Matteo Schiavinato

aln2wig error with pacbio long-read BAM and PSL files

1

Hi, I'm implementing a long-read-based gene prediction pipeline making use of Augustus/3.2.3. I'm using aln2wig to generate a wig track from the pacbio alignment. The alignment was conducted with BLAT...

Hi, I am trying to follow your workflow in [Pryszcz et al., 2016](https://academic.oup.com/nar/article/44/12/e113/2457531?login=true#87015117) but I can't find in the repository the `fasta2diverged.py` script that you mention in the paper (neither...

`nextflow clean` throws `Unexpected error [EOFException]` when attempting to clean previous runs

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## Bug report After a successful run of my pipeline, I am trying to clean the workspace from previous runs. I'm doing so using `nextflow clean -f -before nauseous_cajal`, which...

`Error: no reads found` but the report file contains read counts

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I'm using bracken in a pipeline, and I'm encountering some issues. I have used it before in the same system without any issue, so I'm a bit confused about this....

Sequences not multiple of 3: poor stderr information

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With one of the file sets I'm using in the analysis, I get this error: `/software/python/Python2.7/lib/python2.7/site-packages/Bio/Seq.py:2071: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or...

proposedGenes file not found

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The program seems not able to find a file that it should be internally generated: `grep: path/to/file.fa.proposedGenes: No such file or directory` (I substituted the original file with path/to/file) Checking...

Program crashes but ghosh jobs keep going on

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I recently ran an OrthoFiller process with 28 cores which crashed after some time for some input file problem. I had also **time** to track the timing of the program,...

Installation step fails at copying flye folder

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I am trying to install MaSuRCA and I am getting this error when running the `./install.sh` step: ``` + cp -a ../Flye /opt/MaSuRCA-4.1.1 cp: '../Flye' and '/opt/MaSuRCA-4.1.1/Flye' are the same...