A working command line for Illumina's iSAAC ?

[craczy]

Hi GenoMax,

if you managed to run it under HAS, why don't you use the command line generated by HAS? That command line can be found either on the standard output, or at the beginning of the log file "Logging/Isaac.stderr.txt" that you will find in the HAS output directory.

Regarding the specific behaviour that you observed when trying to run directly from the command line, there is clearly an issue with the memory settings, but it is difficult to diagnose without more information. Could you provide the output of:

ulimit -a
tail -n 9999 /proc/sys/vm/*
cat /proc/meminfo

and also the last couple hundred lines of stderr before the crash.
Thanks,

Come

[GenoMax]

Has anyone managed to get "isaac-align" to work stand-alone on the command line and if so on what OS?

"Isaac-align"er is one of the components of HiSeq Analysis Software (HAS) and I have managed to get it to work when run as a part of a HAS run (but only under SGE, no luck with LSF).

Trying to get it to work stand-alone has been an exercise (Oiiio: I could not get it to work with the options you noted, on individual files etc). I thought I had managed to to it to work using the following command line (on a rocks v. 5.4.2 cluster)

isaac-align -b /Flow_cell_folder/Data/Intensities/BaseCalls -r /path_to/ISAAC_genomes/hg19/Homo_sapiens/UCSC/hg19/Sequence/IsaacIndex/sorted-reference.xml -o /output_dir -m 48

It created binary demultiplexed files (*.dat) (ran for about 8 hours, this was a big flowcell) before it died with following error

Error: boost::exception: Throw location unknown (consider using BOOST_THROW_EXCEPTION)
Dynamic exception type: boost::exception_detail::clone_impl<boost::exception_detail::current_exception_std_exception_wrapper<std::bad_alloc> >
std::exception::what: std::bad_alloc
[boost::tag_original_exception_type*] = St9bad_alloc

Illumina tech support says that the aligner part from HAS is not meant to be run as a standalone program and they pointed me to an open source project (https://github.com/sequencing/isaac_aligner) where the aligner from HAS has been released as a "developer" version i.e. they provide no support. There is no documentation (and as far as I can tell, not all of the command line options seem to work) in the github package.

[craczy]

Hi oiiio

You would need a lot more than 12GB memory. Try "-m 48" instead.

Thanks,

Come

[oiiio]

After downloading the reference I'm now hitting this error:


2013-06-10 17:52:33 [0x11d36a0] __gnu_parallel:sort for 64000000 elements
terminate called recursively
terminate called recursively
./isaac-run.sh: line 5: 40176 Aborted (core dumped) isaac-align --reference-genome IsaacIndex/sorted-reference.xml -b isaac/ --base-calls-format fastq -m 12 --verbosity 3

Has anyone put a successful run through with Isaac yet?

[oiiio]

Thanks I'm downloading it now, although I wonder if this download will finish before my indexing command...

Even though it looks like the downloadable ref is based on the same UCSC hg19 I am using, I can't help but feel a little loss of experimental control when it comes to comparisons against the other software I ran

[GenoMax]

Now just trying to index the hg19 reference with isaac-sort-reference . Seems to be taking quite a long time

Or you could download it from Illumina. It is available along with the HiSeq Analysis Software.

[oiiio]

So I realized that the FASTQ names must be specifically named as lane1_read1.fastq lane1_read2.fastq

Now just trying to index the hg19 reference with isaac-sort-reference . Seems to be taking quite a long time

[sklages]

What problems occured? Did you read the output of

./bin/isaac-align --help

[oiiio]

I just got hold of the iSAAC aligner from Illumina, but it seems to use a very different type of command line than most of the other aligners I have used, particularly when specifying a FASTQ. Does anyone have a command line that has been working for them?