Linux/bin/spades.py --careful -t 20 --pe1-1 /run/media/user1/storage1/5_hari_g/trimgalore_output_2/P5652_PC…
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Hi Roderick!
I'm developing a k-mer counting Python package for internal usage and I'm using needletail as a backend. While developing it, I noticed that `Kmers` and `CanonicalKmers` are inconsiste…
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Hi, I am using the following command to make the index file. However, I am getting an ERROR.
./kallisto index -i /DataAnalysis/kallisto_test/transcripts.idx /DataAnalysis/kallisto_test/Homo_sapien…
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### Description of bug
Spades-hammer is terminating because of a segmentation fault while kmer-counting and reports an "OS return value: 1".
Command line:
```
/lisc/scratch/jmf/internal/Analyse…