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021417-abacus-stdout.txt
steven@emu:~/bioinfo/021417$ java -Xmx16g -jar /home/shared/abacus/abacus.jar -p \
> Abacus-01.param
***********************************
Abacus
Version: 2.5
***********************************
Developed and written by: Damian Fermin and Alexey Nesvizhskii
Copyright 2010 Damian Fermin
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
Parameters for this execution:
Source directory: '/home/steven/bioinfo/021417'
DB name: 'Cg_Giga_cont_AA.fa'
Output file: '/home/steven/bioinfo/021417/ABACUS_output.tsv'
Combined file P: 0.9
iniProb threshold: 0.5
maxIniProb: 0.99
Keep DB files: false
Recalc Pep Wts: false
Output format: Default
Retrieving protein lengths from
'Cg_Giga_cont_AA.fa'
Loading protXML files
Parsing protXML [ 1 of 44 ]: interact-20161205_Sample_51A.prot.xml
Parsing protXML [ 2 of 44 ]: interact-20161205_Sample_36.prot.xml
Parsing protXML [ 3 of 44 ]: interact-20161205_Sample_19A.prot.xml
Parsing protXML [ 4 of 44 ]: interact-20161205_Sample_28.prot.xml
Parsing protXML [ 5 of 44 ]: interact-20161205_Sample_40A.prot.xml
Parsing protXML [ 6 of 44 ]: interact-20161205_Sample_24.prot.xml
Parsing protXML [ 7 of 44 ]: interact-20161205_Sample_40.prot.xml
Parsing protXML [ 8 of 44 ]: interact-20161205_Sample_36A.prot.xml
Parsing protXML [ 9 of 44 ]: interact-20161205_Sample_1A.prot.xml
Parsing protXML [ 10 of 44 ]: interact-20161205_Sample_19.prot.xml
Parsing protXML [ 11 of 44 ]: interact-20161205_Sample_27.prot.xml
Parsing protXML [ 12 of 44 ]: interact-20161205_Sample_48A.prot.xml
Parsing protXML [ 13 of 44 ]: interact-20161205_Sample_16.prot.xml
Parsing protXML [ 14 of 44 ]: interact-20161205_Sample_24A.prot.xml
Parsing protXML [ 15 of 44 ]: interact-20161205_Sample_3.prot.xml
Parsing protXML [ 16 of 44 ]: interact-20161205_Sample_51.prot.xml
Parsing protXML [ 17 of 44 ]: interact-20161205_Sample_56.prot.xml
Parsing protXML [ 18 of 44 ]: interact-20161205_Sample_35A.prot.xml
Parsing protXML [ 19 of 44 ]: interact-20161205_Sample_35.prot.xml
Parsing protXML [ 20 of 44 ]: interact-20161205_Sample_43.prot.xml
Parsing protXML [ 21 of 44 ]: interact-20161205_Sample_8A.prot.xml
Parsing protXML [ 22 of 44 ]: interact-20161205_sample_1.prot.xml
Parsing protXML [ 23 of 44 ]: interact-20161205_Sample_11A.prot.xml
Parsing protXML [ 24 of 44 ]: interact-20161205_Sample_8.prot.xml
Parsing protXML [ 25 of 44 ]: interact-20161205_Sample_43A.prot.xml
Parsing protXML [ 26 of 44 ]: interact-20161205_Sample_32.prot.xml
Parsing protXML [ 27 of 44 ]: interact-20161205_Sample_3A.prot.xml
Parsing protXML [ 28 of 44 ]: interact-20161205_Sample_27A.prot.xml
Parsing protXML [ 29 of 44 ]: interact-20161205_Sample_56A.prot.xml
Parsing protXML [ 30 of 44 ]: interact-20161205_Sample_12.prot.xml
Parsing protXML [ 31 of 44 ]: interact-20161205_Sample_4.prot.xml
Parsing protXML [ 32 of 44 ]: interact-20161205_Sample_11.prot.xml
Parsing protXML [ 33 of 44 ]: interact-20161205_Sample_44.prot.xml
