Question: Deconseq: Malloc error (error code 3)
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gravatar for lobosea
9 months ago by
lobosea0
lobosea0 wrote:

Dear colleagues,

I try to use Deconseq to filter assembly (Fasta file containing contigs after Sparse assembler) from bacterial contamination and get the following message:


Amoeba-2:deconseq asmirnov$ perl deconseq.pl -f PK_new.fasta -dbs 'bactDB' -i 90 -c 90 -out_dir output
[bsw2_aln] read 46 sequences (10130812 bp)...

bwaMAC(24691,0xa2ec5000) malloc: *** mach_vm_map(size=8388608) failed (error code=3)

*** error: can't allocate region

*** set a breakpoint in malloc_error_break to debug

ERROR: system call "/users/asmirnov/deconseq/bwaMAC bwasw -A -f output/1546564095_bactDB_bactDB_s1.tsv /users/asmirnov/deconseq/bactDB_s1 PK_new.fasta" failed: 11.

Try 'deconseq -h' for more information.

Exit program.

DeconSeq.config.pm is following ( I used example from https://vcru.wisc.edu/simonlab/bioinformatics/programs/install/deconseq.htm):


package DeconSeqConfig;

use strict;

use constant DEBUG => 0;
use constant PRINT_STUFF => 1;
use constant VERSION => '0.4.3';
use constant VERSION_INFO => 'DeconSeq version '.VERSION;

use constant ALPHABET => 'ACGTN';

use constant DB_DIR => '/users/asmirnov/deconseq/';
use constant TMP_DIR => '/users/asmirnov/deconseq/tmp/';
use constant OUTPUT_DIR => '/users/asmirnov/deconseq/output/';

use constant PROG_NAME => 'bwaMAC';  # should be either bwa64 or bwaMAC (based on your system architecture)
use constant PROG_DIR => '/users/asmirnov/deconseq/';      # should be the location of the PROG_NAME file (use './' if in the same location at the perl script)

use constant DBS => { hsref => { name => 'Human - Craig Venter (HuRef)',
                                 db =>   'hs_alt_HuRef_s1,hs_alt_HuRef_s2,hs_alt_HuRef_s3' },
                      arch =>  { name => 'Archaeal genomes [155 unique genomes, 02/12/11]',
                                 db =>   'archDB_s1' },
                      bactDB => { name => 'Bacterial genomes [2,206 unique genomes, 02/12/11]',
                                 db =>   'bactDB_s1,bactDB_s2,bactDB_s3' },
                      vir =>   { name => 'Viral genomes in RefSeq 45 [3,761 unique sequences, 02/12/11]',
                                 db =>   'virDB_s1' },                     
              };
use constant DB_DEFAULT => 'bactDB';

#######################################################################

use base qw(Exporter);

use vars qw(@EXPORT);

@EXPORT = qw(
             DEBUG
             PRINT_STUFF
             VERSION
             VERSION_INFO
             ALPHABET
             PROG_NAME
             PROG_DIR
             DB_DIR
             TMP_DIR
             OUTPUT_DIR
             DBS
             DB_DEFAULT
             );

1;

I use terminal and MacOS 10.11.6 (ElCapitan).
Deconseq scripts and databases are located at /users/asmirnov/deconseq
rw permissions to scripts and bwaMAC are granted; /deconseq is in PATH

May I ask a trivial question: what I am doing wrong. Thank you!

Alexey Smirnov, Faculty of Biology, Saint Petersburg State University

deconseq software error • 261 views
ADD COMMENTlink modified 9 months ago by RamRS24k • written 9 months ago by lobosea0
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