yzhernand / vntrseek Goto Github PK

$ ls
bam_14_sorted_griznog.bam  bam_14_sorted_griznog.bam.bai

$ vntrseek 0 19 --dbsuffix ${DB_SUFFIX}
Could not read global config


Executing step #0 (creating MySQL database)...
Warning: Failed to create data directory!

Warning: Failed to create html directory!

Warning: Failed to create output directory!
done!


Executing step #1 (searching for tandem repeats in reads, producing profiles and sorting)...
2 supported files (bam format, assuming uncompressed) found in /tmp/7244420/fasta
Will use 4 processes
Processing bam chunk using: samtools view -F 256 -F 2048 -f 64 /tmp/7244420/fasta/bam_14_sorted_griznog.bam chrM:1-16571
Processing bam chunk using: samtools view -F 256 -F 2048 -f 128 /tmp/7244420/fasta/bam_14_sorted_griznog.bam chrM:1-16571
Processing bam chunk using: samtools view -F 256 -F 2048 -f 64 /tmp/7244420/fasta/bam_14_sorted_griznog.bam chr1:1-249250621
Processing bam chunk using: samtools view -F 256 -F 2048 -f 128 /tmp/7244420/fasta/bam_14_sorted_griznog.bam chr1:1-249250621
Running child, current_file = 1 (HASH(0x1e2e940))...
Running child, current_file = 0 (HASH(0x1e2ea18))...
Running child, current_file = 2 (HASH(0x1e2ebc8))...
Running child, current_file = 3 (HASH(0x1e0fc48))...
Processing bam chunk using: samtools view -F 256 -F 2048 -f 64 /tmp/7244420/fasta/bam_14_sorted_griznog.bam chr2:1-243199373
Running child, current_file = 4 (HASH(0x1e2ea90))...
Processing bam chunk using: samtools view -F 256 -F 2048 -f 128 /tmp/7244420/fasta/bam_14_sorted_griznog.bam chr2:1-243199373
Running child, current_file = 5 (HASH(0x1ffd378))...

--- vntrseek-scg.pl	2019-02-23 10:09:42.652371611 -0800
+++ vntrseek.pl	2019-02-23 12:01:06.717409634 -0800
@@ -667,8 +667,13 @@
 
     write_mysql( $DBNAME, $opts{TMPDIR} );
 
+    my ($db_host, $db_port) = split(/:/, $opts{HOST});
+    if ($db_port ne "") {
+        $db_port = "--port $db_port";
+    }
+
     my $exstring
-        = "mysql -u $opts{LOGIN} --password=$opts{PASS} -h $opts{HOST} < $opts{TMPDIR}/${DBNAME}.sql";
+        = "mysql -u $opts{LOGIN} --password=$opts{PASS} -h ${db_host} ${db_port} < $opts{TMPDIR}/${DBNAME}.sql";
     system($exstring);
 
     $exstring = "rm -f $opts{TMPDIR}/${DBNAME}.sql";
@@ -1099,8 +1104,13 @@
         }
     }
 
+    my ($db_host, $db_port) = split(/:/, $opts{HOST});
+    if ($db_port ne "") {
+        $db_port = "--port $db_port";
+    }
+
     $exstring
-        = "mysql -u $opts{LOGIN} --password=$opts{PASS} -h $opts{HOST} --local-infile=1 $DBNAME < $opts{TMPDIR}/${DBNAME}_2.sql";
+        = "mysql -u $opts{LOGIN} --password=$opts{PASS} -h $db_host $db_port --local-infile=1 $DBNAME < $opts{TMPDIR}/${DBNAME}_2.sql";
     system($exstring);
     if ( $? == -1 ) {
         SetError( $STEP, "command failed: $!", -1 );

29284921 profiles read, 8437576 profiles marked nonredundant. (time: 8097 seconds)

setting additional statistics...
Creating reference sequence database...
DBD::SQLite::db do failed: near "(": syntax error at /scg/apps/software/vntrseek/1.10.0-rc.3/vntrseek1.10.0-rc.3/lib/vutil.pm line 706.
command exited with value 2 at /scg/apps/software/vntrseek/1.10.0-rc.3/bin/vntrseek line 585.
Done vntrseek

$ cat 7258930.vs.cnf
# Database backend
BACKEND=sqlite

# set this to the number of processors on your system 
# (or less if sharing the system with others or RAM is limited)
# eg, 8
NPROCESSES=128

# minimum required flank on both sides for a read TR to be considered
# eg, 10
MIN_FLANK_REQUIRED=10

# maximum flank length used in flank alignments
# set to big number to use all
# if read flanks are long with a lot of errors, 
# it might be useful to set this to something like 50
# max number of errors per flank is currently set to 8 (can be changed in main script only)
# eg, 1000
MAX_FLANK_CONSIDERED=50

# minimum number of mapped reads which agree on copy number to call an allele
# eg, 2
MIN_SUPPORT_REQUIRED=2

# Whether or not to keep reads detected as PCR duplicates. A nonzero (true) value
# means that detected PCR duplicates will not be removed. Default is 0.
KEEPPCRDUPS=1

# server name, used for html generating links
# eg, orca.bu.edu
SERVER=localhost

# for 454 platform, strip leading 'TCAG' 
# eg, 1 - yes
# eg, 0 - no (use no for all other platforms)
STRIP_454_KEYTAGS=0

# data is paired reads
# eg, 0 = no 
# eg, 1 - yes
IS_PAIRED_READS=1

# Sample ploidy. Default is 2. For haploid, set to 1.
PLOIDY=2

# Rebuild reference database
# eg, 0 = no 
# eg, 1 - yes
REDO_REFDB=0

# input data directory 
# (plain or gzipped fasta/fastq files)
# eg, /input
INPUT_DIR=/tmp/7258930/fasta

# output directory (must be writable and executable!)
# eg, /output
OUTPUT_ROOT=/home/username/output/7258930

# temp (scratch) directory (must be executable!)
# eg, /tmp
TMPDIR=/tmp/7258930

# names for the reference files 

# (leb36 file, sequence plus flank data file, indistinguishable references file) 
# files must be in install directory

# eg, hg19. This is the base name for files describing
# reference TR loci (.db, .seq, .leb36, and .indist)
REFERENCE=/tmp/7258930/reference/t26__

# generate a file of indistinguishable references, 
# necessary only if a file is not already available for the reference set
# eg, 1- generate
# eg, 0 - don't generate
REFERENCE_INDIST_PRODUCE=0