Parsing protXML [ 34 of 44 ]: interact-COMBINED.prot.xml
Parsing protXML [ 35 of 44 ]: interact-20161205_Sample_52.prot.xml
Parsing protXML [ 36 of 44 ]: interact-20161205_Sample_20.prot.xml
Parsing protXML [ 37 of 44 ]: interact-20161205_Sample_16A.prot.xml
Parsing protXML [ 38 of 44 ]: interact-20161205_Sample_28A.prot.xml
Parsing protXML [ 39 of 44 ]: interact-20161205_Sample_32A.prot.xml
Parsing protXML [ 40 of 44 ]: interact-20161205_Sample_4A.prot.xml
Parsing protXML [ 41 of 44 ]: interact-20161205_Sample_12A.prot.xml
Parsing protXML [ 42 of 44 ]: interact-20161205_Sample_48.prot.xml
Parsing protXML [ 43 of 44 ]: interact-20161205_Sample_44A.prot.xml
Parsing protXML [ 44 of 44 ]: interact-20161205_Sample_52A.prot.xml
Loading pepXML files
Parsing pepXML [ 1 of 88 ]: interact-20161205_Sample_8A.pep.xml
Parsing pepXML [ 2 of 88 ]: 20161205_Sample_56.pep.xml
Parsing pepXML [ 3 of 88 ]: 20161205_Sample_20.pep.xml
Parsing pepXML [ 4 of 88 ]: interact-20161205_Sample_1A.pep.xml
Parsing pepXML [ 5 of 88 ]: interact-20161205_Sample_4A.pep.xml
Parsing pepXML [ 6 of 88 ]: 20161205_Sample_52.pep.xml
Parsing pepXML [ 7 of 88 ]: interact-20161205_Sample_40.pep.xml
Parsing pepXML [ 8 of 88 ]: 20161205_sample_1.pep.xml
Parsing pepXML [ 9 of 88 ]: 20161205_Sample_27A.pep.xml
Parsing pepXML [ 10 of 88 ]: 20161205_Sample_27.pep.xml
Parsing pepXML [ 11 of 88 ]: interact-20161205_Sample_20A.pep.xml
Parsing pepXML [ 12 of 88 ]: 20161205_Sample_4A.pep.xml
Parsing pepXML [ 13 of 88 ]: 20161205_Sample_43A.pep.xml
Parsing pepXML [ 14 of 88 ]: interact-20161205_Sample_48.pep.xml
Parsing pepXML [ 15 of 88 ]: interact-20161205_Sample_35.pep.xml
Parsing pepXML [ 16 of 88 ]: interact-20161205_Sample_43A.pep.xml
Parsing pepXML [ 17 of 88 ]: 20161205_Sample_1A.pep.xml
Parsing pepXML [ 18 of 88 ]: interact-20161205_Sample_12.pep.xml
Parsing pepXML [ 19 of 88 ]: 20161205_Sample_8.pep.xml
Parsing pepXML [ 20 of 88 ]: 20161205_Sample_48A.pep.xml
Parsing pepXML [ 21 of 88 ]: interact-20161205_Sample_52.pep.xml
Parsing pepXML [ 22 of 88 ]: 20161205_Sample_32.pep.xml
Parsing pepXML [ 23 of 88 ]: 20161205_Sample_19.pep.xml
Parsing pepXML [ 24 of 88 ]: 20161205_Sample_40.pep.xml
Parsing pepXML [ 25 of 88 ]: interact-20161205_Sample_24A.pep.xml
Parsing pepXML [ 26 of 88 ]: interact-20161205_Sample_51.pep.xml
Parsing pepXML [ 27 of 88 ]: 20161205_Sample_20A.pep.xml
Parsing pepXML [ 28 of 88 ]: 20161205_Sample_43.pep.xml
Parsing pepXML [ 29 of 88 ]: 20161205_Sample_3A.pep.xml
Parsing pepXML [ 30 of 88 ]: 20161205_Sample_8A.pep.xml
Parsing pepXML [ 31 of 88 ]: interact-20161205_Sample_32A.pep.xml
Parsing pepXML [ 32 of 88 ]: interact-20161205_Sample_51A.pep.xml
Parsing pepXML [ 33 of 88 ]: interact-20161205_Sample_3.pep.xml
Parsing pepXML [ 34 of 88 ]: interact-20161205_Sample_35A.pep.xml
Parsing pepXML [ 35 of 88 ]: interact-20161205_Sample_56A.pep.xml
Parsing pepXML [ 36 of 88 ]: interact-20161205_Sample_11A.pep.xml
Parsing pepXML [ 37 of 88 ]: 20161205_Sample_51A.pep.xml
Parsing pepXML [ 38 of 88 ]: 20161205_Sample_48.pep.xml
