When i run Scalpel on sample data, I get the following error. I am using a bed file of the format chromosome_number:start-end
Loading targets from BED file...Use of uninitialized value $chr in string eq at /u/home/v/vsarwal/codes/Scalpel/scalpel-0.5.3/SequenceIO.pm line 209, <EXONSLIST> line 2.
Use of uninitialized value in hash element at /u/home/v/vsarwal/codes/Scalpel/scalpel-0.5.3/SequenceIO.pm line 224, <EXONSLIST> line 2.
Use of uninitialized value in string eq at /u/home/v/vsarwal/codes/Scalpel/scalpel-0.5.3/SequenceIO.pm line 209, <EXONSLIST> line 3.
Use of uninitialized value $chr in string eq at /u/home/v/vsarwal/codes/Scalpel/scalpel-0.5.3/SequenceIO.pm line 209, <EXONSLIST> line 3.
Use of uninitialized value in numeric le (<=) at /u/home/v/vsarwal/codes/Scalpel/scalpel-0.5.3/SequenceIO.pm line 209, <EXONSLIST> line 3.
Use of uninitialized value $start in numeric le (<=) at /u/home/v/vsarwal/codes/Scalpel/scalpel-0.5.3/SequenceIO.pm line 209, <EXONSLIST> line 3.
2 targets (filtered 1 overlapping).
Loading genome from FASTA file...1 sequences.
Assembly Exons
Use of uninitialized value $start in subtraction (-) at /u/home/v/vsarwal/codes/Scalpel/scalpel-0.5.3/FindVariants.pl line 363.
Use of uninitialized value $end in addition (+) at /u/home/v/vsarwal/codes/Scalpel/scalpel-0.5.3/FindVariants.pl line 365.
Use of uninitialized value $left in subtraction (-) at /u/home/v/vsarwal/codes/Scalpel/scalpel-0.5.3/FindVariants.pl line 369.
Use of uninitialized value $l in addition (+) at /u/home/v/vsarwal/codes/Scalpel/scalpel-0.5.3/FindVariants.pl line 373.
Use of uninitialized value $start in subtraction (-) at /u/home/v/vsarwal/codes/Scalpel/scalpel-0.5.3/FindVariants.pl line 363.
Use of uninitialized value $end in addition (+) at /u/home/v/vsarwal/codes/Scalpel/scalpel-0.5.3/FindVariants.pl line 365.
Use of uninitialized value $left in subtraction (-) at /u/home/v/vsarwal/codes/Scalpel/scalpel-0.5.3/FindVariants.pl line 369.
Use of uninitialized value $l in addition (+) at /u/home/v/vsarwal/codes/Scalpel/scalpel-0.5.3/FindVariants.pl line 373.
start assembly of 2 regions.
stepSize: 2
Use of uninitialized value $chr in concatenation (.) or string at /u/home/v/vsarwal/codes/Scalpel/scalpel-0.5.3/FindVariants.pl line 484.
Use of uninitialized value $left in concatenation (.) or string at /u/home/v/vsarwal/codes/Scalpel/scalpel-0.5.3/FindVariants.pl line 484.
Use of uninitialized value $chr in exists at /u/home/v/vsarwal/codes/Scalpel/scalpel-0.5.3/FindVariants.pl line 487.
Use of uninitialized value $chr in concatenation (.) or string at /u/home/v/vsarwal/codes/Scalpel/scalpel-0.5.3/FindVariants.pl line 487.
Undefined sequence ()
Command failure: FindVariants (/u/home/v/vsarwal/codes/Scalpel/scalpel-0.5.3/FindVariants.pl --bam /u/home/v/vsarwal/example/alignments.bam --bed regions.bed --ref /u/home/v/vsarwal/example/reference.fa --kmer 25 --covthr 5 --lowcov 2 --mincov 5 --covratio 0.01 --outratio 0.05 --radius 100 --window 400 --maxregcov 10000 --step 100 --mapscore 1 --mismatches 3 --pathlimit 1000000 --dir /u/home/v/vsarwal/codes/Scalpel/scalpel-0.5.3/outdir --numprocs 1 --format vcf --coords null)...
child exited with value 25
Discovery: elapsed time: 0 day(s) 0 hour(s) 0 minute(s) 0 second(s)
Can someone tell me what's wrong
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When i run Scalpel on sample data, I get the following error. I am using a bed file of the format chromosome_number:start-end
Loading targets from BED file...Use of uninitialized value $chr in string eq at /u/home/v/vsarwal/codes/Scalpel/scalpel-0.5.3/SequenceIO.pm line 209, <EXONSLIST> line 2.
