Issue in Carveme

[Sububioinfo]

I am getting an error please help me to solve the issuse. here is my command and error (carveme) bash-4.2$ carve --refseq GCF_000005845.2 -o ecoli_k12_mg1655.xml diamond v0.9.24.125 | by Benjamin Buchfink buchfink@gmail.com Licensed under the GNU GPL https://www.gnu.org/licenses/gpl.txt Check http://github.com/bbuchfink/diamond for updates.

CPU threads: 80

Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) Temporary directory: Opening the database... [0.270249s] Percentage range of top alignment score to report hits: 10 Opening the input file... [0.132084s] Opening the output file... [100.674s] Loading query sequences... [0.019824s] Masking queries... [0.012677s] Building query seed set... [0.000265s] Algorithm: Double-indexed Building query histograms... [0.010517s] Allocating buffers... [0.003047s] Loading reference sequences... [0.321985s] Building reference histograms... [0.132916s] Allocating buffers... [0.002581s] Initializing temporary storage... [0.928057s] Processing query chunk 0, reference chunk 0, shape 0, index chunk 0. Building reference index... [0.042005s] Building query index... [0.015771s] Building seed filter... [0.005057s] Searching alignments... [0.082735s] Processing query chunk 0, reference chunk 0, shape 0, index chunk 1. Building reference index... [0.0361s] Building query index... [0.014717s] Building seed filter... [0.005101s] Searching alignments... [0.071485s] Processing query chunk 0, reference chunk 0, shape 0, index chunk 2. Building reference index... [0.039922s] Building query index... [0.014736s] Building seed filter... [0.005173s] Searching alignments... [0.07394s] Processing query chunk 0, reference chunk 0, shape 0, index chunk 3. Building reference index... [0.033905s] Building query index... [0.014346s] Building seed filter... [0.00526s] Searching alignments... [0.069182s] Processing query chunk 0, reference chunk 0, shape 1, index chunk 0. Building reference index... [0.035161s] Building query index... [0.014272s] Building seed filter... [0.005068s] Searching alignments... [0.0646s] Processing query chunk 0, reference chunk 0, shape 1, index chunk 1. Building reference index... [0.039211s] Building query index... [0.014987s] Building seed filter... [0.005317s] Searching alignments... [0.082725s] Processing query chunk 0, reference chunk 0, shape 1, index chunk 2. Building reference index... [0.03876s] Building query index... [0.014781s] Building seed filter... [0.004944s] Searching alignments... [0.059073s] Processing query chunk 0, reference chunk 0, shape 1, index chunk 3. Building reference index... [0.04098s] Building query index... [0.014577s] Building seed filter... [0.00511s] Searching alignments... [0.071151s] Processing query chunk 0, reference chunk 0, shape 2, index chunk 0. Building reference index... [0.034155s] Building query index... [0.014648s] Building seed filter... [0.005004s] Searching alignments... [0.070215s] Processing query chunk 0, reference chunk 0, shape 2, index chunk 1. Building reference index... [0.0359s] Building query index... [0.014287s] Building seed filter... [0.005131s] Searching alignments... [0.070191s] Processing query chunk 0, reference chunk 0, shape 2, index chunk 2. Building reference index... [0.039502s] Building query index... [0.01476s] Building seed filter... [0.005274s] Searching alignments... [0.110466s] Processing query chunk 0, reference chunk 0, shape 2, index chunk 3. Building reference index... [0.033038s] Building query index... [0.01488s] Building seed filter... [0.005282s] Searching alignments... [0.062097s] Processing query chunk 0, reference chunk 0, shape 3, index chunk 0. Building reference index... [0.035796s] Building query index... [0.014479s] Building seed filter... [0.005376s] Searching alignments... [0.065265s] Processing query chunk 0, reference chunk 0, shape 3, index chunk 1. Building reference index... [0.038651s] Building query index... [0.014879s] Building seed filter... [0.005232s] Searching alignments... [0.067437s] Processing query chunk 0, reference chunk 0, shape 3, index chunk 2. Building reference index... [0.037244s] Building query index... [0.014401s] Building seed filter... [0.004937s] Searching alignments... [0.063721s] Processing query chunk 0, reference chunk 0, shape 3, index chunk 3. Building reference index... [0.038263s] Building query