Parsing pepXML [ 39 of 88 ]: 20161205_Sample_11A.pep.xml
Parsing pepXML [ 40 of 88 ]: 20161205_Sample_32A.pep.xml
Parsing pepXML [ 41 of 88 ]: interact-20161205_Sample_44A.pep.xml
Parsing pepXML [ 42 of 88 ]: 20161205_Sample_11.pep.xml
Parsing pepXML [ 43 of 88 ]: 20161205_Sample_24.pep.xml
Parsing pepXML [ 44 of 88 ]: interact-20161205_Sample_48A.pep.xml
Parsing pepXML [ 45 of 88 ]: 20161205_Sample_44A.pep.xml
Parsing pepXML [ 46 of 88 ]: interact-20161205_Sample_32.pep.xml
Parsing pepXML [ 47 of 88 ]: interact-20161205_Sample_28.pep.xml
Parsing pepXML [ 48 of 88 ]: interact-20161205_Sample_4.pep.xml
Parsing pepXML [ 49 of 88 ]: 20161205_Sample_3.pep.xml
Parsing pepXML [ 50 of 88 ]: interact-20161205_Sample_16A.pep.xml
Parsing pepXML [ 51 of 88 ]: 20161205_Sample_28.pep.xml
Parsing pepXML [ 52 of 88 ]: interact-20161205_Sample_43.pep.xml
Parsing pepXML [ 53 of 88 ]: 20161205_Sample_36.pep.xml
Parsing pepXML [ 54 of 88 ]: interact-20161205_Sample_27.pep.xml
Parsing pepXML [ 55 of 88 ]: interact-20161205_Sample_27A.pep.xml
Parsing pepXML [ 56 of 88 ]: interact-20161205_Sample_19A.pep.xml
Parsing pepXML [ 57 of 88 ]: interact-20161205_Sample_52A.pep.xml
Parsing pepXML [ 58 of 88 ]: interact-20161205_Sample_40A.pep.xml
Parsing pepXML [ 59 of 88 ]: interact-20161205_Sample_16.pep.xml
Parsing pepXML [ 60 of 88 ]: interact-20161205_Sample_24.pep.xml
Parsing pepXML [ 61 of 88 ]: interact-20161205_Sample_11.pep.xml
Parsing pepXML [ 62 of 88 ]: interact-20161205_Sample_56.pep.xml
Parsing pepXML [ 63 of 88 ]: 20161205_Sample_28A.pep.xml
Parsing pepXML [ 64 of 88 ]: 20161205_Sample_24A.pep.xml
Parsing pepXML [ 65 of 88 ]: 20161205_Sample_19A.pep.xml
Parsing pepXML [ 66 of 88 ]: interact-20161205_sample_1.pep.xml
Parsing pepXML [ 67 of 88 ]: 20161205_Sample_51.pep.xml
Parsing pepXML [ 68 of 88 ]: interact-20161205_Sample_20.pep.xml
Parsing pepXML [ 69 of 88 ]: 20161205_Sample_44.pep.xml
Parsing pepXML [ 70 of 88 ]: 20161205_Sample_36A.pep.xml
Parsing pepXML [ 71 of 88 ]: interact-20161205_Sample_44.pep.xml
Parsing pepXML [ 72 of 88 ]: 20161205_Sample_12A.pep.xml
Parsing pepXML [ 73 of 88 ]: interact-20161205_Sample_12A.pep.xml
Parsing pepXML [ 74 of 88 ]: interact-20161205_Sample_3A.pep.xml
Parsing pepXML [ 75 of 88 ]: interact-20161205_Sample_28A.pep.xml
Parsing pepXML [ 76 of 88 ]: 20161205_Sample_52A.pep.xml
Parsing pepXML [ 77 of 88 ]: 20161205_Sample_16A.pep.xml
Parsing pepXML [ 78 of 88 ]: 20161205_Sample_4.pep.xml
Parsing pepXML [ 79 of 88 ]: 20161205_Sample_35A.pep.xml
Parsing pepXML [ 80 of 88 ]: 20161205_Sample_12.pep.xml
Parsing pepXML [ 81 of 88 ]: 20161205_Sample_56A.pep.xml
Parsing pepXML [ 82 of 88 ]: interact-20161205_Sample_36A.pep.xml
Parsing pepXML [ 83 of 88 ]: interact-20161205_Sample_19.pep.xml
Parsing pepXML [ 84 of 88 ]: 20161205_Sample_16.pep.xml
Parsing pepXML [ 85 of 88 ]: 20161205_Sample_40A.pep.xml
Parsing pepXML [ 86 of 88 ]: interact-20161205_Sample_36.pep.xml
Parsing pepXML [ 87 of 88 ]: interact-20161205_Sample_8.pep.xml
Parsing pepXML [ 88 of 88 ]: 20161205_Sample_35.pep.xml
