I found your publication on crossbow, and would be interested in learning more about it. I started following the instructions on your getting-started page (http://bowtie-bio.sourceforge.net/crossbow/tutorial.shtml), but failed at step one, running cb-copy-local. The command proposed by cb-copy-interactive, and the resulting error message are copied below (not sure if this is useful - advice on what would be useful are welcome).
Thanks,
Nick
The full command is:
bash /home/user/crossbow-0.1.3/ec2-local/cb-copy-local -n 5 -i examples/mouse17/copy.manifest -o s3n://mouse17test/test -m 2 -t c1.medium -c crossbowcopy105248285365 -M 2000000
Execute this command now? :
--snippet
10/02/16 10:52:38 INFO streaming.StreamJob: map 100% reduce 0%
10/02/16 10:53:56 INFO streaming.StreamJob: map 90% reduce 0%
10/02/16 10:54:23 INFO streaming.StreamJob: map 80% reduce 0%
10/02/16 10:54:48 INFO streaming.StreamJob: map 70% reduce 0%
10/02/16 10:54:57 INFO streaming.StreamJob: map 80% reduce 0%
10/02/16 10:55:00 INFO streaming.StreamJob: map 90% reduce 0%
10/02/16 10:55:03 INFO streaming.StreamJob: map 80% reduce 0%
10/02/16 10:55:06 INFO streaming.StreamJob: map 100% reduce 100%
10/02/16 10:55:06 INFO streaming.StreamJob: To kill this job, run:
10/02/16 10:55:06 INFO streaming.StreamJob: /usr/local/hadoop-0.20.0/bin/../bin/hadoop job -Dmapred.job.tracker=hdfs://domU-12-31-39-01-95-04.compute-1.internal:50002 -kill job_201002161021_0001
10/02/16 10:55:06 INFO streaming.StreamJob: Tracking URL: http://domU-12-31-39-01-95-04.compute-1.internal:50030/jobdetails.jsp?jobid=job_201002161021_0001
10/02/16 10:55:06 ERROR streaming.StreamJob: Job not Successful!
10/02/16 10:55:06 INFO streaming.StreamJob: killJob…
Streaming Job Failed!
Finished at: Tue Feb 16 16:55:06 CET 2010
-snippet
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I found your publication on crossbow, and would be interested in learning more about it. I started following the instructions on your getting-started page (http://bowtie-bio.sourceforge.net/crossbow/tutorial.shtml), but failed at step one, running cb-copy-local. The command proposed by cb-copy-interactive, and the resulting error message are copied below (not sure if this is useful - advice on what would be useful are welcome).
Thanks,
Nick
The full command is:
bash /home/user/crossbow-0.1.3/ec2-local/cb-copy-local -n 5 -i examples/mouse17/copy.manifest -o s3n://mouse17test/test -m 2 -t c1.medium -c crossbowcopy105248285365 -M 2000000
Execute this command now? :
--snippet
10/02/16 10:52:38 INFO streaming.StreamJob: map 100% reduce 0%
10/02/16 10:53:56 INFO streaming.StreamJob: map 90% reduce 0%
10/02/16 10:54:23 INFO streaming.StreamJob: map 80% reduce 0%
10/02/16 10:54:48 INFO streaming.StreamJob: map 70% reduce 0%
10/02/16 10:54:57 INFO streaming.StreamJob: map 80% reduce 0%
10/02/16 10:55:00 INFO streaming.StreamJob: map 90% reduce 0%
10/02/16 10:55:03 INFO streaming.StreamJob: map 80% reduce 0%
10/02/16 10:55:06 INFO streaming.StreamJob: map 100% reduce 100%
10/02/16 10:55:06 INFO streaming.StreamJob: To kill this job, run:
10/02/16 10:55:06 INFO streaming.StreamJob: /usr/local/hadoop-0.20.0/bin/../bin/hadoop job -Dmapred.job.tracker=hdfs://domU-12-31-39-01-95-04.compute-1.internal:50002 -kill job_201002161021_0001
10/02/16 10:55:06 INFO streaming.StreamJob: Tracking URL: http://domU-12-31-39-01-95-04.compute-1.internal:50030/jobdetails.jsp?jobid=job_201002161021_0001
10/02/16 10:55:06 ERROR streaming.StreamJob: Job not Successful!
10/02/16 10:55:06 INFO streaming.StreamJob: killJob…
Streaming Job Failed!
Finished at: Tue Feb 16 16:55:06 CET 2010
-snippet
Hi Nick,
We'll need the output from the failed task attempt in order to help you debug this. Can you post that?
If what I just said doesn't make sense to you, I would recommend running Crossbow in local (single-computer) mode.
Hope this helps,
Ben
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