Hi,
Need help please, i encountered with the following error while working with JAFFA.
ERROR: stage get_unmapped failed: Command in stage get_unmapped failed with exit status = 1 :
/mnt/data-drive2/Jyoti/Program/JAFFA-version-2.3/tools/bin/bowtie2 -k1 -p 16 --un trimmed/unmapped.fastq -x /mnt/data-drive2/Jyoti/Program/JAFFA-version-2.3/hg19_genCode19 -U trimmed/trimmed_leftover_reads.fastq.1.gz,trimmed/trimmed_leftover_reads.fastq.2.gz | /usr/local/bin/samtools view -s 1.0 -F 4 -S -b - | /usr/local/bin/samtools sort - trimmed/trimmed_discordant_pairs ; /usr/local/bin/samtools index trimmed/trimmed_discordant_pairs.bam ;
========================================= Pipeline Failed ==========================================
In stage Unknown: One or more parallel stages aborted. The following messages were reported:
------------------------------------ get_unmapped ( trimmed ) ------------------------------------
Command in stage get_unmapped failed with exit status = 1 :