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Hi @FRANKSTARLING69 The "junction insertion" is not fully parallelized, so it may use only one thread and take some time, but it should be less < 30min. Cheers |
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Hi,
This is my first time using STAR. I am using the genecode human PRImary genenome sequence and annotation file (.gtf). Here is the command I used to run STAR:
STAR --runMode genomeGenerate --genomeDir ref/ --genomeFastaFiles /Users/matthew/Bioinformatics/index/GRCh38.primary_assembly.genome.fa --sjdbGTFfile /Users/matthew/Bioinformatics/index/gencode.v40.primary_assembly.annotation.gtf --runThreadN 10When I run this command STAR begins to run and generate genome files relatively quickly. STAR reaches "inserting junctions into the genome indices" but then is stuck at this step and does not finish running. I say that STAR is stuck because that is what is shown when I use the 'top' command to monitor the jobs running. Before the 'inserting junctions into the genome indices' step I can see that STAR is using most of the threads provided and the majority of the cpu but when this step is reached threads drop to below 2 and cpu use percentage drops as well. I do not know if that information is relevant but it is something I noticed. I am using an M1 macbook pro and have over 300 gb of ram so I do not think it is a memory issue.
Here is the log.out file as I have seen that is useful for diagnosing problems.
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