[craczy]

This is not working for me:

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

My mistake. Apologies. It is not the sorted-reference.xml but the tarball created by 'isaac-pack-reference':

rm -rf Temp
isaac-unpack-reference -j 1 -w 6 -i packed-reference.tar.gz

[GenoMax]

Commands used for the final steps in a nutshell.

$ 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

The end result was a set of 64 files

kmer-positions-32-00.dat through kmer-positions-32-63.dat

And one

2uniqueness.16bpb.gz

file.

I have started a new isaac2 genome creation job for the MM9 genome with -w 6 option upfront.

[sklages]

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'.

[GenoMax]

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.

[craczy]

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

[sklages]

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):

isaac-sort-reference \
  --output-directory iSAACindex \
  --jobs 1 \
  --mask-width 0 \
  --genome-file genome.fa

That left me with exact 3 files and a 1.1TiB Temp folder:

-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

make reported

[all]    INFO: All done!

At least it is "packable" by isaac-pack-reference.

hg19-packed-reference.tar.gz from BaseSpace (btw, would be fine to have some grch38/grcm38 though) shows:

-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

* Is that a complete and valid index??
* Do I still need Temp for any task after index creation?
* What are the differences compared to isaac2 indices?

best,
Sven

[fznajar]

Dear all,
Can iSAAC work on mac os platform?