Error running SWSCEN output

[Miles Zhang]

Hi I am running SWSCEN for my UCE data, and the first time I did using internal trimming everything worked fine, but when I am running the cfg file SWSCEN gave me for the edge trimmed data on CIPRES I am getting the following errors:

everything up to this point looked regular like this: 

INFO     | 2018-10-06 04:05:03,997 |       Finished subset 3263/28730, 11.36 percent done

INFO     | 2018-10-06 04:05:04,276 |       Finished subset 3264/28730, 11.36 percent done

INFO     | 2018-10-06 04:05:05,209 |       Finished subset 3265/28730, 11.36 percent done

Then error:

Exception in thread Thread-535:

Traceback (most recent call last):

  File "/opt/python/lib/python2.7/threading.py", line 810, in __bootstrap_inner

    self.run()

  File "/share/apps/compute/partitionfinder/partfinder/threadpool.py", line 115, in run

    cmd, args = self.pool.next_task()

  File "/share/apps/compute/partitionfinder/partfinder/threadpool.py", line 81, in next_task

    task = self.tasks[self.curtask]

IndexError: list index out of range

INFO     | 2018-10-06 04:05:05,407 |       Finished subset 3266/28730, 11.37 percent done

Exception in thread Thread-530:

Traceback (most recent call last):

  File "/opt/python/lib/python2.7/threading.py", line 810, in __bootstrap_inner

    self.run()

  File "/share/apps/compute/partitionfinder/partfinder/threadpool.py", line 115, in run

    cmd, args = self.pool.next_task()

  File "/share/apps/compute/partitionfinder/partfinder/threadpool.py", line 81, in next_task

    task = self.tasks[self.curtask]

IndexError: list index out of range

INFO     | 2018-10-06 04:05:05,617 |       Finished subset 3267/28730, 11.37 percent done

Exception in thread Thread-536:

Traceback (most recent call last):

  File "/opt/python/lib/python2.7/threading.py", line 810, in __bootstrap_inner

    self.run()

  File "/share/apps/compute/partitionfinder/partfinder/threadpool.py", line 115, in run

    cmd, args = self.pool.next_task()

  File "/share/apps/compute/partitionfinder/partfinder/threadpool.py", line 81, in next_task

    task = self.tasks[self.curtask]

IndexError: list index out of range

INFO     | 2018-10-06 04:05:06,298 |       Finished subset 3268/28730, 11.37 percent done

Exception in thread Thread-534:

Traceback (most recent call last):

  File "/opt/python/lib/python2.7/threading.py", line 810, in __bootstrap_inner

    self.run()

  File "/share/apps/compute/partitionfinder/partfinder/threadpool.py", line 115, in run

    cmd, args = self.pool.next_task()

  File "/share/apps/compute/partitionfinder/partfinder/threadpool.py", line 81, in next_task

    task = self.tasks[self.curtask]

IndexError: list index out of range

INFO     | 2018-10-06 04:05:07,339 |       Finished subset 3269/28730, 11.38 percent done

Exception in thread Thread-531:

Traceback (most recent call last):

  File "/opt/python/lib/python2.7/threading.py", line 810, in __bootstrap_inner

    self.run()

  File "/share/apps/compute/partitionfinder/partfinder/threadpool.py", line 115, in run

    cmd, args = self.pool.next_task()

  File "/share/apps/compute/partitionfinder/partfinder/threadpool.py", line 81, in next_task

    task = self.tasks[self.curtask]

IndexError: list index out of range

INFO     | 2018-10-06 04:05:07,561 |       Finished subset 3270/28730, 11.38 percent done

Exception in thread Thread-533:

Traceback (most recent call last):

  File "/opt/python/lib/python2.7/threading.py", line 810, in __bootstrap_inner

    self.run()

  File "/share/apps/compute/partitionfinder/partfinder/threadpool.py", line 115, in run

    cmd, args = self.pool.next_task()

  File "/share/apps/compute/partitionfinder/partfinder/threadpool.py", line 81, in next_task

    task = self.tasks[self.curtask]

IndexError: list index out of range

INFO     | 2018-10-06 04:05:07,798 |       Finished subset 3271/28730, 11.39 percent done

Exception in thread Thread-537:

Traceback (most recent call last):

  File "/opt/python/lib/python2.7/threading.py", line 810, in __bootstrap_inner

    self.run()

  File "/share/apps/compute/partitionfinder/partfinder/threadpool.py", line 115, in run

    cmd, args = self.pool.next_task()

  File "/share/apps/compute/partitionfinder/partfinder/threadpool.py", line 81, in next_task

    task = self.tasks[self.curtask]

IndexError: list index out of range

ERROR    | 2018-10-06 04:05:08,863 | A program that Partitionfinder uses failed. Output follows, in case it's helpful for finding the problem

ERROR    | 2018-10-06 04:05:08,864 | raxml.linux: optimizeModel.c:123: setRateModel: Assertion `rate >= 0.0001 && rate <= 1000000.0' failed.