index... [0.014379s] Building seed filter... [0.005113s] Searching alignments... [0.06293s] Processing query chunk 0, reference chunk 0, shape 4, index chunk 0. Building reference index... [0.034804s] Building query index... [0.014281s] Building seed filter... [0.005151s] Searching alignments... [0.064652s] Processing query chunk 0, reference chunk 0, shape 4, index chunk 1. Building reference index... [0.038495s] Building query index... [0.014977s] Building seed filter... [0.005073s] Searching alignments... [0.06529s] Processing query chunk 0, reference chunk 0, shape 4, index chunk 2. Building reference index... [0.039247s] Building query index... [0.014179s] Building seed filter... [0.004931s] Searching alignments... [0.066621s] Processing query chunk 0, reference chunk 0, shape 4, index chunk 3. Building reference index... [0.034255s] Building query index... [0.014757s] Building seed filter... [0.005195s] Searching alignments... [0.059543s] Processing query chunk 0, reference chunk 0, shape 5, index chunk 0. Building reference index... [0.036618s] Building query index... [0.01509s] Building seed filter... [0.005087s] Searching alignments... [0.065938s] Processing query chunk 0, reference chunk 0, shape 5, index chunk 1. Building reference index... [0.038962s] Building query index... [0.014907s] Building seed filter... [0.004963s] Searching alignments... [0.065102s] Processing query chunk 0, reference chunk 0, shape 5, index chunk 2. Building reference index... [0.032782s] Building query index... [0.014598s] Building seed filter... [0.005325s] Searching alignments... [0.05902s] Processing query chunk 0, reference chunk 0, shape 5, index chunk 3. Building reference index... [0.035053s] Building query index... [0.014151s] Building seed filter... [0.004923s] Searching alignments... [0.074683s] Processing query chunk 0, reference chunk 0, shape 6, index chunk 0. Building reference index... [0.035981s] Building query index... [0.01499s] Building seed filter... [0.005155s] Searching alignments... [0.065819s] Processing query chunk 0, reference chunk 0, shape 6, index chunk 1. Building reference index... [0.035685s] Building query index... [0.014827s] Building seed filter... [0.005083s] Searching alignments... [0.060858s] Processing query chunk 0, reference chunk 0, shape 6, index chunk 2. Building reference index... [0.032654s] Building query index... [0.014677s] Building seed filter... [0.005079s] Searching alignments... [0.063812s] Processing query chunk 0, reference chunk 0, shape 6, index chunk 3. Building reference index... [0.035952s] Building query index... [0.01454s] Building seed filter... [0.004969s] Searching alignments... [0.059714s] Processing query chunk 0, reference chunk 0, shape 7, index chunk 0. Building reference index... [0.035636s] Building query index... [0.014528s] Building seed filter... [0.004971s] Searching alignments... [0.062995s] Processing query chunk 0, reference chunk 0, shape 7, index chunk 1. Building reference index... [0.039118s] Building query index... [0.014449s] Building seed filter... [0.005219s] Searching alignments... [0.064226s] Processing query chunk 0, reference chunk 0, shape 7, index chunk 2. Building reference index... [0.032639s] Building query index... [0.014759s] Building seed filter... [0.004991s] Searching alignments... [0.064234s] Processing query chunk 0, reference chunk 0, shape 7, index chunk 3. Building reference index... [0.034936s] Building query index... [0.014147s] Building seed filter... [0.005124s] Searching alignments... [0.070441s] Processing query chunk 0, reference chunk 0, shape 8, index chunk 0. Building reference index... [0.035831s] Building query index... [0.014403s] Building seed filter... [0.005008s] Searching alignments... [0.060733s] Processing query chunk 0, reference chunk 0, shape 8, index chunk 1. Building reference index... [0.037682s] Building query index... [0.015011s] Building seed filter... [0.005278s] Searching alignments... [0.063568s] Processing query chunk 0, reference chunk 0, shape 8, index chunk 2. Building reference index... [0.039566s] Building query index... [0.015131s] Building seed filter... [0.005311s] Searching alignments... [0.075291s] Processing query chunk 0, reference chunk 0, shape 8, index chunk 3. Building reference index... [0.035062s] Building query index... [0.014669s] Building seed filter... [0.005089s] Searching