Creating srcFileTags table
Creating combined table from 'interact-COMBINED.prot.xml'
Curating interact-COMBINED.prot.xml
Recalculating peptide weights for combined
Creating protXML table
Populating protXML table... [ / 2643677 Working... ]
Indexing protXML table (This can take a while...)
Indexing of protXML completed
Mapping peptides to proteins (combined)
Mapping peptides to proteins (combined) [ - 117298 Working... ]
Mapping peptides to proteins (X20161205_SAMPLE_1)
Mapping peptides to proteins (X20161205_SAMPLE_11)
Mapping peptides to proteins (X20161205_SAMPLE_11A)
Mapping peptides to proteins (X20161205_SAMPLE_12)
Mapping peptides to proteins (X20161205_SAMPLE_12A)
Mapping peptides to proteins (X20161205_SAMPLE_16)
Mapping peptides to proteins (X20161205_SAMPLE_16A)
Mapping peptides to proteins (X20161205_SAMPLE_19)
Mapping peptides to proteins (X20161205_SAMPLE_19A)
Mapping peptides to proteins (X20161205_SAMPLE_1A)
Mapping peptides to proteins (X20161205_SAMPLE_20)
Mapping peptides to proteins (X20161205_SAMPLE_24)
Mapping peptides to proteins (X20161205_SAMPLE_24A)
Mapping peptides to proteins (X20161205_SAMPLE_27)
Mapping peptides to proteins (X20161205_SAMPLE_27A)
Mapping peptides to proteins (X20161205_SAMPLE_28)
Mapping peptides to proteins (X20161205_SAMPLE_28A)
Mapping peptides to proteins (X20161205_SAMPLE_3)
Mapping peptides to proteins (X20161205_SAMPLE_32)
Mapping peptides to proteins (X20161205_SAMPLE_32A)
Mapping peptides to proteins (X20161205_SAMPLE_35)
Mapping peptides to proteins (X20161205_SAMPLE_35A)
Mapping peptides to proteins (X20161205_SAMPLE_36)
Mapping peptides to proteins (X20161205_SAMPLE_36A)
Mapping peptides to proteins (X20161205_SAMPLE_3A)
Mapping peptides to proteins (X20161205_SAMPLE_4)
Mapping peptides to proteins (X20161205_SAMPLE_40)
Mapping peptides to proteins (X20161205_SAMPLE_40A)
Mapping peptides to proteins (X20161205_SAMPLE_43)
Mapping peptides to proteins (X20161205_SAMPLE_43A)
Mapping peptides to proteins (X20161205_SAMPLE_44)
Mapping peptides to proteins (X20161205_SAMPLE_44A)
Mapping peptides to proteins (X20161205_SAMPLE_48)
Mapping peptides to proteins (X20161205_SAMPLE_48A)
Mapping peptides to proteins (X20161205_SAMPLE_4A)
Mapping peptides to proteins (X20161205_SAMPLE_51)
Mapping peptides to proteins (X20161205_SAMPLE_51A)
Mapping peptides to proteins (X20161205_SAMPLE_52)
Mapping peptides to proteins (X20161205_SAMPLE_52A)
Mapping peptides to proteins (X20161205_SAMPLE_56)
Mapping peptides to proteins (X20161205_SAMPLE_56A)
Mapping peptides to proteins (X20161205_SAMPLE_8)
Mapping peptides to proteins (X20161205_SAMPLE_8A)
Creating protidSummary table
Collecting list of all proteins identified in interact-COMBINED.prot.xml
Counting protein frequencies across independent files
Getting protein frequencies [ \ 20435 Working... ]
Recording best ProteinProphet scores for each protein
Collecting protein probabilities [ \ 20435 Working... ]
Creating selection heuristics table (This could take a while)... [ - 10486 Working... ]
