ERROR: stage get_unmapped failed: Command in stage get_unmapped failed with exit status = 1 :

[Jyoti Mridha]

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 :

[Nadia Davidson]

Hi Jyoti,

Sorry for the slow reply. Would you mind posting this issue on JAFFA's github site, https://github.com/Oshlack/JAFFA/issues with some more details (see https://github.com/Oshlack/JAFFA/wiki/FAQandTroubleshooting#other-errors for the info you should provide us) and we'll try to have a look at what's gone wrong.

Kind regards,

Nadia.