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archive:bioinformatic_tools:abyss [2010/05/16 01:49] jstjohn |
archive:bioinformatic_tools:abyss [2010/05/17 23:45] jstjohn |
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Also because the makefile crashed, it didn't get a chance to clean up the output from the previous step. I had to manually delete the lane-x-3.hist files (which were all of size 0 anyway). After doing this the makefile was able to pick up where it left off and re-generate the lane-x-3.hist files. | Also because the makefile crashed, it didn't get a chance to clean up the output from the previous step. I had to manually delete the lane-x-3.hist files (which were all of size 0 anyway). After doing this the makefile was able to pick up where it left off and re-generate the lane-x-3.hist files. | ||
+ | |||
+ | There is some error where the laneX.hist files are empty... | ||
+ | |||
+ | ====Attempt 4==== | ||
+ | I have access to kolossus which has 1.1tb of ram. I will now run the program on kolossus to see if it will assemble there... | ||
+ | |||
+ | Step1: | ||
+ | Install ABySS on kolossus. Following the exactly same process as listed above except with --prefix=/scratch/jstjohn on kolossus. The installation was straightforward and went without a hitch. | ||
+ | |||
+ | Binaries and libraries are located here: | ||
+ | /scratch/jstjohn/bin | ||
+ | /scratch/jstjohn/lib | ||
+ | |||
+ | Step2: | ||
+ | Galt has already coppied the banana slug illumina reads to /scratch/galt/bananaSlug, I added the 454 fastq reads to that folder as well. | ||
+ | |||
+ | Step3: | ||
+ | from screen on kolossus execute the following command: | ||
+ | <code> | ||
+ | set path = ( /scratch/jstjohn/bin $path ) | ||
+ | abyss-pe -j j=4 k=35 n=2 mpirun="/scratch/jstjohn/bin/mpirun -machinefile machinefile -x PATH=/scratch/jstjohn/bin:$PATH" np=30 lib='lib1' lib1='/scratch/galt/bananaSlug/slug_1.fastq /scratch/galt/bananaSlug/slug_2.fastq' se='/scratch/galt/bananaSlug/GAZ7HUX02.fastq /scratch/galt/bananaSlug/GAZ7HUX03.fastq /scratch/galt/bananaSlug/GAZ7HUX04.fastq /scratch/galt/bananaSlug/GCLL8Y406.fastq' name=slugAbyss3 | ||
+ | </code> | ||
+ | |||
+ | |||
+ | Note that this run combines both the illumina runs and the 454 data for banana slug. I am also experimenting with a k=35 since galt had better luck with a kmer size of 31 using SOAPdenovo than a kmer size of 23, perhaps the trend continues into larger kmers. If this doesn't work for whatever reason, I will also try shorter and longer kmers. | ||
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