Building reference

[pillailab]

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]

@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.

[asdggr]

Hello, did you find the answer to that issue? I have the exact same problem. I also tried with BuildRefProcess, but it gets stuck at the mapping genome fragments step. I checked that both the gtf and fasta have the same chromosome nomenclatures. I used IRF v 1.3.0, 1.3.1 and even the 2.0

All dependencies are ok..

Thanks in advance for any help.