the preads jobs only posted a part of task inside the 0-rawreads folder

[lilinzhou]

hello when I run the preads $PATH/FALCON/0-rawreads/preads/c_*.sh, Log file shows one of the following tasks can deliver success this folder, the rest delivery failure. why?

[pb-cdunn]

It's hard to debug all problems remotely, but if you post more information, we can try.

• cd FALCON; git rev-parse HEAD
• Content of preads/c_*.sub.sh for the failing job.
• Content of preads/c_*.sh.log for the failing job.
• Content of your fc_run.cfg

[lilinzhou]

there is a new problem about the nearly empty folder 1-preads_ovl and 2-asm-falcon so that the asembly complete in a second when preads produced. here is the folder 1-preads_ovl

0 Apr 13 23:34 da_done
1.3K Apr 13 23:15 input_preads.fofn
 488 Apr 14 09:30 job_c8cfc468/
  30 Apr 13 23:36 las_files/
453 Apr 13 23:36 m_00001/
  0 Apr 13 23:15 pdb_build_done
 0 Apr 14 09:30 pdb_build_done.exit
   0 Apr 13 23:36 p_merge_done
  22 Apr 13 23:36 preads.1.las -> ./m_00001/preads.1.las
47M Apr 13 23:38 preads4falcon.fasta
500 Apr 13 23:15 preads.db
  94 Apr 14 09:30 preads.fofn
 2.1K Apr 14 09:30 prepare_pdb.sh
 719 Apr 13 23:15 run_jobs.sh

and here is the log file, other log file like pypeflow.log, fc_run.log seems have nothing wrong.

2016-04-14 01:30:22,874 - pypeflow.controller - INFO - message for task://localhost/falcon: 'started, runflag: 0'
2016-04-14 01:30:22,875 - pypeflow.controller - WARNING - Got unexpected message 'task://localhost/falcon' from URL 'started, runflag: 0'.
2016-04-14 01:30:22,875 - pypeflow.controller - INFO - message for task://localhost/falcon: 'done'
2016-04-14 01:30:22,875 - pypeflow.controller - INFO - Success ('done'). Joining 'task://localhost/falcon'...
2016-04-14 01:30:22,878 - pypeflow.controller - INFO - #jobsReadyToBeSubmitted: 0
2016-04-14 01:30:22,878 - pypeflow.controller - INFO - _refreshTargets() finished with no thread running and no new job to submit
 No target specified, assuming "assembly" as target

I don't understand why is this happening.

[pb-jchin]

what is the content of 2-falcon_asm?

[lilinzhou]

hi jason, the 2-falcon_asm nearly empty, too.

 0 Apr 13 23:39 a_ctg_all.fa
0 Apr 13 23:39 a_ctg_base.fa
0 Apr 13 23:39 a_ctg_base_tiling_path
 0 Apr 13 23:39 a_ctg.fa
0 Apr 13 23:39 a_ctg_tiling_path
0 Apr 13 23:39 c_path
0 Apr 13 23:39 ctg_paths
 0 Apr 13 23:39 falcon_asm_done
0 Apr 13 23:38 fc_ovlp_to_graph.log
97 Apr 13 23:38 las.fofn
0 Apr 13 23:39 p_ctg.fa
 0 Apr 13 23:39 p_ctg_tiling_path
 93 Apr 13 23:38 preads4falcon.fasta -> WORKDIR/1-preads_ovl/preads4falcon.fasta
0 Apr 13 23:38 preads.ovl
 2.5K Apr 13 23:36 run_falcon_asm.sh
 0 Apr 13 23:39 sg_edges_list
  0 Apr 13 23:39 utg_data

[lilinzhou]

But the preads have already produced successfuly

[pb-jchin]

you might have two processes running at the same time and the confuse the results. Make sure you don't have any process and delete the 2-* direct and re-run it. The size of p-reads seems too small even for bacteria, so it could be that there is no meaningful overlap found for assembly too.

[lilinzhou]

If the second one happened, what can I do ?

[pb-jchin]

You will have to examine the assembly project a little bit more detail to figure where enough coverage data is generated for the organism of interest.