Very long tophat run

[seq_newbie]

Hi,

I have submitted a job to the queue on my cluster with 7 successive tophat jobs in the file. It has been 2 days and only the directory for the first job has been created and there is still no accepted_hits.bam file

(only left_kept_reads.info logs right_kept_reads.info tmp)

There are no error files generated and the job is still on the queue. Does anyone know what might be going on and if I should kill the job and start again? I don't want to kill it if there's a chance it's normal for such a long run.

Thanks,

K.

[dariober]

Hi,
It might be normal if you have lots of reads (can't tell how many, but I guess hundreds of millions would take days on a single thread/processor).

Also, could it be that you submitted the job two days ago but stayed in the queue waiting to start for several hours?

If you post more details (number of reads, log files etc...) someone in SEQanswers might give some insights...

Dario

[seq_newbie]

Hi Dariober,

Thanks for your reply. I'm pretty sure the job started running straight away. I'm not sure of the number of reads but I reckon it would be in the millions. I tried uploading log files but I get invalid file message. I'll just wait and see I suppose.

K.

[jeales]

You can do "wc -l my_reads.fastq" on one of the fastq files then divide by 4 and that is the number of reads in the file