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MonashBioinformaticsPlatform / RNAsik-pipe

RNAsik - more than just a pipeline
https://monashbioinformaticsplatform.github.io/RNAsik-pipe/
Apache License 2.0
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declaring the reference file directory with -refFiles throws an error #28

Open methylnick opened 6 years ago

methylnick commented 6 years ago

Using The Lot command in the docs to point to the reference file directory with -refFiles throws an error

RNAsik version 1.5.0 00:00:00.207 Error (/mnt/software/apps/RNAsik-pipe-1.5.0/bin/../src/sikRefFiles.bds, line 165, pos 31): Too many or too little refFiles were found, '{ fa => /mnt/cephfs/scratch/nick.wong/mark.shackleton/gamze.abali/referenceFiles/genome.fa, gtf => /mnt/cephfs/scratch/nick.wong/mark.shackleton/gamze.abali/referenceFiles/genes.gtf }'. Try using -fastaRef and -gtfFile options instead

However, using the -fastaRef and -gtfFile options worked.

serine commented 6 years ago

thanks @methylnick this is likely a bug. It's on my todo to make -refFiles better, will get up to it soon, thanks for reporting

alexyfyf commented 6 years ago

How is your progress on this? 1.5.2 still not working for this parameter