Question: Problem with Abyss 2.0
0
gravatar for Pierre
16 months ago by
Pierre0
France
Pierre0 wrote:

Hi everyone,

I try to do a draft genome assembly (the input data are OK and worked fine to do an assembly with Platanus assembler)

Now, I want to test Abyss 2.0 assembler.

The command line was :

nohup abyss-pe k=64 np=64 name=abyss-mullus lib='pea peb' mp='mpc mpd' pea='paired/paired350_R1.fastq paired/paired350_R2.fastq' peb='paired2/paired550_R1.fastq paired2/paired550_R2.fastq' mpc='mate-pair/mp3kb_R1.fastq mate-pair/mp3kb_R2.fastq' mpd='mate-pair2/mp5kb_R1.fastq mate-pair2/mp5kb_R2.fastq' q=15 c=3 N=6 k=64 v=-v 2> abyss2_test.log &

My computer have ~500G RAM and 64 cores. The input data are 30-50G for paired end reads files and 1-5G for mate-pair reads files

I try 2 times to launch and get the following :

warning: -c,--coverage was specified, but -e,--erode was not specified Previously, the default was -e2 (or --erode=2). make: *** [abyss-mullus-1.fa] Erreur 137

/usr/local/bin/abyss-pe:334 : la recette pour la cible « error » a échouée /usr/bin/mpirun -np 64 ABYSS-P -k64 -q15 -c3 -v  
--coverage-hist=coverage.hist -s abyss-mullus-bubbles.fa  -o abyss-mullus-1.fa paired/paired350_R1.fastq paired/paired350_R2.fastq paired2/paired550_R1.fastq paired2/paired550_R2.fastq  ABySS 2.0.2 ABYSS-P -k64 -q15 -c3 -v --coverage-hist=coverage.hist -s abyss-mullus-bubbles.fa -o abyss-mullus-1.fa paired/paired350_R1.fastq paired/paired350_R2.fastq paired2/paired550_R1.fastq paired2/paired550_R2.fastq Running on 64 processors 19: Running on host lxcbigmem3 21: Running on host lxcbigmem3 23: Running on host lxcbigmem3 25: Running on host lxcbigmem3 ... 34: Running on host lxcbigmem3 36: Running on host lxcbigmem3 0: Reading `paired/paired350_R1.fastq'... 2: Reading `paired2/paired550_R1.fastq'... 1: Reading `paired/paired350_R2.fastq'... 3: Reading `paired2/paired550_R2.fastq'... 2: Read 100000 reads. 2: Hash load: 474335 / 4294967296 = 0.00011 using 1.54 GB 3: Read 100000 reads. 3: Hash load: 480132 / 4294967296 = 0.000112 using 1.54 GB 1: Read 100000 reads. 1: Hash load: 488910 / 4294967296 = 0.000114 using 1.54 GB 0: Read 100000 reads. 0: Hash load: 520430 / 4294967296 = 0.000121 using
1.54 GB 2: Read 200000 reads. 2: Hash load: 907661 / 4294967296 = 0.000211 using 1.56 GB 3: Read 200000 reads. 3: Hash load: 944496 / 4294967296 = 0.00022 using 1.56 GB 1: Read 200000 reads. 1: Hash load: 953017 / 4294967296 = 0.000222 using 1.56 GB 0: Read 200000 reads. 0: Hash load: 1037204 / 4294967296 = 0.000241 using 1.56 GB 2: Read 300000 reads. 2: Hash load: 1319412 / 4294967296 = 0.000307 using 1.58 GB 1: Read 300000 reads. 1: Hash load: 1348134 / 4294967296 = 0.000314 using 1.58 G: ... something like several hundreds lines of this type ... 1: Read 106200000 reads. 1: Hash load: 144524647 / 4294967296 =
0.0336 using 8.4 GB 2: Read 112400000 reads. 2: Hash load: 146281960 / 4294967296 = 0.0341 using 8.48 GB 3: Read 124900000 reads. 3: Hash load: 144829638 / 4294967296 = 0.0337 using 8.43 GB 2: Read 112500000 reads. 2: Hash load: 146391174 / 4294967296 = 0.0341 using 8.49 GB 1: Read 106300000 reads. 1: Hash load: 144640498 / 4294967296 = 0.0337 using 8.41 GB 0: Read 114700000 reads. 0: Hash load: 147404170 / 4294967296 = 0.0343 using 8.54 GB 1: Read 106400000 reads. 1: Hash load: 144719128 / 4294967296 = 0.0337 using 8.41 GB 3: Read 125000000 reads. 3: Hash load: 144948742 / 4294967296 = 0.0337 using 8.44 GB
-------------------------------------------------------------------------- mpirun noticed that process rank 36 with PID 41106 on node lxcbigmem3 exited on signal 9 (Killed).
-------------------------------------------------------------------------- /usr/local/bin/abyss-pe:501 : la recette pour la cible « abyss-mullus-1.fa » a échouée

I translate : target recipe « abyss-mullus-1.fa » failed

I have to mention that i installed the 4 required libraries as recommended in the gitub.

sudo ./configure --with-boost=/usr/local/include/boost --with-mpi=/usr/lib/openmpi --with-sparsehash=/usr/include/sparsehash --with-sqlite=/usr/bin/sqlite3
make AM_CXXFLAGS=-Wall
sudo make install AM_CXXFLAGS=-Wall

It seems to be a problem of memory but i'am not enough expert to manage the problem. Can anyone help me please ?

By the way I don't understand the interest and how to use (properly) the bloom filter in abyss 2.0. If anyone can explain me ?

Thanks you in advance !

abyss assembly • 728 views
ADD COMMENTlink written 16 months ago by Pierre0
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