archive:bioinformatic_tools:abyss
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archive:bioinformatic_tools:abyss [2010/05/17 23:45] jstjohn |
archive:bioinformatic_tools:abyss [2010/05/19 20:55] jstjohn |
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| There is some error where the laneX.hist files are empty... | There is some error where the laneX.hist files are empty... | ||
| - | |||
| ====Attempt 4==== | ====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... | 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... | ||
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| - | 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. | + | 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. |
| + | We combined all fastq files into two large files representing the two read pairs. Each of these files is approximately 50GB and contain roughly 20GB of reads. Even on kolossus I am getting some out of disk space errors in the following step: | ||
| + | |||
| + | <code> | ||
| + | KAligner -j4 -k35 /scratch/galt/bananaSlug/slug_1.fastq /scratch/galt/bananaSlug/slug_2.fastq slugAbyss3-3.fa \ | ||
| + | |ParseAligns -k35 -h lib1-3.hist \ | ||
| + | |sort -nk2,2 \ | ||
| + | |gzip >lib1-3.pair.gz | ||
| + | </code> | ||
| + | |||
| + | Near the height I have observed this is eating up about 50G of ram, but the issue appears to be in available space for the sort algorithm in kolossus's /tmp/ directory. I am trying this again so I can copy down the error and send it to cluster-admin because kolossus should have around 400GB free of local HD space on top of its 1.1TB of ram. (kolossus has more ram than HD space: 1.1TB of ram vs 750GB hd) | ||
| + | |||
| + | To get around the issue of sort running out of memory in its temp directory, I found an alternate command where you can supply your own temp directory to sort. Since there is plenty of room left on the hive I issue the following command to generate the files myself. The nice thing is that since this is a makefile, once I have done this I can simply re-start the assembler, and it will see the files I have manually generated and move on to the next step. | ||
| + | <code> | ||
| + | KAligner -j4 -k35 /scratch/galt/bananaSlug/slug_1.fastq /scratch/galt/bananaSlug/slug_2.fastq slugAbyss3-3.fa \ | ||
| + | |ParseAligns -k35 -h lib1-3.hist \ | ||
| + | |sort -T /hive/users/jstjohn/slugAssembly/tmp -nk2,2 \ | ||
| + | |gzip >lib1-3.pair.gz | ||
| + | </code> | ||
archive/bioinformatic_tools/abyss.txt · Last modified: 2015/07/28 06:23 by ceisenhart
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