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mhammell-laboratory / TElocal

A package for quantifying transposable elements at a locus level for RNAseq datasets.
GNU General Public License v3.0
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Error in building gene index #9

Closed whiteorchid closed 3 years ago

whiteorchid commented 3 years ago

Hi,

May I know "Error in building gene index" is caused by the gene gtf file, which I used : ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/gencode.v34.primary_assembly.annotation.gtf.gz

Thanks!

log file content as below:

INFO  @ Mon, 10 Aug 2020 11:39:51: 
# ARGUMENTS LIST:
# name = test
# BAM file = test.bam
# GTF file = gencode.v34.primary_assembly.annotation.gtf 
# TE file = hg38_rmsk_TE.gtf.locInd 
# multi-mapper mode = multi 
# stranded = reverse 
# number of iteration = 100
# Alignments grouped by read ID = False

INFO  @ Mon, 10 Aug 2020 11:39:51: Processing annotation files ...

INFO  @ Mon, 10 Aug 2020 11:39:51: Building gene index ....... 

Error in building gene index
olivertam commented 3 years ago

Hi,

Thank you for your interest in the software. We are now taking a look at the error and see if we can replicate it. Could you confirm that the version of TElocal is 1.1.0?

Thanks.

whiteorchid commented 3 years ago

Thanks,

Yes, the version used is TElocal 1.1.0, thanks a lot!

olivertam commented 3 years ago

Thanks for your quick response. I have another question (apologies): which python version are you using? All the best.

whiteorchid commented 3 years ago

python 2.7.15, thanks!

olivertam commented 3 years ago

Thanks. We have been able to replicate the issue, and are now looking into it. We'll let you know once we have a solution.

whiteorchid commented 3 years ago

Thanks so much, appreciate!

talithaforcier commented 3 years ago

Hi! Thanks for the information, it looks like there was an extra call for the strandedness parameter, and with that removed it should build the index properly.

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