Duplicate overlap

[emmanuelconstantino19]

I kept on restarting Falcon but there are always 6 jobs that kept on failing. It didn't seem to show any error but I noticed that there's something similar in the stderr file of the jobs.

.. raw_reads.22.raw_reads.3.C0: Duplicate overlap (868 vs 102) raw_reads.22.raw_reads.3.C1: 5 all OK ..

touch /home/ebconstantino/Desktop/FALCON-integrate/FALCON-examples/run/synth0/0-rawreads/job_0033/job_0033_done.exit

• touch /home/ebconstantino/Desktop/FALCON-integrate/FALCON-examples/run/synth0/0-rawreads/job_0033/job_0033_done.exit returned: 256

Do you have any idea what seems to be the problem here?

[pb-jchin]

there is a related ( issue https://github.com/thegenemyers/DALIGNER/issues/43 ) that LACheck might fail in some case. You can comment out the LACheck comment to push it through and generate the correct sentinel files and restart the jobs.

[emmanuelconstantino19]

Where do I comment out the LAcheck comment?

[pb-jchin]

check the *.sh files inside the pre-job working dir.

[emmanuelconstantino19]

I tried doing that and it worked. but another error popped up.

2016-07-19 06:52:48,377[INFO] Queued 'task://localhost/cns_check' ... 2016-07-19 06:52:48,377[INFO] Success ('done'). Joining 'task://localhost/cns_check'... 2016-07-19 06:52:48,441[INFO] tick: 16, #updatedTasks: 32, sleep_time=0.100000 2016-07-19 06:52:48,442[INFO] Running task from function task_report_pre_assembly() 2016-07-19 06:52:48,442[INFO] length_cutoff=1891 from '/home/ebconstantino/Desktop/FALCON-integrate/FALCON-examples/run/synth0/0-rawreads/length_cutoff' 2016-07-19 06:52:48,442[INFO] Report inputs: {'i_raw_reads_db_fn': '/home/ebconstantino/Desktop/FALCON-integrate/FALCON-examples/run/synth0/0-rawreads/raw_reads.db', 'i_preads_fofn_fn': '/home/ebconstantino/Desktop/FALCON-integrate/FALCON-examples/run/synth0/1-preads_ovl/input_preads.fofn', 'length_cutoff': 1891, 'genome_length': 5000} [18704]$ DBdump -h /home/ebconstantino/Desktop/FALCON-integrate/FALCON-examples/run/synth0/0-rawreads/raw_reads.db > 2016-07-19 06:52:48,511[CRITICAL] Any exception caught in RefreshTargets() indicates an unrecoverable error. Shutting down... /home/ebconstantino/Desktop/FALCON-integrate/pypeFLOW/pypeflow/controller.py:537: UserWarning: "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!" "! Please wait for all threads / processes to terminate !" "! Also, maybe use 'ps' or 'qstat' to check all threads,!" "! processes and/or jobs are terminated cleanly. !" "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!"

it's hard to know which job caused the error.

[emmanuelconstantino19]

File "/home/ebconstantino/Desktop/FALCON-integrate/FALCON/falcon_kit/stats_preassembly.py", line 191, in calc_dict stats_preads = stats_from_sorted_readlengths(preads) File "/home/ebconstantino/Desktop/FALCON-integrate/FALCON/falcon_kit/stats_preassembly.py", line 101, in stats_from_sorted_readlengths p95 = percentile(read_lens, 0.95) File "/home/ebconstantino/Desktop/FALCON-integrate/FALCON/falcon_kit/stats_preassembly.py", line 95, in percentile return read_lens[int(len(read_lens)*p)] IndexError: list index out of range

It seems that the error occurred in this part of the code. I tried printing the read_lens:

[100, 100, 100, 100, 100, 100, 243, 251, 258, 263, 264, 302, 359, 395, 407, 408, 424, 426, 436, 438, 451, 460, 473, 475, 475, 485, 492, 493, 506, 534, 535, 545, 547, 548, 565, 571, 574, 587, 587, 593, 595, 598, 601, 605, 605, 617, 620, 623, 628, 632, 634, 646, 650, 655, 655, 667, 668..............

[1891, 1891, 1891, 1891, 1891, 1891, 1891, 1891, 1891, 1892, 1892, 1892, 1892, 1892, 1892, 1892, 1892, 1892, 1892, 1893, 1893, 1893, 1893, 1893, 1893, 1894, 1894, 1894, 1894, 1894, 1894, 1894, 1894, 1895, 1895, 1895, 1895, 1895, 1896, 1896,.....................

[ ]

At the 3rd part. read_lens had no value. What could have caused this??

[pb-cdunn]

'length_cutoff': 1891, 'genome_length': 5000

You might need to clean the work-directory before running a different example.