ERROR: Command failed with exit status = 1, not solved when switch to version 1.08

54 views

Skip to first unread message

guo.j...@dhs.sg

unread,

May 10, 2018, 12:32:28 PM5/10/18

to jaffa-project

Hi there

I was trying to set up JAFFA and running it on the provided demo data.

1. The command I used is
./bpipe run /home/ubuntu/jaffa/JAFFA-version-1.08/JAFFA_assembly.groovy /home/ubuntu/jaffa/BT474-demo_*.fastq.gz /home/ubuntu/jaffa/MCF7-demo_*.fastq.gz
as provided by the website

2. The error I am getting is
=============================== Stage filter_transcripts (MCF7-demo) ===============================
ERROR: Command failed with exit status = 1 :

time /usr/bin/R --vanilla --args BT474-demo/BT474-demo.psl BT474-demo/BT474-demo.txt 1000 /home/ubuntu/jaffa/JAFFA-version-1.08/hg19_genCode19.tab < /home/ubuntu/jaffa/JAFFA-version-1.08/process_transcriptome_blat_table.R &> BT474-demo/log_filter

ERROR: Command failed with exit status = 1 :

time /usr/bin/R --vanilla --args MCF7-demo/MCF7-demo.psl MCF7-demo/MCF7-demo.txt 1000 /home/ubuntu/jaffa/JAFFA-version-1.08/hg19_genCode19.tab < /home/ubuntu/jaffa/JAFFA-version-1.08/process_transcriptome_blat_table.R &> MCF7-demo/log_filter

========================================= Pipeline Failed ==========================================

One or more parallel stages aborted. The following messages were reported:

Branch BT474-demo in stage Unknown reported message:

Command failed with exit status = 1 :

Branch MCF7-demo in stage Unknown reported message:

Command failed with exit status = 1 :

Use 'bpipe errors' to see output from failed commands.

3. I have seen in previous questions whereby the problem was solved by using an older version of JAFFA, but mine still show the same error even with different versions of JAFFA. I am using R version 3.4.4 and IRanges version 2.12.0

Looking forward to any advice on how to solve this issue.

Thanks!
Allyson

Reply all

Reply to author

Forward

0 new messages