alignments... [0.063826s] Processing query chunk 0, reference chunk 0, shape 9, index chunk 0. Building reference index... [0.035052s] Building query index... [0.014675s] Building seed filter... [0.005029s] Searching alignments... [0.064393s] Processing query chunk 0, reference chunk 0, shape 9, index chunk 1. Building reference index... [0.038267s] Building query index... [0.014543s] Building seed filter... [0.005249s] Searching alignments... [0.064676s] Processing query chunk 0, reference chunk 0, shape 9, index chunk 2. Building reference index... [0.041149s] Building query index... [0.01579s] Building seed filter... [0.005371s] Searching alignments... [0.064081s] Processing query chunk 0, reference chunk 0, shape 9, index chunk 3. Building reference index... [0.034576s] Building query index... [0.01493s] Building seed filter... [0.005194s] Searching alignments... [0.061006s] Processing query chunk 0, reference chunk 0, shape 10, index chunk 0. Building reference index... [0.038963s] Building query index... [0.014092s] Building seed filter... [0.004982s] Searching alignments... [0.064211s] Processing query chunk 0, reference chunk 0, shape 10, index chunk 1. Building reference index... [0.038693s] Building query index... [0.014487s] Building seed filter... [0.005399s] Searching alignments... [0.0605s] Processing query chunk 0, reference chunk 0, shape 10, index chunk 2. Building reference index... [0.040189s] Building query index... [0.014756s] Building seed filter... [0.005142s] Searching alignments... [0.067102s] Processing query chunk 0, reference chunk 0, shape 10, index chunk 3. Building reference index... [0.035658s] Building query index... [0.014408s] Building seed filter... [0.005102s] Searching alignments... [0.064701s] Processing query chunk 0, reference chunk 0, shape 11, index chunk 0. Building reference index... [0.035278s] Building query index... [0.014448s] Building seed filter... [0.005266s] Searching alignments... [0.063701s] Processing query chunk 0, reference chunk 0, shape 11, index chunk 1. Building reference index... [0.038791s] Building query index... [0.014677s] Building seed filter... [0.004956s] Searching alignments... [0.064083s] Processing query chunk 0, reference chunk 0, shape 11, index chunk 2. Building reference index... [0.038761s] Building query index... [0.014666s] Building seed filter... [0.005119s] Searching alignments... [0.062955s] Processing query chunk 0, reference chunk 0, shape 11, index chunk 3. Building reference index... [0.031915s] Building query index... [0.014462s] Building seed filter... [0.005263s] Searching alignments... [0.062516s] Processing query chunk 0, reference chunk 0, shape 12, index chunk 0. Building reference index... [0.036111s] Building query index... [0.01511s] Building seed filter... [0.004846s] Searching alignments... [0.069028s] Processing query chunk 0, reference chunk 0, shape 12, index chunk 1. Building reference index... [0.038727s] Building query index... [0.014816s] Building seed filter... [0.00499s] Searching alignments... [0.060112s] Processing query chunk 0, reference chunk 0, shape 12, index chunk 2. Building reference index... [0.041982s] Building query index... [0.015132s] Building seed filter... [0.005216s] Searching alignments... [0.067827s] Processing query chunk 0, reference chunk 0, shape 12, index chunk 3. Building reference index... [0.030766s] Building query index... [0.014174s] Building seed filter... [0.005095s] Searching alignments... [0.061464s] Processing query chunk 0, reference chunk 0, shape 13, index chunk 0. Building reference index... [0.037362s] Building query index... [0.014797s] Building seed filter... [0.005111s] Searching alignments... [0.063288s] Processing query chunk 0, reference chunk 0, shape 13, index chunk 1. Building reference index... [0.03849s] Building query index... [0.014405s] Building seed filter... [0.004985s] Searching alignments... [0.062075s] Processing query chunk 0, reference chunk 0, shape 13, index chunk 2. Building reference index... [0.040666s] Building query index... [0.014735s] Building seed filter... [0.005009s] Searching alignments... [0.065542s] Processing query chunk 0, reference chunk 0, shape 13, index chunk 3. Building reference index... [0.034991s] Building query index... [0.014875s] Building seed filter... [0.005005s] Searching alignments... [0.065143s] Processing