Optitype not predicting HLA-C alleles
alexanderwhatley opened this issue · comments
I ran optitype, and everything looked fine, but the output file did not give any predictions for the HLA-C alleles. Here is the output log:
mapping with 8 threads...
0:01:14.27 Mapping filtered_fished.fastq to GEN reference...
0:03:26.66 Generating binary hit matrix.
0:03:26.70 Loading optitype_outdir/2017_04_25_02_02_55/2017_04_25_02_02_55_1.bam started. Number of HLA reads loaded (updated every thousand):
1K...
0:03:26.97 1255 reads loaded. Creating dataframe...
0:03:27.18 Dataframes created. Shape: 1255 x 11179, hits: 22073 (22250), sparsity: 1 in 630.55
0:03:33.52 temporary pruning of identical rows and columns
0:03:33.63 Size of mtx with unique rows and columns: (50, 59)
0:03:33.63 determining minimal set of non-overshadowed alleles
0:03:33.78 Keeping only the minimal number of required alleles (12,)
0:03:33.78 Creating compact model...
starting ilp solver with 1 threads...
0:03:33.83 Initializing OptiType model...
Welcome to the CBC MILP Solver
Version: 2.9
Build Date: Mar 7 2017
command line - /n/sw/fasrcsw/apps/Core/Cbc/2.9-fasrc01/bin/cbc -printingOptions all -import /tmp/tmpext6iepo.pyomo.lp -import -stat=1 -solve -solu /tmp/tmpext6iepo.pyomo.soln (default strategy 1)
Option for printingOptions changed from normal to all
CoinLpIO::readLp(): Maximization problem reformulated as minimization
Current default (if $ as parameter) for import is /tmp/tmpext6iepo.pyomo.lp
Presolve 103 (-9) rows, 61 (-3) columns and 285 (-15) elements
Statistics for presolved model
Original problem has 37 integers (37 of which binary)
Presolved problem has 35 integers (35 of which binary)
==== 8 zero objective 32 different
==== absolute objective values 32 different
==== for integers 7 zero objective 17 different
==== for integers absolute objective values 17 different
===== end objective counts
Problem has 103 rows, 61 columns (53 with objective) and 285 elements
Column breakdown:
25 of type 0.0->inf, 1 of type 0.0->up, 0 of type lo->inf,
0 of type lo->up, 0 of type free, 0 of type fixed,
0 of type -inf->0.0, 0 of type -inf->up, 35 of type 0.0->1.0
Row breakdown:
0 of type E 0.0, 0 of type E 1.0, 0 of type E -1.0,
0 of type E other, 0 of type G 0.0, 3 of type G 1.0,
0 of type G other, 73 of type L 0.0, 0 of type L 1.0,
27 of type L other, 0 of type Range 0.0->1.0, 0 of type Range other,
0 of type Free
Continuous objective value is -429.083 - 0.00 seconds
Cgl0004I processed model has 102 rows, 61 columns (35 integer (35 of which binary)) and 279 elements
Cbc0038I Initial state - 0 integers unsatisfied sum - 1.44329e-15
Cbc0038I Solution found of -429.083
Cbc0038I Relaxing continuous gives -429.083
Cbc0038I Before mini branch and bound, 35 integers at bound fixed and 5 continuous
Cbc0038I Mini branch and bound did not improve solution (0.01 seconds)
Cbc0038I After 0.01 seconds - Feasibility pump exiting with objective of -429.083 - took 0.00 seconds
Cbc0012I Integer solution of -429.083 found by feasibility pump after 0 iterations and 0 nodes (0.01 seconds)
Cbc0001I Search completed - best objective -429.083, took 0 iterations and 0 nodes (0.01 seconds)
Cbc0035I Maximum depth 0, 0 variables fixed on reduced cost
Cuts at root node changed objective from -429.083 to -429.083
Probing was tried 0 times and created 0 cuts of which 0 were active after adding rounds of cuts (0.000 seconds)
Gomory was tried 0 times and created 0 cuts of which 0 were active after adding rounds of cuts (0.000 seconds)
Knapsack was tried 0 times and created 0 cuts of which 0 were active after adding rounds of cuts (0.000 seconds)
Clique was tried 0 times and created 0 cuts of which 0 were active after adding rounds of cuts (0.000 seconds)
MixedIntegerRounding2 was tried 0 times and created 0 cuts of which 0 were active after adding rounds of cuts (0.000 seconds)
FlowCover was tried 0 times and created 0 cuts of which 0 were active after adding rounds of cuts (0.000 seconds)
TwoMirCuts was tried 0 times and created 0 cuts of which 0 were active after adding rounds of cuts (0.000 seconds)
Result - Optimal solution found
Objective value: -429.08300000
Enumerated nodes: 0
Total iterations: 0
Time (CPU seconds): 0.01
Time (Wallclock seconds): 0.02
Total time (CPU seconds): 0.02 (Wallclock seconds): 0.03
The output file looks like this:
A1 A2 B1 B2 C1 C2 Reads Objective
0 A*11:01 A*11:01 B*07:02 B*07:02 433 429.083
Any idea why this is?
Hi Alexander, can you e-mail me the intermediate bam file? You can tell OT to keep them with deletebam=false in the config file.
Hello,
I encountered the same problem. Wonder if anyone could advise what the problem was and how to fix it? Thank you!
I can look at the intermediate bam file if you e-mail it to me.
Thank you for offering help. Please find the intermediate files and the output attached. ?
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From: andras86 <notifications@github.com>
Sent: 30 November 2018 13:38
To: FRED-2/OptiType
Cc: Phuc Hoang; Comment
Subject: Re: [FRED-2/OptiType] Optitype not predicting HLA-C alleles (#49)
I can look at the intermediate bam file if you e-mail it to me.
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