archive:bioinformatic_tools:abyss
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archive:bioinformatic_tools:abyss [2010/05/10 22:21] jstjohn |
archive:bioinformatic_tools:abyss [2010/05/10 23:15] jstjohn |
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| [[http://www.open-mpi.org/software/ompi|OpenMPI]] \\ | [[http://www.open-mpi.org/software/ompi|OpenMPI]] \\ | ||
| [[http://code.google.com/p/google-sparsehash/downloads/list|Google sparsehash]] | [[http://code.google.com/p/google-sparsehash/downloads/list|Google sparsehash]] | ||
| + | |||
| + | ===== Slug Assembly ===== | ||
| + | In the directory: | ||
| + | /campus/BME235/assemblies/slug/ABySS-assembly1 | ||
| + | I ran the following command to start the assembly process on this file in parallel MPI mode. note that the binaries for abyss were installed with open-mpi 1.4, but I am using mpirun 1.3. When we re-install open-mpi 1.4 so that it has SGE support, I will re-run this with that if there are problems. Here is the command executed to start the process: | ||
| + | /campus/BME235/assemblies/slug/ABySS-assembly1 | ||
| + | |||
| + | And here are the contents of the script I use to run everything: | ||
| + | |||
| + | #!/bin/bash | ||
| + | # | ||
| + | #$ -cwd | ||
| + | #$ -j y | ||
| + | #$ -S /bin/bash | ||
| + | #$ -V | ||
| + | #$ -l mem_free=15g | ||
| + | # | ||
| + | /opt/openmpi/bin/mpirun -np $NSLOTS abyss-pe -j j=2 np=$NSLOTS n=8 k=25 name=slugAbyss lib='lane1 lane2 lane3 lane5 lane6 lane7 lane8' lane1='/campus/BME235/data/slug/Illumina/illumina_run_1/CeleraReads/s_1_1_all_qseq.fastq /campus/BME235/data/slug/Illumina/illumina_run_1/CeleraReads/s_1_2_all_qseq.fastq' lane2='/campus/BME235/data/slug/Illumina/illumina_run_1/CeleraReads/s_2_1_all_qseq.fastq /campus/BME235/data/slug/Illumina/illumina_run_1/CeleraReads/s_2_2_all_qseq.fastq' lane3='/campus/BME235/data/slug/Illumina/illumina_run_1/CeleraReads/s_3_1_all_qseq.fastq /campus/BME235/data/slug/Illumina/illumina_run_1/CeleraReads/s_3_2_all_qseq.fastq' lane5='/campus/BME235/data/slug/Illumina/illumina_run_1/CeleraReads/s_5_1_all_qseq.fastq /campus/BME235/data/slug/Illumina/illumina_run_1/CeleraReads/s_5_2_all_qseq.fastq' lane6='/campus/BME235/data/slug/Illumina/illumina_run_1/CeleraReads/s_6_1_all_qseq.fastq /campus/BME235/data/slug/Illumina/illumina_run_1/CeleraReads/s_6_2_all_qseq.fastq' lane7='/campus/BME235/data/slug/Illumina/illumina_run_1/CeleraReads/s_7_1_all_qseq.fastq /campus/BME235/data/slug/Illumina/illumina_run_1/CeleraReads/s_7_2_all_qseq.fastq' lane8='/campus/BME235/data/slug/Illumina/illumina_run_1/CeleraReads/s_8_1_all_qseq.fastq /campus/BME235/data/slug/Illumina/illumina_run_1/CeleraReads/s_8_2_all_qseq.fastq' | ||
| + | |||
| + | Unfortunately this command crashes. The error states that the LD_LIBRARY_PATH might need to be set to point to shared MPI libraries. Also it would probably be best to use our version of "mpirun" once we get it compiled with sge support. | ||
| ===== References ===== | ===== References ===== | ||
| <refnotes>notes-separator: none</refnotes> | <refnotes>notes-separator: none</refnotes> | ||
| ~~REFNOTES cite~~ | ~~REFNOTES cite~~ | ||
archive/bioinformatic_tools/abyss.txt · Last modified: 2015/07/28 06:23 by ceisenhart
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