I'm running Scalpel but getting almost immediate failure/exit from the program and I'm not sure why. Red flags are "undefined sequence" and "command failure" I'm quite new to Linux commands so I can't really tell if it's my input files or an installation problem . Here's the detailed output, can anyone assist?
I'm running Scalpel but getting almost immediate failure/exit from the program and I'm not sure why. Red flags are "undefined sequence" and "command failure" I'm quite new to Linux commands so I can't really tell if it's my input files or an installation problem . Here's the detailed output, can anyone assist?
INPUT:
$ perl /mnt/d/scalpel-0.5.4/scalpel-discovery --single --bam /mnt/d/scalpel-0.5.4/MC-files/MC-fish.marked_duplicates.bam --bed 15:1-48040578 --ref /mnt/d/scalpel-0.5.4/MC-files/danRer11.fa --window 600 --numprocs 4
OUTPUT:
Program: scalpel-discovery (micro-assembly variant detection)
Version: 0.5.4 (beta), January 11 2018
Contact: Giuseppe Narzisi gnarzisi@nygenome.org
START ANALYSIS
-- Print parameters to /mnt/d/scalpel-0.5.4/outdir/parameters.txt
Loading targets region: 15:1-48040578
Loading genome from FASTA file...1923 sequences.
Assembly Exons
start assembly of 480402 regions.
stepSize: 120101
Undefined sequence (15)
Command failure: FindVariants (/mnt/d/scalpel-0.5.4/FindVariants.pl --bam /mnt/d/scalpel-0.5.4/MC-files/MC-fish.marked_duplicates.bam --bed 15:1-48040578 --ref /mnt/d/scalpel-0.5.4/MC-files/danRer11.fa --kmer 25 --covthr 5 --lowcov 2 --mincov 5 --covratio 0.01 --outratio 0.05 --radius 100 --window 600 --maxregcov 10000 --step 100 --mapscore 1 --mismatches 3 --pathlimit 1000000 --dir /mnt/d/scalpel-0.5.4/outdir --numprocs 4 --format vcf --seed 0 --coords null)...
child exited with value 25
Discovery: elapsed time: 0 day(s) 0 hour(s) 0 minute(s) 16 second(s)