EarlGrey

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EG4.0.8 vs EG 4.2.4

2

I ran the earlGrey pipeline version 4.0.8 (using RM4.1.5) on a genome and now I ran earlGrey 4.2.4 (with RM4.1.6) on the same genome. The resulting plots look very different...

ekaralashvili

runtime in TEstrainer ultralong for *some* genomes

6

Hi, After running EG with v4.2.4 for a while without major problems, we upgraded to 4.4.0 recently and have a couple issues. It seems one issue is with TEstrainer where...

estolle

Warning: malformed fasta index file

1

Hi, looks like I am having a similar problem to #121 installed earlgrey via conda ```bash earlgrey 4.4.4 h4ac6f70_0 bioconda ``` I've uploaded the fasta index file [here](https://github.com/JonEilers/error_logs/blob/main/PyrusCommunis_BartlettDHv2.0.pilon.fasta.fai) ```bash >...

JonEilers

RepeatModeler always runs with 1 thread, does not reuse earlier round results

2

I'm running EarlGrey on my chromosome-level plant assembly with a size of 890Mbp. Estimated repeat content from the first few runs of RepeatModeler is around 60%. I am using the...

mjacksonhill

Conda install error

1

Hi all, Installing version 4.0.0 via conda triggers the following error: ``` Preparing transaction: done Verifying transaction: done Executing transaction: done ERROR conda.core.link:_execute(950): An error occurred while installing package 'bioconda::bioconductor-genomeinfodbdata-1.2.11-r43hdfd78af_1'....

Glfrey

Out of Memory but the job seemed already finished

10

Hello! I ran EarlGrey (v4.4.4) for multiple genomes (size between 500-600 Mb) using Slurm. Some jobs were completed but the others showed Out Of Memory (exit code 0). For those...

ting-hsuan-chen

Hi, Thank you for this very complete tool! When I run it in SLURM HPC using a conda environment, it seems that EarlGrey writes a lot of files in the...

jeankeller

RepeatMasker complains about invalid species search term (but runs at Gitpod)

6

Hi TobyBaril. I would like to ask for you help concerning a RepeatMasker error. We are trying to annotate a new genome assembly of Trypanosoma cruzi, whose NCBI Taxid is...

trypchromics

Resume from in-progress TEStrainer iterations

2

Hello! One of my genomes with a recent whole-genome duplication in the sunflower family (notoriously repeat-rich) has spent 26 days so far in the straining step, making it to round...

mjacksonhill

RepeatModeler or RepeatMasker failed with EarlGrey v4.4.0 and RepeatMasker v4.15, lanscape.pdf missed and an extended runtime of RepeatModeler round with EarlGrey v4.4.0 and RepeatMasker v4.15

4

1. The first time, I installed EarlGrey **v4.4.0** and RepeatMasker **v4.16**, and I ran around 50 species using this version. The running time of every species was less than 3...

manwensu