Picking representative protids
Loading protidSummary table... [ / 9077 Working... ]
Creating results
Appending protein lengths
Creating peptide usage table
Peptide usage index (X20161205_SAMPLE_1)... [ | 32888 Working... ]
Peptide usage index (X20161205_SAMPLE_11)... [ / 31713 Working... ]
Peptide usage index (X20161205_SAMPLE_11A)... [ \ 32223 Working... ]
Peptide usage index (X20161205_SAMPLE_12)... [ | 35724 Working... ]
Peptide usage index (X20161205_SAMPLE_12A)... [ - 35762 Working... ]
Peptide usage index (X20161205_SAMPLE_16)... [ / 31921 Working... ]
Peptide usage index (X20161205_SAMPLE_16A)... [ | 31256 Working... ]
Peptide usage index (X20161205_SAMPLE_19)... [ \ 33611 Working... ]
Peptide usage index (X20161205_SAMPLE_19A)... [ \ 35019 Working... ]
Peptide usage index (X20161205_SAMPLE_1A)... [ / 33993 Working... ]
Peptide usage index (X20161205_SAMPLE_20)... [ / 34069 Working... ]
Peptide usage index (X20161205_SAMPLE_24)... [ / 28665 Working... ]
Peptide usage index (X20161205_SAMPLE_24A)... [ - 29158 Working... ]
Peptide usage index (X20161205_SAMPLE_27)... [ \ 25807 Working... ]
Peptide usage index (X20161205_SAMPLE_27A)... [ | 25892 Working... ]
Peptide usage index (X20161205_SAMPLE_28)... [ / 32449 Working... ]
Peptide usage index (X20161205_SAMPLE_28A)... [ / 34189 Working... ]
Peptide usage index (X20161205_SAMPLE_3)... [ \ 32407 Working... ]
Peptide usage index (X20161205_SAMPLE_32)... [ | 32124 Working... ]
Peptide usage index (X20161205_SAMPLE_32A)... [ / 32369 Working... ]
Peptide usage index (X20161205_SAMPLE_35)... [ \ 10991 Working... ]
Peptide usage index (X20161205_SAMPLE_35A)... [ / 10653 Working... ]
Peptide usage index (X20161205_SAMPLE_36)... [ / 31221 Working... ]
Peptide usage index (X20161205_SAMPLE_36A)... [ \ 30931 Working... ]
Peptide usage index (X20161205_SAMPLE_3A)... [ \ 32611 Working... ]
Peptide usage index (X20161205_SAMPLE_4)... [ / 34429 Working... ]
Peptide usage index (X20161205_SAMPLE_40)... [ | 31096 Working... ]
Peptide usage index (X20161205_SAMPLE_40A)... [ | 30744 Working... ]
Peptide usage index (X20161205_SAMPLE_43)... [ \ 15299 Working... ]
Peptide usage index (X20161205_SAMPLE_43A)... [ | 15300 Working... ]
Peptide usage index (X20161205_SAMPLE_44)... [ \ 26003 Working... ]
Peptide usage index (X20161205_SAMPLE_44A)... [ | 26656 Working... ]
Peptide usage index (X20161205_SAMPLE_48)... [ - 33974 Working... ]
Peptide usage index (X20161205_SAMPLE_48A)... [ - 35738 Working... ]
Peptide usage index (X20161205_SAMPLE_4A)... [ \ 34643 Working... ]
Peptide usage index (X20161205_SAMPLE_51)... [ \ 27651 Working... ]
Peptide usage index (X20161205_SAMPLE_51A)... [ / 27553 Working... ]
Peptide usage index (X20161205_SAMPLE_52)... [ \ 29111 Working... ]
Peptide usage index (X20161205_SAMPLE_52A)... [ / 28541 Working... ]
Peptide usage index (X20161205_SAMPLE_56)... [ | 32604 Working... ]
Peptide usage index (X20161205_SAMPLE_56A)... [ | 32292 Working... ]
Peptide usage index (X20161205_SAMPLE_8)... [ | 33204 Working... ]
