search

arq5x / lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery
MIT License
306 stars 118 forks source link

lumpyexpress exited with "Could not retrieve index file for '-'" #370

Open Ceonham opened 2 years ago

Ceonham commented 2 years ago

Hello, I met this error when I used lumpyexpress to generate SV vcf file for next genotyping. The command I used is: lumpyexpress -B 19S669_sv_sorted.bam -S 19S669.splitter.bam -D 19S669.discordants.bam -o 19S669_sv.vcf

And soon the following information appeared: Sourcing executables from /home/qh/BioSoft/IndelEnsembler/lumpy-sv/bin/lumpyexpress.config ... Checking for required python modules (/usr/bin/python)... Calculating insert distributions... Library read groups: 19S669 Library read length: 150 [E::idx_find_and_load] Could not retrieve index file for '-'

Finally no vcf file was created and I have no idea what "the index file for '-'" is. Do you have any suggestions to solve this problem? Many thanks!

Han Qin

ryanlayer commented 2 years ago

That is strange. It is as if it did not grab the command line argument correctly.

I suggest you use smooch. https://github.com/brentp/smoove

It is a much better wrapper than lumpyexpress

On Nov 28, 2021, at 2:49 AM, Ceonham @.***> wrote:

[E::idx_find_and_load] Could not retrieve index file for '-'

Ceonham commented 2 years ago

That's really good. I'm trying it. Thank you so much!

liujiaxin7 commented 1 year ago

nd_and_load] Could not retrieve index file for '-'

Hello, have you solved this problem? I had the same problem.

Ceonham commented 1 year ago

Hi,

Sorry for the late reply. It appears an unsolved bug in lumpy and you could choose the new softwore recommended by the author below my comments. Hope it helps :)

Han Qin

---------- Origin message ----------

From："liujiaxin7" @.> To："arq5x/lumpy-sv" @.> Subject：Re: [arq5x/lumpy-sv] lumpyexpress exited with "Could not retrieve index file for '-'" (Issue #370) Date：2022-10-07 11:07:44> nd_and_load] Could not retrieve index file for '-'

Hello, have you solved this problem? I had the same problem.

-- Reply to this email directly or view it on GitHub: https://github.com/arq5x/lumpy-sv/issues/370#issuecomment-1271061006 You are receiving this because you authored the thread.

Message ID: @.***>

liujiaxin7 commented 1 year ago

Thank you very much. I'll try it.