Ondov, thanks for the notes!
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Hi ondovb,
Many thanks for the notes! That was actually my concern.. My team had a discussion over the running time as we were not looking at Arabidopsis samples.
Which brings me to something else I just thought of: What is the difference between running on multiple threads and multiple nodes? I currently put threads=1 while total nodes=10..
On a side note, I realised that my processes that have been split into 10 nodes are all going into sleep mode.. Could this be because I didn't allocate enough RAM?
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Threads: should be the number of cores you want to use on each node. You mentioned you have 8 cores per node, so you'll want 8 threads to use them all.
Running time: will be linear with respect to genome length. Our data took 480 cpu hours, so yours (assuming a similar # of reads) should take 480 * 30 = 14400 cpu hours. If you use all 40 * 8 cores on your cluster, you're looking at about 45 hours.
Sleeping: if you remembered to include the -p flag, I'm not sure what else could cause this. Have you tried running it locally with the same settings and watching the output?
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Hi ondovb,
Yes, Im running it locally but it seems to be stuck at the aligning stage:
Round 1 / 4 (2101986 reads):
Sensitivity 4:
EDIT: I have used strace on the process and found it to be at the following state:
futex(0x40dd79d0, FUTEX_WAIT, 25312, NULLLast edited by Haneko; 07-01-2010, 07:06 PM.
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I think each instance might appear to be sleeping to the OS because the parent thread just sits and waits for the child threads to finish their computation (even if only one thread is chosen). What does the CPU usage look like?
Sensitivity 4 will take a pretty long time (even on your cluster), which could make it appear to be stuck. I wouldn't recommend going higher than 3. If you set the trim to at least 3, that should get rid of a lot of the errors and you should still be able to align a lot of reads.
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I have aligned a subset of the reads on my machine and have some questions.
I received several warnings (e.g. '5719579 substrings of chr1.fa ignored due to 5718003 character(s) other than [ACGTacgt]'). The Ns in the reference file(s) cause this problem and I don't know the impact of the warnings on the overall analysis.
At the end of the aligning part is says 'computing error frequencies'. What does this mean?
Does SOCS-B run faster, if all reference files would be merged into one multiFASTA reference file?
I struggle to understand the difference between the mismatch sensitivity (s) and the tolerance (t). Could you briefly explain these two parameters? Can I set them independently?
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Originally posted by fwessely View PostI received several warnings (e.g. '5719579 substrings of chr1.fa ignored due to 5718003 character(s) other than [ACGTacgt]'). The Ns in the reference file(s) cause this problem and I don't know the impact of the warnings on the overall analysis.
Originally posted by fwessely View PostAt the end of the aligning part is says 'computing error frequencies'. What does this mean?
Originally posted by fwessely View PostDoes SOCS-B run faster, if all reference files would be merged into one multiFASTA reference file?
Originally posted by fwessely View PostI struggle to understand the difference between the mismatch sensitivity (s) and the tolerance (t). Could you briefly explain these two parameters? Can I set them independently?
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