deFuse / Discussion / deFuse Help: success and failure for defuse command

I'm trying to run deFuse on an SGE cluster with the following code:
sge ./defuse.pl -c /defuse/scripts/config.txt -1 sample1.R1.fastq -2 sample1.R2.fastq -o /defuse_out/sample1 -s sge -p 8

deFuse splits in multiple nodes, and some appear to run fine, while others throw an error. I would expect that if something is wrong, nothing would run at all, instead of some that do and others that don't.

Below an example of a successful command:
tarting 1 defuse command(s) on cnpew17
Starting defuse command:
/cm/shared/apps/defuse/current/scripts/index_paired_fastq.pl #<1 #<2 #>1 #>2 #>3 #>4
Reasons:
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/reads.1.fastq missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/reads.2.fastq missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/reads.fqi missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/reads.names missing
Success for defuse command:
/cm/shared/apps/defuse/current/scripts/index_paired_fastq.pl /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/GC011094.R1.fastq /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/GC011094.R2.fastq /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/reads.1.fastq.tmp /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/reads.2.fastq.tmp /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/reads.fqi.tmp /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/reads.names.tmp
Return codes: 0
Job output:
Running on cnpew17.uz.kuleuven.ac.be
Imported 49830874 reads
Finished Import

real    12m49.462s
user    5m48.029s
sys 1m8.944s

Completed in 776 seconds
Starting 1 defuse command(s) on cnpew17
Starting defuse command:
/cm/shared/apps/defuse/current/scripts/split_fastq.pl /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/reads 1000000 /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads > #>1
Reasons:
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/reads.split.catalog missing
Success for defuse command:
/cm/shared/apps/defuse/current/scripts/split_fastq.pl /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/reads 1000000 /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads > /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/reads.split.catalog.tmp
Return codes: 0
Job output:
Running on cnpew17.uz.kuleuven.ac.be

real    32m21.770s
user    19m15.722s
sys 0m56.304s

Completed in 1947 seconds
Starting 50 defuse command(s) on cnpew17
Starting defuse command:
/cm/shared/apps/defuse/current/scripts/alignjob.pl -c /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse/scripts/config3.txt -j reads.split.049 -l /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/tmp -o /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094 -n GC011094 -p /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.049
Reasons:
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.049.concordant.read.stats missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.049.spanlength.samples missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.049.splitpos.samples missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.049.splitmin.samples missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.049.expression.txt missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.049.cdna.pair.sam missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.049.improper.sam missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.049.spanning.filelist missing
Starting defuse command:
/cm/shared/apps/defuse/current/scripts/alignjob.pl -c /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse/scripts/config3.txt -j reads.split.048 -l /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/tmp -o /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094 -n GC011094 -p /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.048
Reasons:
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.048.concordant.read.stats missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.048.spanlength.samples missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.048.splitpos.samples missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.048.splitmin.samples missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.048.expression.txt missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.048.cdna.pair.sam missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.048.improper.sam missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.048.spanning.filelist missing
Starting defuse command:
/cm/shared/apps/defuse/current/scripts/alignjob.pl -c /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse/scripts/config3.txt -j reads.split.047 -l /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/tmp -o /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094 -n GC011094 -p /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.047
Reasons:
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.047.concordant.read.stats missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.047.spanlength.samples missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.047.splitpos.samples missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.047.splitmin.samples missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.047.expression.txt missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.047.cdna.pair.sam missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.047.improper.sam missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.047.spanning.filelist missing
Starting defuse command:
/cm/shared/apps/defuse/current/scripts/alignjob.pl -c /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse/scripts/config3.txt -j reads.split.046 -l /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/tmp -o /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094 -n GC011094 -p /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.046
Reasons:
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.046.concordant.read.stats missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.046.spanlength.samples missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.046.splitpos.samples missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.046.splitmin.samples missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.046.expression.txt missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.046.cdna.pair.sam missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.046.improper.sam missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.046.spanning.filelist missing
Starting defuse command:
/cm/shared/apps/defuse/current/scripts/alignjob.pl -c /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse/scripts/config3.txt -j reads.split.045 -l /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/tmp -o /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094 -n GC011094 -p /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.045
Reasons:
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.045.concordant.read.stats missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.045.spanlength.samples missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.045.splitpos.samples missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.045.splitmin.samples missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.045.expression.txt missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.045.cdna.pair.sam missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.045.improper.sam missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.045.spanning.filelist missing
Starting defuse command:
/cm/shared/apps/defuse/current/scripts/alignjob.pl -c /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse/scripts/config3.txt -j reads.split.044 -l /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/tmp -o /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094 -n GC011094 -p /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.044
Reasons:
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.044.concordant.read.stats missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.044.spanlength.samples missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.044.splitpos.samples missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.044.splitmin.samples missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.044.expression.txt missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.044.cdna.pair.sam missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.044.improper.sam missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.044.spanning.filelist missing
Starting defuse command:
/cm/shared/apps/defuse/current/scripts/alignjob.pl -c /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse/scripts/config3.txt -j reads.split.043 -l /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/tmp -o /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094 -n GC011094 -p /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.043
Reasons:
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.043.concordant.read.stats missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.043.spanlength.samples missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.043.splitpos.samples missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.043.splitmin.samples missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.043.expression.txt missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.043.cdna.pair.sam missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.043.improper.sam missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.043.spanning.filelist missing
Starting defuse command:
/cm/shared/apps/defuse/current/scripts/alignjob.pl -c /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse/scripts/config3.txt -j reads.split.042 -l /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/tmp -o /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094 -n GC011094 -p /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.042
Reasons:
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.042.concordant.read.stats missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.042.spanlength.samples missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.042.splitpos.samples missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.042.splitmin.samples missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.042.expression.txt missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.042.cdna.pair.sam missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.042.improper.sam missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.042.spanning.filelist missing
Success for defuse command:
/cm/shared/apps/defuse/current/scripts/alignjob.pl -c /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse/scripts/config3.txt -j reads.split.049 -l /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/tmp -o /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094 -n GC011094 -p /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.049
Return codes: 0
Job output:
Running on cnpew17.uz.kuleuven.ac.be
Starting alignjob reads.split.049
Finding concordant alignments to cdna
Finding concordant alignments to dna
Calculating read statistics
Calculating covariance samples
Calculating expression
Trimming and filtering reads
Finding all cdna alignments
Finding all dna alignments
Finding same gene concordant read ids for cdna
Finding same region concordant read ids for dna
Finding alignments to rRNA
Finding rrna anchored concordant read ids
Finding concordant alignments to prefilter fasta /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse/Hs.seq.uniq
Excluding IG rearrangements
Coallating concordant read ids
Creating list of improper reads
Dividing sam output files
Finished Alignments
Cleaning Up