ERROR    | 2018-10-06 04:05:08,864 | Warning, you specified a working directory via "-w" Keep in mind that RAxML only accepts absolute path names, not relative ones! IMPORTANT WARNING: Sequences NylaM01_bibadia and NylaM03_caerula are exactly identical IMPORTANT WARNING: Sequences NylaM02_caerula and NylaM15_pini are exactly identical IMPORTANT WARNING: Sequences NylaM06_caerula and NylaM07_disatra are exactly identical IMPORTANT WARNING: Sequences NylaM104_steinheili_minuta and NylaM86_cf_fulva are exactly identical IMPORTANT WARNING: Sequences NylaM104_steinheili_minuta and NylaM93_steinheili are exactly identical IMPORTANT WARNING: Sequences NylaM104_steinheili_minuta and NylaM103_steinheili are exactly identical IMPORTANT WARNING: Sequences NylaM104_steinheili_minuta and NylaM87_pubens are exactly identical IMPORTANT WARNING: Sequences NylaM104_steinheili_minuta and NylaM89_guatemalensis are exactly identical IMPORTANT WARNING: Sequences NylaM104_steinheili_minuta and NylaM101_steinheili are exactly identical IMPORTANT WARNING: Sequences NylaM104_steinheili_minuta and NylaM88_lucayana are exactly identical IMPORTANT WARNING: Sequences NylaM20_cf_birmana and NylaM46_cf_amia are exactly identical IMPORTANT WARNING: Sequences NylaM27_faisonensis and NylaM34_parvula are exactly identical IMPORTANT WARNING: Sequences NylaM29_natalensis and NylaM95_steinheili are exactly identical IMPORTANT WARNING Found 13 sequences that are exactly identical to other sequences in the alignment. Normally they should be excluded from the analysis. Just in case you might need it, an alignment file with sequence duplicates removed is printed to file ./analysis/phylofiles/aaf195ef8c8bf97fbcfe0917b86f4962.phy.reduced Using BFGS method to optimize GTR rate parameters, to disable this specify "--no-bfgs" This is RAxML version 8.2.3 released by Alexandros Stamatakis on August 12 2015. With greatly appreciated code contributions by: Andre Aberer (HITS) Simon Berger (HITS) Alexey Kozlov (HITS) Kassian Kobert (HITS) David Dao (KIT and HITS) Nick Pattengale (Sandia) Wayne Pfeiffer (SDSC) Akifumi S. Tanabe (NRIFS) Alignment has 399 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 29.71% RAxML Branch length scaler and other model parameter optimization up to an accuracy of 1.000000 log likelihood units Using 1 distinct models/data partitions with individual per partition branch length optimization All free model parameters will be estimated by RAxML GAMMA model of rate heteorgeneity, ML estimate of alpha-parameter GAMMA Model parameters will be estimated up to an accuracy of 1.0000000000 Log Likelihood units Partition: 0 Alignment Patterns: 399 Name: No Name Provided DataType: DNA Substitution Matrix: GTR RAxML was called as follows: /share/apps/compute/partitionfinder/programs/raxml.linux -f B -s ./analysis/phylofiles/aaf195ef8c8bf97fbcfe0917b86f4962.phy -t ./analysis/start_tree/RAxML_result.BLTREE -m GTRGAMMA -n aaf195ef8c8bf97fbcfe0917b86f4962_GTR+G.txt -w /projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-PARTITIONFINDER2_XSEDE-880CA369F7E848E1AD62EE3C8DB639CD/analysis/phylofiles -e 1.0 -O

[Rob Lanfear]

Hi Miles,

This is an issue with RAxML that I do not think is fixed.

It's been discussed at length here:

https://groups.google.com/forum/#!searchin/partitionfinder/rate$20%3E$3D$200.0001$20$26$26$20rate$20%3C$3D$201000000.0%7Csort:date/partitionfinder/F9hQ4ZUNREk/vXX6zCbJAgAJ

Rob

[Miles Zhang]

Hi Rob,

Thank you I will also follow Ethan's advice on the other chat.