query chunk 0, reference chunk 0, shape 14, index chunk 0. Building reference index... [0.03679s] Building query index... [0.01468s] Building seed filter... [0.004932s] Searching alignments... [0.070252s] Processing query chunk 0, reference chunk 0, shape 14, index chunk 1. Building reference index... [0.036266s] Building query index... [0.014815s] Building seed filter... [0.004861s] Searching alignments... [0.064723s] Processing query chunk 0, reference chunk 0, shape 14, index chunk 2. Building reference index... [0.039814s] Building query index... [0.014502s] Building seed filter... [0.005094s] Searching alignments... [0.06294s] Processing query chunk 0, reference chunk 0, shape 14, index chunk 3. Building reference index... [0.035184s] Building query index... [0.014779s] Building seed filter... [0.005282s] Searching alignments... [0.064733s] Processing query chunk 0, reference chunk 0, shape 15, index chunk 0. Building reference index... [0.036195s] Building query index... [0.014941s] Building seed filter... [0.004802s] Searching alignments... [0.064931s] Processing query chunk 0, reference chunk 0, shape 15, index chunk 1. Building reference index... [0.03997s] Building query index... [0.014342s] Building seed filter... [0.004966s] Searching alignments... [0.059839s] Processing query chunk 0, reference chunk 0, shape 15, index chunk 2. Building reference index... [0.040311s] Building query index... [0.014951s] Building seed filter... [0.005054s] Searching alignments... [0.079221s] Processing query chunk 0, reference chunk 0, shape 15, index chunk 3. Building reference index... [0.034127s] Building query index... [0.014636s] Building seed filter... [0.005098s] Searching alignments... [0.061396s] Deallocating buffers... [0.010819s] Computing alignments... [0.508285s] Deallocating reference... [0.003416s] Loading reference sequences... [1.5e-05s] Deallocating buffers... [0.000398s] Deallocating queries... [0.000131s] Loading query sequences... [9e-06s] Closing the input file... [0.000521s] Closing the output file... [0.056322s] Closing the database file... [1.2e-05s] Deallocating taxonomy... [3e-06s] Total time = 111.108s Reported 81059 pairwise alignments, 81060 HSPs. 2108 queries aligned. Traceback (most recent call last): File "/storage/dhome/jsankarasubramani/miniconda3/envs/carveme/bin/carve", line 364, in ref_score=args.reference_score File "/storage/dhome/jsankarasubramani/miniconda3/envs/carveme/bin/carve", line 198, in main debug_output=debug_output) File "/storage/dhome/jsankarasubramani/miniconda3/envs/carveme/lib/python3.6/site-packages/carveme/reconstruction/carving.py", line 236, in carve_model ref_reactions=ref_reactions, ref_score=ref_score, debug_output=debug_output) File "/storage/dhome/jsankarasubramani/miniconda3/envs/carveme/lib/python3.6/site-packages/carveme/reconstruction/carving.py", line 123, in minmax_reduction solver.update() File "/storage/dhome/jsankarasubramani/miniconda3/envs/carveme/lib/python3.6/site-packages/framed/solvers/cplex_interface.py", line 206, in update self.add_variables(var_ids, lbs, ubs, vartypes) File "/storage/dhome/jsankarasubramani/miniconda3/envs/carveme/lib/python3.6/site-packages/framed/solvers/cplex_interface.py", line 105, in add_variables self.problem.variables.add(names=var_ids, lb=lbs, ub=ubs, types=vartypes) File "/storage/dhome/jsankarasubramani/miniconda3/envs/carveme/lib/python3.6/site-packages/cplex/_internal/_subinterfaces.py", line 456, in add obj, lb, ub, types, names, columns) File "/storage/dhome/jsankarasubramani/miniconda3/envs/carveme/lib/python3.6/site-packages/cplex/_internal/_baseinterface.py", line 41, in _add_iter addfun(*args, **kwargs) File "/storage/dhome/jsankarasubramani/miniconda3/envs/carveme/lib/python3.6/site-packages/cplex/_internal/_subinterfaces.py", line 378, in _add types, names) File "/storage/dhome/jsankarasubramani/miniconda3/envs/carveme/lib/python3.6/site-packages/cplex/_internal/_procedural.py", line 967, in newcols xctype, colname) File "/storage/dhome/jsankarasubramani/miniconda3/envs/carveme/lib/python3.6/site-packages/cplex/_internal/_pycplex.py", line 1785, in CPXXnewcols return _pycplex_platform.CPXXnewcols(env, lp, ccnt, py_obj, py_lb, py_ub, xctype, colname) TypeError: not a list

[cdanielmachado]

This is a duplicated issue, please check https://github.com/cdanielmachado/carveme/issues/48