Error in Stage extract_fusion_sequences

[zacharop...@gmail.com]

Hi all,

I seem to have a problem in the Stage extract_fusion_sequences.

I get this message:

============================ Stage extract_fusion_sequences (Sample2) ============================
java -ea -Xmx200m -cp /home/hassan/panagiota/JAFFA/tools/bbmap/current/ jgi.ReformatReads in=Sample2.fastq/Sample2.fastq.fasta out=stdout.fasta fastawrap=0
Executing jgi.ReformatReads [in=Sample2.fastq/Sample2.fastq.fasta, out=stdout.fasta, fastawrap=0]
Input is being processed as unpaired
Input: 62 reads 57437 bases
Output: 62 reads (100.00%) 57437 bases (100.00%)
Time: 0.466 seconds.
Reads Processed: 62 0.13k reads/sec
Bases Processed: 57437 0.12m bases/sec
ERROR: Command failed with exit status = 1 :

cat Sample2.fastq/Sample2.fastq.txt | awk '{print $1}' | sed 's/^/>/g' > Sample2.fastq/Sample2.fastq.fusions.fa.temp ; /home/hassan/panagiota/JAFFA/tools/bin/reformat in=Sample2.fastq/Sample2.fastq.fasta out=stdout.fasta fastawrap=0 | awk '{print $1}' | grep -F -A1 -f Sample2.fastq/Sample2.fastq.fusions.fa.temp | grep -v "^\-\-" > Sample2.fastq/2Illumina.fastq.fusions.fa ; rm Sample2.fastq/Sample2.fastq.fusions.fa.temp ;

I have run the command piece by piece but still I can't get any results and my Sample2.fastq.fusions.fa file is empty. Do you think that this is because it can't find any fusions or is it another problem?

Thanks!

Peny