archive:bioinformatic_tools:abyss
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archive:bioinformatic_tools:abyss [2010/05/19 20:55] jstjohn |
archive:bioinformatic_tools:abyss [2010/05/20 20:48] jstjohn |
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| <code> | <code> | ||
| - | /campus/BME235/programs/abyss_tmp/bin/abyss-pe mpirun="/opt/openmpi/bin/mpirun -machinefile machines -x PATH=/campus/BME235/bin/programs/abyss_tmp/bin:$PATH" np=23 n=8 k=28 name=slugAbyss lib='lane1 lane2 lane3 lane5 lane6 lane7 lane8' lane1='/campus/BME235/data/slug/Illumina/illumina_run_1/CeleraReads/s_1_1_all_qseq.fastq /campus/BME235/data/slug/Illumina/illumina_run_1/CeleraReads/s_1_2_all_qseq.fastq' lane2='/campus/BME235/data/slug/Illumina/illumina_run_1/CeleraReads/s_2_1_all_qseq.fastq /campus/BME235/data/slug/Illumina/illumina_run_1/CeleraReads/s_2_2_all_qseq.fastq' lane3='/campus/BME235/data/slug/Illumina/illumina_run_1/CeleraReads/s_3_1_all_qseq.fastq /campus/BME235/data/slug/Illumina/illumina_run_1/CeleraReads/s_3_2_all_qseq.fastq' lane5='/campus/BME235/data/slug/Illumina/illumina_run_1/CeleraReads/s_5_1_all_qseq.fastq /campus/BME235/data/slug/Illumina/illumina_run_1/CeleraReads/s_5_2_all_qseq.fastq' lane6='/campus/BME235/data/slug/Illumina/illumina_run_1/CeleraReads/s_6_1_all_qseq.fastq /campus/BME235/data/slug/Illumina/illumina_run_1/CeleraReads/s_6_2_all_qseq.fastq' lane7='/campus/BME235/data/slug/Illumina/illumina_run_1/CeleraReads/s_7_1_all_qseq.fastq /campus/BME235/data/slug/Illumina/illumina_run_1/CeleraReads/s_7_2_all_qseq.fastq' lane8='/campus/BME235/data/slug/Illumina/illumina_run_1/CeleraReads/s_8_1_all_qseq.fastq /campus/BME235/data/slug/Illumina/illumina_run_1/CeleraReads/s_8_2_all_qseq.fastq' | + | /campus/BME235/programs/abyss_tmp/bin/abyss-pe mpirun="/opt/openmpi/bin/mpirun -machinefile machines -x PATH=/campus/BME235/bin/programs/abyss_tmp/bin:$PATH" np=60 n=8 k=28 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' |
| </code> | </code> | ||
| 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... | + | Campusrocks-0-6.local is back up so I am re-starting this task. At its peak the KAligner step (where it crashed previously when the -j option was enabled) requires quite a lot of ram. I am hoping that the 30GB available on this node is sufficient. |
| ====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... | ||
archive/bioinformatic_tools/abyss.txt · Last modified: 2015/07/28 06:23 by ceisenhart
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