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--- archive:bioinformatic_tools:abyss [2010/05/19 20:55]
jstjohn
+++ archive:bioinformatic_tools:abyss [2015/04/16 10:31]
jaredc [Sources with Binaries and Documentation]
@@ Line 96: / Line 96: @@
 </code>
+=== Yet Another Install (1.2.7) ===
+On 7 Jun 2011, Kevin Karplus tried installing abyss-1.2.7 from /campusdata/BME235/programs/abyss-1.2.7/ using
+<code>
+configure --prefix=/campusdata/BME235 \
+        CPPFLAGS='-I/opt/openmpi/include -I/campusdata/BME235/include' \
+        LDFLAGS=-L/campusdata/BME235/lib  \
+        CC=gcc44 CXX=g++44 \
+        --with-mpi=/opt/openmpi
+</code>
+Before this configure could work, sparsehash-1.10 was installed from /campusdata/BME235/programs/google/sparsehash-1.10/
 ==== Websites ====
 [[http://www.bcgsc.ca/platform/bioinfo/software/abyss|ABySS]] \\
 [[http://www.open-mpi.org|OpenMPI]] \\
-[[http://code.google.com/p/google-sparsehash|Google sparsehash]]
+[[http://code.google.com/p/google-sparsehash|Google sparsehash]] \\
+[[http://www.boost.org/|Boost]]
 ==== Sources with Binaries and Documentation ====
 [[http://www.bcgsc.ca/platform/bioinfo/software/abyss/releases|ABySS]] \\
 [[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]] \\
+[[http://www.boost.org/users/history/version_1_57_0.html|Boost]]
 ===== Slug Assembly =====
@@ Line 238: / Line 251: @@
 <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>
 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====
 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...
@@ Line 285: / Line 298: @@
                 |gzip >lib1-3.pair.gz
 </code>
+This step takes a lot of time. After running for approximately 24 hours it finally finished, and then when I tried to restart the makefile I accidently executed the previous KAligner command and the lib1-3.pair.gz file was written over... For now I am going to let the Ray assembly finish on Kolossus, and then I will re-run this step. Note that since campusrocks-0-6.local is back online I am also re-trying this stage in "Attempt 3" above. Since the run on campusrocks is split up between the 7 lanes rather than one large run, it is possible that it will work even with limited ram. One of the selling points of ABySS is that it is supposed to run on "commodity hardware" so we will see if it lives up to that claim.

Banana Slug Genomics

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