Peptide usage index (X20161205_SAMPLE_8A)... [ | 34304 Working... ]
Indexing pepUsage_ table
Updating adjusted spectral counts
Retrieving data from individual experiments
Adding data from X20161205_SAMPLE_1
Adding data from X20161205_SAMPLE_11
Adding data from X20161205_SAMPLE_11A
Adding data from X20161205_SAMPLE_12
Adding data from X20161205_SAMPLE_12A
Adding data from X20161205_SAMPLE_16
Adding data from X20161205_SAMPLE_16A
Adding data from X20161205_SAMPLE_19
Adding data from X20161205_SAMPLE_19A
Adding data from X20161205_SAMPLE_1A
Adding data from X20161205_SAMPLE_20
Adding data from X20161205_SAMPLE_24
Adding data from X20161205_SAMPLE_24A
Adding data from X20161205_SAMPLE_27
Adding data from X20161205_SAMPLE_27A
Adding data from X20161205_SAMPLE_28
Adding data from X20161205_SAMPLE_28A
Adding data from X20161205_SAMPLE_3
Adding data from X20161205_SAMPLE_32
Adding data from X20161205_SAMPLE_32A
Adding data from X20161205_SAMPLE_35
Adding data from X20161205_SAMPLE_35A
Adding data from X20161205_SAMPLE_36
Adding data from X20161205_SAMPLE_36A
Adding data from X20161205_SAMPLE_3A
Adding data from X20161205_SAMPLE_4
Adding data from X20161205_SAMPLE_40
Adding data from X20161205_SAMPLE_40A
Adding data from X20161205_SAMPLE_43
Adding data from X20161205_SAMPLE_43A
Adding data from X20161205_SAMPLE_44
Adding data from X20161205_SAMPLE_44A
Adding data from X20161205_SAMPLE_48
Adding data from X20161205_SAMPLE_48A
Adding data from X20161205_SAMPLE_4A
Adding data from X20161205_SAMPLE_51
Adding data from X20161205_SAMPLE_51A
Adding data from X20161205_SAMPLE_52
Adding data from X20161205_SAMPLE_52A
Adding data from X20161205_SAMPLE_56
Adding data from X20161205_SAMPLE_56A
Adding data from X20161205_SAMPLE_8
Adding data from X20161205_SAMPLE_8A
Creating NSAF values table (protein-centric)
NSAF_FACTOR = 10^5 = 100000.0
java.sql.SQLSyntaxErrorException: user lacks privilege or object not found: NAN
at org.hsqldb.jdbc.JDBCUtil.sqlException(Unknown Source)
at org.hsqldb.jdbc.JDBCUtil.sqlException(Unknown Source)
at org.hsqldb.jdbc.JDBCStatement.fetchResult(Unknown Source)
at org.hsqldb.jdbc.JDBCStatement.executeUpdate(Unknown Source)
at abacus.hyperSQLObject.getNSAF_values_prot(hyperSQLObject.java:2961)
at abacus.abacus.main(abacus.java:221)
at mainFunction.mainFunction.main(mainFunction.java:49)
Caused by: org.hsqldb.HsqlException: user lacks privilege or object not found: NAN
at org.hsqldb.error.Error.error(Unknown Source)
at org.hsqldb.error.Error.error(Unknown Source)
at org.hsqldb.ExpressionColumn.checkColumnsResolved(Unknown Source)
at org.hsqldb.ParserDML.resolveUpdateExpressions(Unknown Source)
at org.hsqldb.ParserDML.compileUpdateStatement(Unknown Source)
at org.hsqldb.ParserCommand.compilePart(Unknown Source)
at org.hsqldb.ParserCommand.compileStatements(Unknown Source)
at org.hsqldb.Session.executeDirectStatement(Unknown Source)
at org.hsqldb.Session.execute(Unknown Source)
... 5 more
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