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In the *.cls.tsv file, the header is listed in the following format. However, in the place of "Order", the true classification should be in the "Subclass" level. For the order level, it probably shoul…
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Hi,
I am assembling a heterozygous 2.5 Gb (haploid size, so we expect a ~5 Gb assembly) plant genome. We have about 35x coverage per allele and many copies of a very few repeats (LTR-retrotransposons…
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Hello,
I am running LTR retriever, and I am coming across these errors:
1.when i run /LTR_retriever/LTR_retriever,It displays the following error, but it can continue to run.
Fri Oct 25 06:19:16 Lo…
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(LTR_retriever) [00:07:33]rzhao@magnus-2:~/LTR_retriever$ 'LTR_retriever -genome /scratch/pawsey0149/rzhao/wheatProject/LTR_file/refKA_polished/refKA_polished.fasta'
##########################
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Hello @zhangrengang,
Thank you so much for developing this neat package. I improved the `LTR_retriever` classification scheme based on your [suggestions](https://github.com/oushujun/LTR_retriever/i…
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Hi Mikhail,
Thanks for making this tool available. I'm working on a medium size plant genome (~ 1.2 GB). It's highly inbred, but also full of repeats. I'm wondering if you recommend that we filter…
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I am getting the following error while running v2.0. I don't know what caused it. Please help me.
Error: Argument "num_threads". Illegal value, expected (>=1 and =
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Hi,
I've downloaded `dfamscan.pl` here: `/usr/local/bin/dfamscan.pl`. Then, I tried to pull out the help but I got an error:
`perl /usr/local/bin/dfamscan.pl -help
Can't locate Dfamscan.pm in @…
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Running with harvest and finder inputs. The errors are produced when the program is executed with just harvest outputs, just finder outputs and when both are run together. The command utilized to run …
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Hi. LTR_retriever stops with a RepeatMasker error resulting from a sequence ID longer than 50 characters in the file xxx.fa.mod.ltrTE.trunc. The ID in question is >LSRX01000097.1:1074794..1082843|LSRX…