real    103m15.988s
user    97m46.969s
sys 2m31.687s

And from a failed command:
Failure for defuse command:
/cm/shared/apps/defuse/current/scripts/alignjob.pl -c /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse/scripts/config3.txt -j reads.split.012 -l /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/tmp -o /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094 -n GC011094 -p /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.012
Reason:
Job command with nonzero return code
Finding concordant alignments to dna
Job output:
Running on cnpew02.uz.kuleuven.ac.be
Starting alignjob reads.split.012
Finding concordant alignments to cdna
Starting defuse command:
/cm/shared/apps/defuse/current/scripts/alignjob.pl -c /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse/scripts/config3.txt -j reads.split.000 -l /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/tmp -o /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094 -n GC011094 -p /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.000
Reasons:
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.000.concordant.read.stats missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.000.spanlength.samples missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.000.splitpos.samples missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.000.splitmin.samples missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.000.expression.txt missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.000.cdna.pair.sam missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.000.improper.sam missing
/uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.000.spanning.filelist missing
Failure for defuse command:
/cm/shared/apps/defuse/current/scripts/alignjob.pl -c /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse/scripts/config3.txt -j reads.split.000 -l /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/tmp -o /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094 -n GC011094 -p /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.000
Reason:
Failure for defuse command:
/cm/shared/apps/defuse/current/scripts/alignjob.pl -c /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse/scripts/config3.txt -j reads.split.002 -l /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/tmp -o /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094 -n GC011094 -p /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.002
Reason:
Job command with nonzero return code
Return codes: 25
Job output:
Running on cnpew06.uz.kuleuven.ac.be
Starting alignjob reads.split.002
Finding concordant alignments to cdna
Failure for alignjob.reads.split.002 command:
/cm/shared/apps/bowtie/current/bowtie --phred33-quals --sam-nohead -S -t -X 500 /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse/defuse.cdna.fa -1 /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.002.1.fastq -2 /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.002.2.fastq /uz/data/avalok/symbiosys/gcpi_r_uz_peter_vandenberghe/lspans0/defuse_out/GC011094/jobs/reads.split.002.cdna.pair.sam.tmp
Reason:
Job command with nonzero return code

I've also tried in default status, without assigning a certain number to the -p parameter, but this also fails.
Any suggestions?
Thanks!

success and failure for defuse command

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success and failure for defuse command