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guigolab / sQTLseekeR

R package to detect splicing QTLs (sQTLs)
http://big.crg.cat/computational_biology_of_rna_processing/sqtlseeker
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error message from index.genotype in sQTLseekeR #11

Open tingqi opened 4 years ago

tingqi commented 4 years ago

Hi,

I was running sQTLseekeR and got an error message "[E::get_intv] Failed to parse TBX_GENERIC, was wrong -p [type] used? The offending line was: "chr start end snpId". It seems that there is some issue about this function "Rsamtools::indexTabix(file.final, format = "bed")". This error message seems to be the newly generated error. Previously, I also run sQTLseekeR using tested data and real data, and it works well. Could you please help have a check? Thank you.

Cheers, Ting

chz31 commented 2 years ago

I got the same error. I wonder if anyone got an answer to this? Thanks!

sklarame commented 1 year ago

I got the same error. I wonder if anyone got an answer to this? Thanks!

I got this error too. Checking of the source code showed that such errors were caused by the inconsistency in regarding the header line of the genotyping table between sQTLseekeR and the tabix program (called by the Rsamtools::indexTabix). sQTLseekeR requires a header line with the first 4 fields as "chr\tstart\tend\tsnpId", which is however regarded as "offending of the BED format" in the tabix program, since the header does not start with a "#". But further test with my data showed that the whole pipeline can be completed despite the error message.