Dear all,
Can iSAAC work on mac os platform?
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Hallo again ;-)
we are now with Isaac3. Cool .. ;-)
Creating indices for grch38 and grcm38 leaves some open questions:
I have run index creation as follows (mask-width 0 is the default, I just put it there as a "reminder" for future index creation runs):
Code:isaac-sort-reference \ --output-directory iSAACindex \ --jobs 1 \ --mask-width 0 \ --genome-file genome.fa
Code:-rw-rw-r-- 1 klages klages 618M 2016.08.26 01:05:08 2repeatness.8bpb.gz -rw-rw-r-- 1 klages klages 678M 2016.08.25 22:19:13 2uniqueness.8bpb.gz -rw-rw-r-- 1 klages klages 108K 2016.08.26 01:05:09 sorted-reference.xml drwxrwxr-x 2 klages klages 8.0K 2016.08.26 01:05:09 Temp
Code:[all] INFO: All done!
hg19-packed-reference.tar.gz from BaseSpace (btw, would be fine to have some grch38/grcm38 though) shows:
Code:-rwxr-x--- rpetrovski/aladdin 644685308 2014-11-19 21:38 2uniqueness.16bpb.gz -rw-r--r-- rpetrovski/aladdin 386961748 2014-11-20 13:03 neighbors-1or2-16.1bpb -rw-r--r-- rpetrovski/aladdin 386961748 2014-11-20 13:06 neighbors-1or2-32.1bpb -rwxr-xr-- rpetrovski/aladdin 3157608038 2014-11-20 12:53 genome.fa -rw-r--r-- rpetrovski/aladdin 48044 2014-11-20 12:54 sorted-reference.xml
* Do I still need Temp for any task after index creation?
* What are the differences compared to isaac2 indices?
best,
Sven
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In an attempt to make it easier to use Isaac2, we will make the packed index reference for commonly used genomes on BaseSpace. At the moment, the only 2 genomes available are hg19 and mm9. Feel free to request other genomes.
Also, the issues and recommendations around indexing genomes are summarized on the isaac2 github wiki page "Reference Indexes".
The link to the already indexed genomes in basespace might change in the future, please refer to the wiki page on github for updates.
Hopefully, this will help.
Come
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I had started an isaac2 index creation job for mm9 genome (with -w 6). It has been running for a week and still making files in Temp directory.
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Got the same just 5 minutes ago :-)
So the default for isaac-sort-reference should be changed or, alternatively, it should always be called with '--mask-width 6'.
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Commands used for the final steps in a nutshell.
Code:$ isaac-pack-reference -j 1 -r ./sorted-reference.xml -o ./packed-reference.tar.gz $ isaac-unpack-reference -j 1 -w 6 -i ./packed-reference.tar.gz
kmer-positions-32-00.dat through kmer-positions-32-63.dat
Code:2uniqueness.16bpb.gz
I have started a new isaac2 genome creation job for the MM9 genome with -w 6 option upfront.Last edited by GenoMax; 07-29-2015, 03:11 AM.
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Originally posted by GenoMax View PostThis is not working for me:
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
Code:rm -rf Temp isaac-unpack-reference -j 1 -w 6 -i packed-reference.tar.gz
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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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The 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
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@sven: A new thread has been created for posts related to isaac2 genome index creation.
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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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@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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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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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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