Re: gnumaps setup problem

[Brent Pedersen]

The machines have 47GB of memory. I have made all of that available.
The err log is attached.

On Mon, Feb 24, 2014 at 11:07 AM, changjin hong <cjh...@bu.edu> wrote:
> Hi,
>
> Can you check what is the max memory available in the machine you run gnumap?
>
>
> On Monday, February 24, 2014 10:39:25 AM you wrote:
>> Now I get this (still running)
>>
>> Command Line Arguments:
>> /software/cgeh/gnumap/gnumap/dep/gnumap_MPI_opt/bin/gnumap-stl -g
>> /misc2/data/Schwartz/brentp/mm10/ref/mm10.fa
>> --save=/misc2/data/Schwartz/brentp/mm10/ref/idxGnu/mm10-ct-m17-s1-h500.gnu
>> -o /home/brentp/src/bwa-meth/compare/results/gnumapbs-sim/tmp/nullReadOutTmp
>> -m 17 -s 1 -c 1 -h 500 -t 1 -a 0.95 -b --up_strand -y 2
>> /software/cgeh/gnumap/gnumap/scripts/gnuIdxRead.fq
>> Hashing Genome...
>>
>> ===========================================
>> GNUMAP_PIPELINE(v0.1)
>> -http://jlab.bu.edu
>> -cjh...@bu.edu
>> -running at /software/cgeh/gnumap/gnumap
>> -elapsed time: 0.0
>> ===========================================
>> In progress ...
>> # Using STL genome type: unsigned int
>> This is GNUMAP, Version 3.1.0 BETA, for public and private use.
>> # Using STL version to hash.
>> Size of genome: 2730871774
>> [0/-] Converting to Vector...
>> [0/-] Trying to create hash of size 108193685
>> Trying to create entire array of size 8405958600 (1050744825 total
>> positions of size 8)
>> [0/-] Finished create hash.
>> [0/-] Stats: Total hashes is 1050744825, Longest hash is 500, shortest
>> is 1, and average is 9.711702
>> [0/-] Trying to create a new genome with a size of 2730871776...Success!
>> ERROR:
>> Could not malloc genome
>> Matching 1 file(s):
>> Reads per processor: 2048
>> Minimum Read Length to Process : 0
>>
>> #Finished.
>> # Total Time: 3995.49 seconds.
>> # Found 1 sequences.
>> # Sequences matched: 0
>> # Sequences not matched: 1
>> # Output written to
>> /home/brentp/src/bwa-meth/compare/results/gnumapbs-sim/tmp/nullReadOutTmp.sa
>> m # Using STL genome type: unsigned int
>> This is GNUMAP, Version 3.1.0 BETA, for public and private use.
>> # Using STL version to hash.
>>
>> On Mon, Feb 24, 2014 at 10:10 AM, Brent Pedersen <bped...@gmail.com> wrote:
>> > Hi, sample commands are working. On our cluster /data/Schwartz is
>> > symlinked from /misc2/data/Schwartz/ so maybe it doesn't like the
>> > symlink? I am still looking in to this but thought that might be a
>> > problem.
>> > -Brent
>> >
>> > On Fri, Feb 21, 2014 at 5:09 PM, changjin hong <cjh...@bu.edu> wrote:
>> >> Hi,
>> >>
>> >> Can you check if you specify a reference genome file in full path with
>> >> '--
>> >> genome'? Also, make sure that the file exist!
>> >>
>> >> Check some sample command line in the example directory.
>> >>
>> >> -CJ
>> >>
>> >> On Friday, February 21, 2014 04:21:57 PM you wrote:
>> >>> Hi, Now I can build but I get the error below. There is nothing in
>> >>> /misc2/data/Schwartz/brentp/mm10/ref/idxGnu
>> >>>
>> >>>
>> >>> Matching 1 file(s):
>> >>> Reads per processor: 2048
>> >>> Minimum Read Length to Process : 0
>> >>>
>> >>> #Finished.
>> >>> # Total Time: 1.87687 seconds.
>> >>> # Found 0 sequences.
>> >>> # Sequences matched: 0
>> >>> # Sequences not matched: 0
>> >>> # Output written to
>> >>> /home/brentp/src/bwa-meth/compare/results/gnumapbs-sim/13230.r1/aligned/
>> >>> gnu/ gen/watson/1.sam # Using STL genome type: unsigned int
>> >>> This is GNUMAP, Version 3.1.0 BETA, for public and private use.
>> >>> # Using STL version to hash.
>> >>>
>> >>> Reading from file:
>> >>> /misc2/data/Schwartz/brentp/mm10/ref/idxGnu/mm10-ga-m17-s1-h500.gnu
>> >>> and iproc:0 nproc:1
>> >>> File wouldn't open: No such file or directory
>> >>>
>> >>> ERROR:
>> >>> Could not open Genome read file
>> >>>
>> >>> On Thu, Feb 20, 2014 at 1:59 PM, changjin hong <cjh...@bu.edu> wrote:
>> >>> > Hi, Brent
>> >>> >
>> >>> >
>> >>> >
>> >>> > Sorry for the inconvinience!
>> >>> >
>> >>> >
>> >>> >
>> >>> > Updated gnumap is available at
>> >>> >
>> >>> >
>> >>> >
>> >>> > ftp://oligomer.bumc.bu.edu/software/gnumaps.tar.gz
>> >>> >
>> >>> >
>> >>> >
>> >>> > Then, try
>> >>> >
>> >>> >
>> >>> >
>> >>> > ./install_gnumaps.sh qc blat 2>&1 | tee gnu_setup.log
>> >>> >
>> >>> >
>> >>> >
>> >>> > Then, can you send "gnu_setup.log" to me?
>> >>> >
>> >>> >
>> >>> >
>> >>> > Thanks,
>> >>> >
>> >>> >
>> >>> >
>> >>> > -CJ