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Check this library for more details
https://github.com/Dfam-consortium/FamDB
This will remove the hmm and the unpacking of the large file. Pante requires quite a lot of disk space for each step
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I have installed EarlGrey using conda, took a while but seemed to install without errors (on Ubuntu 18.04 with miniconda3 and python 3.6).
I have separately installed RepeatMasker and RepeatModeler…
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Hi,
I'm running Earlgrey on chymomyza amoena (~380mb) assembly but the repeatmodeler is taking too much runtime. Is there a way to limit repeatmodeler rounds in this pipeline. I have around 300 ge…
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When I run the program EDTA, an error occurred during the initial process: Invalid value for shared scalar at /lustre/home/huli/micromamba/envs/edta/share/LTR_retriever/bin/LTR.identifier.pl line 114,…
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I am trying to run the `CNVkit 0.9.11.dev0` copy number calling pipeline for a whole exome sequencing sample. However, I am encountering a type error `TypeError:batch_run_sample() takes from 16 to 17…
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Hi,
Thanks for developing freddie tool!
I was trying to apply freddie to our cancer dataset, however, currently I'm experiencing some issues.
1) Our data are nanopore long reads and previously w…
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```
Can't locate WUBlastSearchEngine.pm in @INC (you may need to install the WUBlastSearchEngine module) (@INC contains: /usr/local/bin /Users/ohon_ad/Documents/Tools/RepeatModeler/RepeatModeler-2.0.…
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I used the `makeTEgtf.pl` script you wrote (thank you very much for sending it) to create a GTF file for my transposon records. I got a few warning messages, but the resulting GTF file looks OK to me…
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Singularity> ls
Dfam.h5 Dfam.h5.gz config.ini dnapipete.img famdb.py
Singularity>
Singularity> famdb.py -i Dfam.h5 families -f fasta_name -a Panarthropoda --include-class-in-name > library.fas…
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Dear [jebrosen](https://github.com/jebrosen)
Thank you for tools. If I use this docker image, can I run the following comment
1. RepeatModeler -help
BuildDatabase -name demo_index -engine nc…