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clemgoub / dnaPipeTE

dnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline designed to find, annotate and quantify Transposable Elements in small samples of NGS datasets. It is very useful to quantify the proportion of TEs in newly sequenced genomes since it does not require genome assembly and works on small datasets (< 1X).
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RepeatMasker.lib #31

Closed dlata closed 4 years ago

dlata commented 4 years ago

I am using dnaPipeTE to see what transposable elements are present in the genome of the insect species I am studying. I was having an issue with it, I will be really thankful if you can please help me through this.

I get the following error whenever I run ./test_config.sh.

"RepeatMasker.lib doesn't include the Repbase sequences! Follow instruction to install RepeatMasker libraries on https://github.com/clemgoub/dnaPipeTE"

If anyone say how can this be resolved??

niconm89 commented 4 years ago

Hi, since the last version of RepBase is payed and you need a subscription to get it, you just can avoid this error message. Did you try to run a test?

python3 ./dnaPipeTE.py -input test/test_dataset.fastq -output test/output_folder -genome_size 2000000 -genome_coverage 0.5 -sample_number 2

You should be careful about the installation process because some of the dependencies downloads are not working (several links had changed), so you must manually install them in the bin folder.

Nicolás

clemgoub commented 4 years ago

Yes Nicolás you are right. I need to update dnaPipeTE absolutely to take this into account. 2019 was a crazy year, but 2020 should be more open... Hopefully!