I'm trying to run the scalpel-discovery --somatic analysis, however the process does not seem to complete. I submit the following shell to our server with %qsub -l h_vmem=40g shell.sh
Program: scalpel-discovery (micro-assembly variant detection)
Version: 0.5.3 (beta), January 25 2016
Contact: Giuseppe Narzisi gnarzisi@nygenome.org
MAIN ANALYSIS
-- Print parameters to /home/dcameron/outdir/main/parameters.txt
-- Detect mutations on normal
-- Print parameters to /home/dcameron/outdir/main/normal/parameters.txt
Indexing BAM file...
Loading targets from BED file...389758 targets (filtered 25027 overlapping).
Loading genome from FASTA file...66 sequences.
Assembly Exons
start assembly of 544399 regions.
stepSize: 54440
While the job completes, there is no database file created. Only 10 very large fasta files in the outdir/main/normal directory, one example being "regions-0-54440.fa", and assorted log files.
I'd appreciate any advice you could give. Also, I wanted to check if the software worked using the examples in the Fang, 2016 paper. However, the ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR194/ERR194151 folder no longer exists.
Thanks,
Don
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Hi,
I'm trying to run the scalpel-discovery --somatic analysis, however the process does not seem to complete. I submit the following shell to our server with %qsub -l h_vmem=40g shell.sh
~/Programs/scalpel-0.5.3/scalpel-discovery --somatic --normal ~/Projects/Scalpel/scalpel_01vehicle_sort_markdup.bam --tumor ~/Projects/Scalpel/scalpel_11combo_sort_markdup.bam --bed ~/Projects/Scalpel/mm10_codingexons.bed --ref ~/Projects/Scalpel/mm10.fa --numprocs 10 --two-pass
The output is as follows:
Local date and time: Mon Dec 18 10:27:59 2017
Program: scalpel-discovery (micro-assembly variant detection)
Version: 0.5.3 (beta), January 25 2016
Contact: Giuseppe Narzisi gnarzisi@nygenome.org
MAIN ANALYSIS
-- Print parameters to /home/dcameron/outdir/main/parameters.txt
-- Detect mutations on normal
-- Print parameters to /home/dcameron/outdir/main/normal/parameters.txt
Indexing BAM file...
Loading targets from BED file...389758 targets (filtered 25027 overlapping).
Loading genome from FASTA file...66 sequences.
Assembly Exons
start assembly of 544399 regions.
stepSize: 54440
** 0 started, pid: 7832
** 54440 started, pid: 7833
** 108880 started, pid: 7834
** 163320 started, pid: 7837
** 217760 started, pid: 7841
** 272200 started, pid: 7843
** 326640 started, pid: 7846
** 381080 started, pid: 7848
** 435520 started, pid: 7850
** 489960 started, pid: 7852
While the job completes, there is no database file created. Only 10 very large fasta files in the outdir/main/normal directory, one example being "regions-0-54440.fa", and assorted log files.
I'd appreciate any advice you could give. Also, I wanted to check if the software worked using the examples in the Fang, 2016 paper. However, the ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR194/ERR194151 folder no longer exists.
Thanks,
Don