Hi all,
I have a STAR alignment job that has been running for 2 days. Here is command:
STAR --genomeDir GENOME_DIR --readFilesIn $FASTAQ_DIR/read_1.fastq $FASTAQ_DIR/read_2.fastq --runThreadN 16
And in the end of Log.out file, it just shows "Create thread #..." No error massage and any complaints were found. Any ideas?
Thank you in advance!
Can you see the job running/using memory or is it completely dead?
I also spot a likely error in your command: you specify GENOME_DIR but that should probably be the environmental variable $GENOME_DIR
Thank you for pointing it out. That was just a typo. I use $GENOME_DIR in my command. I check the job status. It shows running, but hangs on the 'create thread' step Still no idea why that happened...
Have you tried with just one thread?
If nothing has happened for 2 days this is not going anywhere. You would be best off killing the job and restarting. Are you trying to use more cores than are available to you/on your server?
Thank you for reply.
I have run this job twice. For the second time, I used option -pe as 16, but it still got me nowhere. I found a similar post on google groups. They seemed to have no answer. I killed the job anyway. similar post
How much memory do you have available on this server? STAR needs a minimum of 30G.
Are you using pre-compiled STAR or did you compile the program yourself? Are you using the the latest version?