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williamritchie / IRFinder

Detecting intron retention from RNA-Seq experiments
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Building reference #172

Open pillailab opened 1 year ago

pillailab commented 1 year ago

Hello, I have been trying to build a new refernce for hg19 (my bam files are hg19) and i have tried the STAR variation, singularity install, older 1.3 version - all of it just runs for several days and times out. Can you let me know what may help ? Down is the latest iteration Launching reference build process. The full build might take hours. <Phase 1: STAR Reference Preparation> STAR --runMode genomeGenerate --genomeDir /home/mp758/project/GenomeBuilds/IRfinder/IRFinder_hg19/STAR --genomeFastaFiles /home/mp758/project/GenomeBuilds/IRfinder/IRFinder_hg19/genome.fa --sjdbGTFfile /home/mp758/project/GenomeBuilds/IRfinder/IRFinder_hg19/transcripts.gtf --sjdbOverhang 150 --runThreadN 20 &>> log-star-build-ref.log STAR version: 2.7.10a compiled: 2022-01-14T18:50:00-05:00 :/home/dobin/data/STAR/STARcode/STAR.master/source May 17 15:15:07 ..... started STAR run May 17 15:15:07 ... starting to generate Genome files May 17 15:15:47 ..... processing annotations GTF May 17 15:16:14 ... starting to sort Suffix Array. This may take a long time... May 17 15:16:31 ... sorting Suffix Array chunks and saving them to disk... May 17 15:34:31 ... loading chunks from disk, packing SA... May 17 15:35:45 ... finished generating suffix array May 17 15:35:45 ... generating Suffix Array index May 17 15:39:31 ... completed Suffix Array index May 17 15:39:32 ..... inserting junctions into the genome indices May 17 15:43:32 ... writing Genome to disk ... May 17 15:43:35 ... writing Suffix Array to disk ... May 17 15:43:56 ... writing SAindex to disk May 17 15:43:59 ..... finished successfully <Phase 2: Mapability Calculation> May 17 15:44:00 ... mapping genome fragments back to genome... slurm-42586915.out (END)

Thanks Manoj

dg520 commented 1 year ago

@pillailab Sorry for the super-late reply. Have you checked if the chromosome nomenclatures in the transcripts.gtf and the genome.fa are the same? For example, both start with "chr", or neither has so.