Scalpel Error - INDELS

Question

[agata88]

Hi all,

I am using scalpel for detection of indels. It works fine for small panels, but right now I am running whole exome according to bed file downloaded from UCSC. Here is an error which appeared during analysis (after 3h of running)

Program: scalpel-discovery (micro-assembly variant detection)
Version: 0.5.2 (beta), September 29 2015
Contact: Giuseppe Narzisi <[e-mail]>

***START ANALYSIS***
-- Print parameters to /var/bioshare/P41/Intermediates/Indels/Scalpel/P41/parameters.txt
Loading targets from BED file...Use of uninitialized value $chr in string eq at /home/agata/VariantAnnotationPipeline/Programs/scalpel-0.5.2/SequenceIO.pm line 209, <EXONSLIST> line 398302.
Use of uninitialized value in hash element at /home/agata/VariantAnnotationPipeline/Programs/scalpel-0.5.2/SequenceIO.pm line 224, <EXONSLIST> line 398302.
376315 targets (filtered 21987 overlapping).
Loading genome from FASTA file...93 sequences.
Indexing BAM file...
Assembly Exons
Use of uninitialized value $start in subtraction (-) at /home/agata/VariantAnnotationPipeline/Programs/scalpel-0.5.2/FindVariants.pl line 360.
Use of uninitialized value $end in addition (+) at /home/agata/VariantAnnotationPipeline/Programs/scalpel-0.5.2/FindVariants.pl line 362.
Use of uninitialized value $left in subtraction (-) at /home/agata/VariantAnnotationPipeline/Programs/scalpel-0.5.2/FindVariants.pl line 366.
Use of uninitialized value $l in addition (+) at /home/agata/VariantAnnotationPipeline/Programs/scalpel-0.5.2/FindVariants.pl line 370.
start assembly of 510343 regions.
stepSize: 42529
Use of uninitialized value $chr in concatenation (.) or string at /home/agata/VariantAnnotationPipeline/Programs/scalpel-0.5.2/FindVariants.pl line 481.
Use of uninitialized value $left in concatenation (.) or string at /home/agata/VariantAnnotationPipeline/Programs/scalpel-0.5.2/FindVariants.pl line 481.
Use of uninitialized value $chr in exists at /home/agata/VariantAnnotationPipeline/Programs/scalpel-0.5.2/FindVariants.pl line 484.
Use of uninitialized value $chr in concatenation (.) or string at /home/agata/VariantAnnotationPipeline/Programs/scalpel-0.5.2/FindVariants.pl line 484.
Undefined sequence ()
Command failure: FindVariants (/home/agata/VariantAnnotationPipeline/Programs/scalpel-0.5.2/FindVariants.pl --bam /var/bioshare/P41/Intermediates/BamSamFiles/P41_sorted_bed.bam --bed /home/agata/VariantAnnotationPipeline/InputFiles/BedFiles/UCSC_RefSeq_hg19_3_chr.bed --ref /home/agata/VariantAnnotationPipeline/Reference/hg19.fa --kmer 25 --covthr 5 --lowcov 30 --mincov 5 --covratio 0.01 --outratio 0.05 --radius 100 --window 400 --maxregcov 10000 --step 100 --mapscore 1 --mismatches 3 --pathlimit 1000000 --dir /var/bioshare/P41/Intermediates/Indels/Scalpel/P41 --numprocs 12 --format vcf --coords null)...
child exited with value 25
Discovery: elapsed time: 0 day(s) 3 hour(s) 6 minute(s) 5 second(s)

Could anyone help me to solve this problem? I am running this analysis on 132GB computer.

I would really appriciate for help,

Best

Agata

[Mitch Bekritsky]

Why not email the contact?

[agata88]

Yeap, I'll probably contact the author. But I was wondering if anybody had this problem and know the solution.

Answer 1

[sydaileen]

Hi， Agata， I ran into the same error with you ,have you solved the problem?

Best, Aileen

[agata88]

No, I used varScan (instead of Scalpel) for indeed discovery :)

Best,

Agata

[zouxiaohui19]

Check you bed file. I get the same problem and the cause is my bed file content was split with blank and the bed file required tab seperation. So change the blank with tab and the process work well.