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