Originally posted by sklages
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I did not specify a value for seed-length so the process is creating all possible combinations [--annotation-seed-lengths arg (=16 20 24 28 32 36 40 44 48 52 56 60 64 68 72 76 80]. It looks like the end may be in sight today for the process I am running since the files for 80 are being made now.
@sven: Expect a multi-day turnaround.
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@Semyon/Come: Can one of you confirm if the following files represent the correct isaac2 index for hg19 genome? My isaac-sort-reference job appeared to have finished (no errors) but these are the only files I see in the top level directory (Temp directory is still there with files within)
Code:1.1G 2uniqueness.16bpb.gz 47G kmer-positions-32-0.dat 50K sorted-reference.xml
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Originally posted by sklages View PostWell, .. for now .. the server crashed overnight, just three hours ago ..
We now have to investigate what event caused this crash. Maybe it is just "Murphy's Law" .. we'll see.
We had a failure on a network interface .. that made at least one process going frenzy and pushed the load beyond 1000...
So I'll restart indexing today.
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Originally posted by GenoMax View Post@Semyon/Come: Can one of you confirm if the following files represent the correct isaac2 index for hg19 genome? My isaac-sort-reference job appeared to have finished (no errors) but these are the only files I see in the top level directory (Temp directory is still there with files within)
Code:1.1G 2uniqueness.16bpb.gz 47G kmer-positions-32-0.dat 50K sorted-reference.xml
All the kmers are indexed in on single data file (kmer-positions-32-0.dat), which is not a very good thing as it prevents parallelisation when searching for mapping candidates.
You can use the "isaac-pack-reference" and then "isaac-unpack-reference -w 6" to split the index into smaller files without having to re-doing the reference sorting.
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Originally posted by craczy View PostThis looks correct, but surprising. Did you specify something like "-w 1" on the command line by any chance?
Code:$ isaac-sort-reference -g /path_to/HG19_UCSC/Sequence/WholeGenomeFasta/genome.fa -o .
Originally posted by craczy View PostYou can use the "isaac-pack-reference" and then "isaac-unpack-reference -w 6" to split the index into smaller files without having to re-doing the reference sorting.
Update: I think I need to move the "Temp" directory out of the way (just realized that and trying it now) for "pack-reference" to work.
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Well, I can confirm that.
It took ~64h on a 48 core "Opteron 6176 SE" (fast local storage, RAID) to build a hg19 index.
Code:isaac-sort-reference --genome-file fa_hg19/genome.fa --jobs 1 --output-directory iSAAC2Index.32 --quiet
Code:938M 2015.07.27 06:21:35 2uniqueness.16bpb.gz 42G 2015.07.27 06:54:45 kmer-positions-32-0.dat 15K 2015.07.27 06:54:51 sorted-reference.xml 8.0K 2015.07.27 06:54:51 Temp
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@come:
I tried the "isaac-unpack-reference" (relevant part of the command line below)
Code:$ isaac-unpack-reference -j 8 -w 6 -i .
Code:tar: .: Cannot read: Is a directory tar: At beginning of tape, quitting now tar: Error is not recoverable: exiting now make: *** [Temp/sorted-reference.xml] Error 2
BTW: "Temp" directory is required for the unpack-reference.
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Just tried,
Code:isaac-unpack-reference -j 1 -w 6 -i . --dry-run
Code:warning: failed to load external entity "Temp/sorted-reference.xml" unable to parse Temp/sorted-reference.xml warning: failed to load external entity "Temp/sorted-reference.xml" unable to parse Temp/sorted-reference.xml
Code:isaac-unpack-reference -j 1 -w 6 -i .
Code:tar -C Temp --touch -xvf . tar: .: Cannot read: Is a directory tar: At beginning of tape, quitting now tar: Error is not recoverable: exiting now make: *** [Temp/sorted-reference.xml] Error 2
Code:make[1]: Entering directory `/path/to/iSAACindexBuildDir/iSAAC2Index.32' make[1]: *** No rule to make target `Temp/genome.fa', needed by `/path/to/iSAACindexBuildDir/iSAAC2Index.32/genome.fa'. Stop. make[1]: Leaving directory `/path/to/iSAACindexBuildDir/iSAAC2Index.32' make: *** [all] Error 2
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Originally posted by craczy View PostThe input file should be the 'sorted-reverence.xml', not the current directory:
This should work:
Code:isaac-unpack-reference -j 1 -w 6 -i sorted-reference.xml
Come
Code:tar: This does not look like a tar archive tar: Skipping to next header tar: Read 4461 bytes from ./sorted-reference.xml tar: Error exit delayed from previous errors make: *** [Temp/sorted-reference.xml] Error 2
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