ValueError: 'd223af7fbf34f5a5111bb1542d8b925c' is not in list

[stsmall]

Hi @simonhmartin, Thank you for a great program! I have run twisst many times without an error, but now seem to be receiving error messages on a few trees. Initially I used BioNJ trees with the same individual sample labels and had no issues. These BioNJ trees did not have bootstrap values. I have switched over to using max likelihood trees generated with RAxML and FastTree. FastTree produces aLRT support values, could this be causing the below errors? thanks, scott

Traceback (most recent call last): File "/afs/crc.nd.edu/user/s/ssmall2/anaconda2/lib/python2.7/multiprocessing/process.py", line 267, in _bootstrap self.run() File "/afs/crc.nd.edu/user/s/ssmall2/anaconda2/lib/python2.7/multiprocessing/process.py", line 114, in run self._target(*self._args, self._kwargs) File "/afs/crc.nd.edu/user/s/ssmall2/programs_that_work/twisst/run_twisst_parallel.py", line 44, in weightTree_wrapper weightsData = twisst.weightTreeSimp(tree=tree, taxa=taxa, taxonNames=taxonNames, topos=topos, getDists=getDists, abortCutoff=args.abortCutoff) File "/afs/crc.nd.edu/user/s/ssmall2/programs_that_work/twisst/twisst.py", line 383, in weightTreeSimp x = topoIDs.index(prunedID) ValueError: 'dd1ccb7098f363bc0cab5e347c4987a7' is not in list 2234 trees queued | 2182 results received | 1664 results written. 4368 trees queued | 4317 results received | 1664 results written. Process Process-4: Traceback (most recent call last): File "/afs/crc.nd.edu/user/s/ssmall2/anaconda2/lib/python2.7/multiprocessing/process.py", line 267, in _bootstrap self.run() File "/afs/crc.nd.edu/user/s/ssmall2/anaconda2/lib/python2.7/multiprocessing/process.py", line 114, in run self._target(*self._args, *self._kwargs) File "/afs/crc.nd.edu/user/s/ssmall2/programs_that_work/twisst/run_twisst_parallel.py", line 44, in weightTree_wrapper weightsData = twisst.weightTreeSimp(tree=tree, taxa=taxa, taxonNames=taxonNames, topos=topos, getDists=getDists, abortCutoff=args.abortCutoff) File "/afs/crc.nd.edu/user/s/ssmall2/programs_that_work/twisst/twisst.py", line 383, in weightTreeSimp x = topoIDs.index(prunedID) ValueError: '5b339154d31bc114b9db4f34f955306e' is not in list 6528 trees queued | 6476 results received | 1664 results written. Process Process-1: Traceback (most recent call last): File "/afs/crc.nd.edu/user/s/ssmall2/anaconda2/lib/python2.7/multiprocessing/process.py", line 267, in _bootstrap self.run() File "/afs/crc.nd.edu/user/s/ssmall2/anaconda2/lib/python2.7/multiprocessing/process.py", line 114, in run self._target(self._args, self._kwargs) File "/afs/crc.nd.edu/user/s/ssmall2/programs_that_work/twisst/run_twisst_parallel.py", line 44, in weightTree_wrapper weightsData = twisst.weightTreeSimp(tree=tree, taxa=taxa, taxonNames=taxonNames, topos=topos, getDists=getDists, abortCutoff=args.abortCutoff) File "/afs/crc.nd.edu/user/s/ssmall2/programs_that_work/twisst/twisst.py", line 383, in weightTreeSimp x = topoIDs.index(prunedID) ValueError: 'd223af7fbf34f5a5111bb1542d8b925c' is not in list

[stsmall]

UPDATE: I removed the aLRT values by rerunning a test using FastTree with the option of -nosupport. However, I am still getting the error at 3 very specific trees. Here is 1 of the trees causing the error:

((funestus_Ugf401:0.00055,((funestuscf_MALAF105_7:0.0,funestuscf_MALAF99_4:0.0,funestuscf_MALF98_2:0.0):0.00055,((funestus_GhaF265:0.0,funestus_MozF29:0.0,funestus_Ugf399:0.0,longipalpusC_11:0.0,longipalpusC_13:0.0,longipalpusC_16:0.0,longipalpusC_4:0.0,longipalpusC_551_12634:0.0,parensis_KwaF761:0.0,parensis_KwaF768:0.0,parensis_KwaF769:0.0,parensis_KwaF851:0.0,vaneedeni_KwaF774:0.0,vaneedeni_KwaF783:0.0):0.00055,(longipalpusC_15:0.00055,vaneedeni_KwaF784:0.00055):0.00055):0.00055):0.00054):0.00054,(funestus_Zam281:0.00055,funestus_TanF601:0.00055):0.00055,((((((parensis_KwaF762:0.0,parensis_KwaF766:0.0,vaneedeni_KwaF780:0.0,vaneedeni_KwaF782:0.0):0.00055,(longipalpusC_551_12533:0.01646,rivulorum_F790:0.25145):0.01065):0.00425,funestus_Ken4590:0.00055):0.00055,funestus_TanF561:0.00055):0.00055,funestus_Ugf403:0.00055):0.00055,(((funestus_MozF260:0.00086,vaneedeni_KwaF773:0.00055):0.00055,((longipalpusC_12:0.0,parensis_KwaF767:0.0,parensis_KwaF835:0.0):0.00055,(vaneedeni_KwaF775:0.00055,vaneedeni_KwaF786:0.06689):0.00055):0.00054):0.00063,(funestus_GhaF264:0.00055,(funestus_MozF123:0.0,funestus_MozF35:0.0,funestus_MozF804:0.0):0.00055):0.00051):0.00100):0.00055);

[simonhmartin]

Dear Scott, Apologies - I missed this email from you. I will look into this issue and try to figure out what's gone wrong. Best wishes, Simon

On Thu, Jan 18, 2018 at 12:27 AM, Scott T Small notifications@github.com wrote:

UPDATE: I removed the aLRT values by rerunning a test using FastTree with the option of -nosupport. However, I am still getting the error at 3 very specific trees. Here is 1 of the trees causing the error:

(((((longipalpusC_15:0.00055,(longipalpusC_4:0.00055,( longipalpusC_11:0.00055,((parensis_KwaF769:0.00055, parensis_KwaF851:0.00055):0.00055,(longipalpusC_551_12533: 0.00055,(parensis_KwaF766:0.00115,(parensis_KwaF762:0. 00055,((parensis_KwaF767:0.0,parensis_KwaF835:0.0):0.00055, (parensis_KwaF761:0.00055,parensis_KwaF768:0.00555):0. 00055):0.00153):0.00189):0.00059):0.00059):0.00055):0. 00055):0.00055):0.00055,longipalpusC_13:0.00055):0. 00055,longipalpusC_16:0.00055):0.00055,(longipalpusC551 12634:0.00208,longipalpusC_12:0.00055):0.00054):0.00142, vaneedeni_KwaF783:0.00055,(vaneedeni_KwaF773:0.00055,( vaneedeni_KwaF775:0.00055,(vaneedeni_KwaF780:0.00055,(( vaneedeni_KwaF782:0.00055,vaneedeni_KwaF786:0.00569):0. 00055,(vaneedeni_KwaF774:0.00055,(((funestuscf_MALF98_2: 0.00055,(funestuscf_MALAF105_7:0.00055,funestuscfMALAF99 4:0.00055):0.00055):0.01010,(funestus_Ken4590:0.00053,( rivulorum_F790:0.26756,(((funestus_Ugf401:0.00055,( funestus_GhaF264:0.00055,funestus_GhaF265:0.00055):0. 00055):0.00055,funestus_Ugf399:0.00055):0.00055,(funestus_Ugf403:0.00108,( funestus_TanF561:0.00055,(funestus_TanF601:0.00055,(( funestus_MozF260:0.0,funestus_MozF29:0.0):0.00055,(( funestus_MozF123:0.0,funestus_MozF35:0.0,funestus_Zam281:0. 0):0.00054,funestus_MozF804:0.00055):0.00053):0.00415):0. 00096):0.00058):0.00104):0.00123):0.00053):0.00287):0. 01492,vaneedeni_KwaF784:0.00053):0.00054):0.00087):0. 00055):0.00055):0.00055):0.00055);

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