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xunchen85 / ERVcaller

ERVcaller is a tool designed to accurately detect and genotype non-reference unfixed endogenous retroviruses (ERVs) and other transposable elements (TEs) in the human genome using next-generation sequencing (NGS) data. We evaluated the tools using both simulated and real benchmark whole-genome sequencing (WGS) datasets. ERVcaller is capable to accurately detect various TE insertions of any lengths, particularly ERVs. It allows for the use of a TE reference library regardless of sequence complexity, such as the entire RepBase database. It is easy to install and use with command lines.
http://www.uvm.edu/genomics/software/ERVcaller.html
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Argument "-" isn't numeric in subtraction (-) at ERVcaller_v.1.3.pl line 1305, <OUT3> line 2. #15

Open Biojenifer opened 2 years ago

Biojenifer commented 2 years ago

Hi!

Although I am getting a vcf with HERV-K insertions after running ERVcaller with some bam files (sorted by coordinate and with duplicates marked), I still have the sampleID_temp directory. Shouldn't this directory be erased when the program finishes?

In addition, I have been looking the logs and I get some errors in different samples:

One of the errors is this:

Argument "-" isn't numeric in subtraction (-) at ERVcaller_v.1.3.pl line 1305, <OUT3> line 2.

In another sample, I get this error:

Error in `[<-.data.frame`(`*tmp*`, , 2, value = NA_real_) :
  replacement has 1 row, data has 0
Calls: [<- -> [<-.data.frame
Execution halted

Do you know how can I solve this?

By the way, I am still getting the output vcf in these samples, so I was wondering if maybe I could ignore it.

Thanks!

xunchen85 commented 2 years ago

Hi,

Yes, if the running is successful, you could remove the entire temp folder.

The first error may be due to some format issue, such as empty temp files. it is about the detection of integration breakpoints. You could check ".out3" files in the temp files

It seems like the second error is due to an empty output, it should be about the R script used for the genotyping. Could you share a bit more details about the input?

btw, I would suggest using the latest version rather than 1.3.

Xun