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nghiavtr / FuSeq_WES

GNU General Public License v3.0
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error when trying to load ensmbl_paralogs_grch38.RData #10

Open hvelab opened 1 year ago

hvelab commented 1 year ago

Good morning,

After an installation from source cloning the repo and downloading the data, when attempting to run the code within the commands:

#extract mapped reads and split reads
python3 /apps/FUSEQ/1.0.0/fuseq_wes.py --bam $bamfile  --gtf $ref_json --mapq-filter --outdir $output_dir

#process the reads
Rscript /apps/FUSEQ/1.0.0/process_fuseq_wes.R in=$output_dir sqlite=$gtfSqlite fusiondb=$fusiondbFn paralogdb=$paralogdb out=$output_dir

This error arises: 

Error in load(paralogdbFn) :
  bad restore file magic number (file may be corrupted) -- no data loaded
In addition: Warning message:
file ‘ensmbl_paralogs_grch38.RData’ has magic number ''
  Use of save versions prior to 2 is deprecated
Execution halted

Being run in an Intel system, with R 4.0.2, all the dependencies are compiled and installed using Intel compilers. Any idea of what might be the issue? With ensmbl_paralogs_grch37.RData runs properly.

Best regards,

nghiavtr commented 1 year ago

Hi @hvelab

Thank you for using FuSeq_WES and pointing out the issue. We have no problem with R version 4.2.0 but likely it happens for lower version of R. I have updated ensmbl_paralogs_grch38.RData file, please download the new one from the Data folder (https://github.com/nghiavtr/FuSeq_WES/blob/main/Data/ensmbl_paralogs_grch38.RData)

let me know if you have any further issues when running FuSeq_WES

Good lucks with your research!

Best, Nghia