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I ran into this in October and was able to solve by setting the memory to 60GB, however this time running `sh run.sh make refresh-merge` (following these docs: https://mondo.readthedocs.io/en/latest/e…
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Hi, I am trying to run the sequences section of Trinotate but run into an error with the tmhmmv2 command:
```
[Wed Sep 11 15:47:29 2024] Running CMD: tmhmm --short /data/putnamlab/dbecks/Heatwave_…
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In semi-model organisms, NCBI and Ensembl usually provide annotations based on ab initio gene prediction and orthology based evidence. With cheap RNAseq, we can build RNA based gene models using Cuffl…
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Hi,
First, congratulations on the development of Anchorwave, it seems a great addition to the Comparative Genomics toolkit!
I have several questions, the majority linked to the "Empty CDS file f…
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Hello, everyone
I used the PASA (v2.5.3) pipeline to update the annotations from EVM with the following command: `/vol2/YL_group/YL/software/PASApipeline-master/Launch_PASA_pipeline.pl -c alignAssemb…
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I met an error like this when I try to update me annotation using Launch_PASA_pipeline.pl, please help me fix it or give me some advice.
* [Fri Sep 15 01:56:05 2023] Running CMD: /home/MCY/App/PASApi…
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### Description of the bug
From terminal output (see below) I see that nextflow tries unsuccessfully to run this:
`singularity pull --name nf-core-bedtools_coreutils-a623c13f66d5262b.img.pulling.1…
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The current GRCh38 RefSeq annotation (GCF_000001405.40-RS_2023_10) has [368 transcripts for BRCA1](https://www.ncbi.nlm.nih.gov/datasets/gene/id/672/products/) - up from 6 the previous version.
I c…
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Hi,
I'm using drop 1.3.3 in order to do aberrant expression analysis. However during outrider execution with 2 bam data and 9 external counts, I'm getting the following error:
```
[Tue May 30 16:…
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This Ensembl pipeline is probably one of the largest sources of incorrect IEA annotation.
One major issue that could be fixed is that the relationships appear to be ignored.
So in this case…