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CarineRey / pcoc

Convergent substitution detection tool based on the PCOC model
GNU General Public License v3.0
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Ask help for the Error report #19

Open shujiangping opened 4 years ago

shujiangping commented 4 years ago

hello Carine,

I got a Error report when I performed the command below:

CMD_PCOC_DOCKER pcoc_num_tree.py -t Case.nw -o Case.pdf cam="17/31/43,33,34,35,36,37,38,39,40,41,42/54,50,51,52,53/92,84,85,86,87,88,89,90,91/103/136" CMD_PCOC_DOCKER pcoc_num_tree.py -t Case.nw -o Case.pdf -m $cam

these 3 commands were OK, but the next meet the error:

CMD_PCOC_DOCKER pcoc_det.py -t Case.nw -aa Case_mafft.fa -o Case_detc -m $cam -f 0.8

Working directory : /home/jiangping.shu User / docker Starting with UID : 1001 2020-06-05 09:35:43,663 - INFO - alignment: Case_mafft.fa 2020-06-05 09:35:43,783 - INFO - Alphabet usage: A(5.42%), C(0.84%), E(6.08%), D(4.76%), G(4.38%), F(2.88%), I(3.86%), -(24.49%), K(4.02%), M(2.04%), L(8.79%), N(2.03%), Q(3.22%), P(3.78%), S (4.52%), R(5.60%), T(4.06%), H(1.72%), V(4.28%), Y(2.15%), W(1.08%) 2020-06-05 09:35:43,783 - INFO - alignment ok after checking 2020-06-05 09:35:43,783 - INFO - tree: Case.nw 2020-06-05 09:35:43,791 - INFO - tree ok after checking 2020-06-05 09:35:43,792 - INFO - Sequence and leaf names match. 2020-06-05 09:35:44,017 - ERROR - Case_detc/RUN_20200605_093543/Estimations/Case_mafft.fa_1_1_noOneChange.infos does not exist 2020-06-05 09:35:44,017 - ERROR - command: bppml param=Case_detc/RUN_20200605_093543/bpp_config/CATseq_estim.bpp NAME=Case_mafft.fa SUFF IX=_noOneChange REP_SEQ=. TREE=Case_detc/RUN_20200605_093543/Trees/tree.nhx REP_EST=Case_detc/RUN_20200605_093543/Estimations 'input.sequence.file=./Case_mafft.fa' NBCAT=10 model1='LGL08_CAT_C1(nbCat=$(NBCAT))' model1.nodes_id='0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,18,19,20,21,22,23,24,25,26,27,28,29,30,32,44,45,46,47,48,49,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,93,94,95,96,97,98,99,100,101,102,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211' model2='LGL08_CAT_C1(nbCat=$(NBCAT))' model2.nodes_id='17,31,43,54,92,103,136,33,34,35,36,37,38,39,40,41,42,50,51,52,53,84,85,86,87,88,89,90,91' rate_distribution='Constant()' MAX_GAP_ALLOWED=5 Ne1=1 Ne2=1 nonhomogeneous.number_of_models=2 out:

Parsing options: Parsing file Case_detc/RUN_20200605_093543/bpp_config/CATseq_estim.bpp for options. Alphabet type .........................: Proteic Sequence file .........................: ./Case_mafft.fa Sequence format .......................: FASTA file Sites to use...........................: all Remove sites with gaps.................: [======================================] 100%Done. Number of sequences....................: 107 Number of sites........................: 739 Input tree.............................: user Input tree file .......................: Case_detc/RUN_20200605_093543/Trees/tree.nhx Input tree format .....................: Nhx Number of leaves.......................: 107 Output tree file ......................: Case_detc/RUN_20200605_093543/Estimations/Case_mafft.fa_noOneChange.dnd Output tree format ....................: Newick Branch lengths.........................: Input Heterogeneous model....................: general Number of distinct models..............: 2 Root frequencies ......................: FromModel Stationarity assumed...................: no Substitution model.....................: LGL08_CAT Substitution model.....................: LGL08_CAT_C1 Frequencies Initialization for model...: None Model1 is associated to................: 183 node(s). Substitution model.....................: LGL08_CAT Substitution model.....................: LGL08_CAT_C1 Frequencies Initialization for model...: None Model2 is associated to................: 29 node(s). Distribution...........................: Constant Number of classes......................: 1

all of my operations are based on your Readme.md, so I don't know what's happened. I am looking forward to your help!

Yours Sincerely

Jiangping

ozguldogan commented 3 years ago

I have also the same problem. Can anybody help me please?

I am looking forward to your help!

Sincerely, Ozgul

1221li commented 2 years ago

I have also the same problem!Have you solved this problem? Can you help me out