Use of uninitialized value in hash element at /u/home/v/vsarwal/codes/Scalpel/scalpel-0.5.3/SequenceIO.pm line 224, <EXONSLIST> line 2.
Use of uninitialized value in string eq at /u/home/v/vsarwal/codes/Scalpel/scalpel-0.5.3/SequenceIO.pm line 209, <EXONSLIST> line 3.
Use of uninitialized value $chr in string eq at /u/home/v/vsarwal/codes/Scalpel/scalpel-0.5.3/SequenceIO.pm line 209, <EXONSLIST> line 3.
Use of uninitialized value in numeric le (<=) at /u/home/v/vsarwal/codes/Scalpel/scalpel-0.5.3/SequenceIO.pm line 209, <EXONSLIST> line 3.
Use of uninitialized value $start in numeric le (<=) at /u/home/v/vsarwal/codes/Scalpel/scalpel-0.5.3/SequenceIO.pm line 209, <EXONSLIST> line 3.
2 targets (filtered 1 overlapping).
Loading genome from FASTA file...1 sequences.
Assembly Exons
Use of uninitialized value $start in subtraction (-) at /u/home/v/vsarwal/codes/Scalpel/scalpel-0.5.3/FindVariants.pl line 363.
Use of uninitialized value $end in addition (+) at /u/home/v/vsarwal/codes/Scalpel/scalpel-0.5.3/FindVariants.pl line 365.
Use of uninitialized value $left in subtraction (-) at /u/home/v/vsarwal/codes/Scalpel/scalpel-0.5.3/FindVariants.pl line 369.
Use of uninitialized value $l in addition (+) at /u/home/v/vsarwal/codes/Scalpel/scalpel-0.5.3/FindVariants.pl line 373.
Use of uninitialized value $start in subtraction (-) at /u/home/v/vsarwal/codes/Scalpel/scalpel-0.5.3/FindVariants.pl line 363.
Use of uninitialized value $end in addition (+) at /u/home/v/vsarwal/codes/Scalpel/scalpel-0.5.3/FindVariants.pl line 365.
Use of uninitialized value $left in subtraction (-) at /u/home/v/vsarwal/codes/Scalpel/scalpel-0.5.3/FindVariants.pl line 369.
Use of uninitialized value $l in addition (+) at /u/home/v/vsarwal/codes/Scalpel/scalpel-0.5.3/FindVariants.pl line 373.
start assembly of 2 regions.
stepSize: 2
Use of uninitialized value $chr in concatenation (.) or string at /u/home/v/vsarwal/codes/Scalpel/scalpel-0.5.3/FindVariants.pl line 484.
Use of uninitialized value $left in concatenation (.) or string at /u/home/v/vsarwal/codes/Scalpel/scalpel-0.5.3/FindVariants.pl line 484.
Use of uninitialized value $chr in exists at /u/home/v/vsarwal/codes/Scalpel/scalpel-0.5.3/FindVariants.pl line 487.
Use of uninitialized value $chr in concatenation (.) or string at /u/home/v/vsarwal/codes/Scalpel/scalpel-0.5.3/FindVariants.pl line 487.
Undefined sequence ()
Command failure: FindVariants (/u/home/v/vsarwal/codes/Scalpel/scalpel-0.5.3/FindVariants.pl --bam /u/home/v/vsarwal/example/alignments.bam --bed regions.bed --ref /u/home/v/vsarwal/example/reference.fa --kmer 25 --covthr 5 --lowcov 2 --mincov 5 --covratio 0.01 --outratio 0.05 --radius 100 --window 400 --maxregcov 10000 --step 100 --mapscore 1 --mismatches 3 --pathlimit 1000000 --dir /u/home/v/vsarwal/codes/Scalpel/scalpel-0.5.3/outdir --numprocs 1 --format vcf --coords null)...
child exited with value 25
Discovery: elapsed time: 0 day(s) 0 hour(s) 0 minute(s) 0 second(s)
Can someone tell me what's wrong