williamritchie / IRFinder

Detecting intron retention from RNA-Seq experiments
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ref-cover.bed missing #19

Closed OSchwich closed 7 years ago

OSchwich commented 7 years ago

Dear all,

I am currently establishing IRFinder 1.2.0 in our lab. I ran the Ref-Building process using our own FASTA and gtf-file and in addition ran the suggested pipeline via the ensembl-FTP. In both cases the building process seemed to work.

/home/Apps/IRFinder/bin/IRFinder -m BuildRef \ -r /home/Apps/IRFinder/REF/Mouse-mm10-release81 \ -S /home/Apps/STAR-2.5.2b/bin//Linux_x86_64/STAR \ -e /home/Apps/IRFinder/REF/extra-input-files/RNA.SpikeIn.ERCC.fasta.gz \ -R /home/Apps/IRFinder/REF/extra-input-files/Mouse_mm10_nonPolyA_ROI.bed \ ftp://ftp.ensembl.org/pub/release-81/gtf/mus_musculus/Mus_musculus.GRCm38.81.gtf.gz

2017-07-27 09:32:30 (2.74 MB/s) - 'Mus_musculus.GRCm38.81.gtf.gz' saved [277875$

Jul 27 09:33:41 ..... started STAR run Jul 27 09:33:41 ... starting to generate Genome files Jul 27 09:35:01 ... starting to sort Suffix Array. This may take a long time... Jul 27 09:35:20 ... sorting Suffix Array chunks and saving them to disk... Jul 27 09:57:32 ... loading chunks from disk, packing SA... Jul 27 10:05:56 ... finished generating suffix array Jul 27 10:05:56 ... generating Suffix Array index Jul 27 10:09:25 ... completed Suffix Array index Jul 27 10:09:25 ..... processing annotations GTF Jul 27 10:09:43 ..... inserting junctions into the genome indices Jul 27 10:13:32 ... writing Genome to disk ... Jul 27 10:14:07 ... writing Suffix Array to disk ... Jul 27 10:18:11 ... writing SAindex to disk Jul 27 10:18:28 ..... finished successfully Star genome build result: 0 Mapability result: -1 Ref build result: -1

Now I wanted to start my first IRFinder run and got (using both reference folders) the same error:

Argument error: -r /home/Apps/IRFinder/REF/Mouse-mm10-release81, Does not appear to be a valid IRFinder reference. Could not find /home/Apps/IRFinder/REF/Mouse-mm10-release81/IRFinder/ref-cover.bed

I checked the folder and the file is truly missing. Is there a way to work this out?

Kind regards

dg520 commented 7 years ago

Hi,

The problem comes from the failure of running mapabillity. Very likely you don't have the permission to call the script. You can use chmod to give execute permission to all the script under bin and bin/util. Please follow the instruction on Wiki page. Then you need to rebuild the IRFinder reference.

Best, Dadi

OSchwich commented 7 years ago

That really was an easy solution to my issue. Thank you, IRFinder is working fine now.

Best