Defuse Calculating spanning p-values Failure

zslee · 11-28-2013, 10:59 PM

Hey, could anyone help me with one problem:
when I run defuse to find gene fusions based on fastq data (illumina HISEQ, paired-end, trimed by trimglore), the software goes well until Calculating spanning p-values:

Importing fastq files
Splitting fastq files
Discordant alignments
Read Stats
Fragment mean 182.171678030117 stddev 43.6861609169054
Read length min 20 max 100
Generating discordant alignment clusters
Remove mitochondrial-genomic clusters
Generating maximum parsimony solution
Selecting fusion clusters
Preparing sequences for local realignment
Performing local realignment
Filtering concordant clusters
Generating spanning alignment regions file
Initializing split read alignments
Calculating split read alignments
Evaluating split reads
Calculating spanning stats
Calculating spanning p-values
Failure for defuse command:
/home/local/bin/Rscript ./defuse-0.6.1//scripts/evaluate_fraglength_mean.R ./temp/defuse/concordant.read.stats ./temp/defuse/spanlength.cov 50 ./temp/defuse/splitreads.span.stats ./temp/defuse/splitreads.span.pval.tmp
Reason:
Job command with nonzero return code
Job output:
Running on node4
Rscript execution error: No such file or directory

real 0m0.099s
user 0m0.000s
sys 0m0.003s
Return codes: 255
Commands failed after 1 seconds

when I check I found there is no ./temp/defuse/splitreads.span.pval.tmp produced, what is the reason?
thanks in advance for anyone's reply.

code as bellow:
~/programs/defuse-0.6.1/scripts/defuse.pl -c ~/programs/defuse-0.6.1/scripts/config.txt -1 $inputdir/$file1 -2 $inputdir/$file2 -o $outputdir -p 24

NKAkers · 01-31-2014, 03:30 PM

/home/local/bin/Rscript ./defuse-0.6.1//scripts/evaluate_fraglength_mean.R

This is your problem, I believe. The double forward slash betweeen defuse-0.6.1 and scripts.

Check your config.txt file to make sure you named your directories without a slash at the end. ie:

/home/usr/defuse-0.6.1
NOT:
/home/usr/defuse-0.6.1/

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11-28-2013, 10:59 PM	#1
zslee Member Location: shanghai of china Join Date: May 2009 Posts: 29	Defuse Calculating spanning p-values Failure Hey, could anyone help me with one problem: when I run defuse to find gene fusions based on fastq data (illumina HISEQ, paired-end, trimed by trimglore), the software goes well until Calculating spanning p-values: Importing fastq files Splitting fastq files Discordant alignments Read Stats Fragment mean 182.171678030117 stddev 43.6861609169054 Read length min 20 max 100 Generating discordant alignment clusters Remove mitochondrial-genomic clusters Generating maximum parsimony solution Selecting fusion clusters Preparing sequences for local realignment Performing local realignment Filtering concordant clusters Generating spanning alignment regions file Initializing split read alignments Calculating split read alignments Evaluating split reads Calculating spanning stats Calculating spanning p-values Failure for defuse command: /home/local/bin/Rscript ./defuse-0.6.1//scripts/evaluate_fraglength_mean.R ./temp/defuse/concordant.read.stats ./temp/defuse/spanlength.cov 50 ./temp/defuse/splitreads.span.stats ./temp/defuse/splitreads.span.pval.tmp Reason: Job command with nonzero return code Job output: Running on node4 Rscript execution error: No such file or directory real 0m0.099s user 0m0.000s sys 0m0.003s Return codes: 255 Commands failed after 1 seconds when I check I found there is no ./temp/defuse/splitreads.span.pval.tmp produced, what is the reason? thanks in advance for anyone's reply. code as bellow: ~/programs/defuse-0.6.1/scripts/defuse.pl -c ~/programs/defuse-0.6.1/scripts/config.txt -1 $inputdir/$file1 -2 $inputdir/$file2 -o $outputdir -p 24

01-31-2014, 03:30 PM	#2
NKAkers Member Location: New York, NY Join Date: Sep 2011 Posts: 26	/home/local/bin/Rscript ./defuse-0.6.1//scripts/evaluate_fraglength_mean.R This is your problem, I believe. The double forward slash betweeen defuse-0.6.1 and scripts. Check your config.txt file to make sure you named your directories without a slash at the end. ie: /home/usr/defuse-0.6.1 NOT: /home/usr/defuse-0.6.1/