[SERVER-21599] Unknown cause of error - String field in insert Created: 20/Nov/15  Updated: 21/Nov/15  Resolved: 20/Nov/15

Status: Closed
Project: Core Server
Component/s: Shell
Affects Version/s: None
Fix Version/s: None

Type: Question Priority: Major - P3
Reporter: Rodrigo Laigner Assignee: Unassigned
Resolution: Done Votes: 0
Labels: None
Remaining Estimate: Not Specified
Time Spent: Not Specified
Original Estimate: Not Specified

Participants:

 Description   

Hi everybody,

I've been trying to insert a Document in a collection, however, the known error 2015-11-20T18:51:02.061-0200 E QUERY SyntaxError: Unexpected token ILLEGAL always appear.

The insert contains a giant string:

db.eactivation.insert({_id :{taskid : 41272, actid : 831},emachine_id:134,processor:4,exitstatus:0,commandline:"./experiment.cmd",workspace:"/root/exp_SciPhy2/exp/raxml/235/",failure_tries:0,tout:"Current working directory /root/exp_SciPhy2/exp/raxml/235raxmlHPC -s ORTHOMCL1973.phylip -n ORTHOMCL1973.phylip_raxml_tree1.singleTree -c 4 -f d -m PROTGAMMARTREV -p 1IMPORTANT WARNING: Sequences 1 and 6 are exactly identicalIMPORTANT WARNING: Sequences 2 and 7 are exactly identicalIMPORTANT WARNING: Sequences 3 and 8 are exactly identicalIMPORTANT WARNING: Sequences 4 and 9 are exactly identicalIMPORTANT WARNING: Sequences 5 and 10 are exactly identicalIMPORTANT WARNINGFound 5 sequences that are exactly identical to other sequences in the alignment.Normally they should be excluded from the analysis.Just in case you might need it, an alignment file with sequence duplicates removed is printed to file ORTHOMCL1973.phylip.reducedYou are using RAxML version 7.2.2 released by Alexandros Stamatakis in August 2009Alignment has 103 distinct alignment patternsProportion of gaps and completely undetermined characters in this alignment: 0.111565RAxML rapid hill-climbing modeUsing 1 distinct models/data partitions with joint branch length optimizationExecuting 1 inferences on the original alignment using 1 distinct randomized MP treesAll free model parameters will be estimated by RAxMLGAMMA model of rate heteorgeneity, ML estimate of alpha-parameterGAMMA Model parameters will be estimated up to an accuracy of 0.1000000000 Log Likelihood unitsPartition: 0Alignment Patterns: 103Name: No Name ProvidedDataType: AASubstitution Matrix: RTREVFixed Base Frequencies:RAxML was called as follows:/usr/local/bin/raxmlHPC -s ORTHOMCL1973.phylip -n ORTHOMCL1973.phylip_raxml_tree1.singleTree -c 4 -f d -m PROTGAMMARTREV -p 1 Inference[0]: Time 7.478738 GAMMA-based likelihood -917.790168, best rearrangement setting 5Conducting final model optimizations on all 1 trees under GAMMA-based models ....Inference[0] final GAMMA-based Likelihood: -917.790099 tree written to file /root/exp_SciPhy2/exp/raxml/235/RAxML_result.ORTHOMCL1973.phylip_raxml_tree1.singleTreeStarting final GAMMA-based thorough Optimization on tree 0 likelihood -917.790099 .... Final GAMMA-based Score of best tree -917.790099Program execution info written to /root/exp_SciPhy2/exp/raxml/235/RAxML_info.ORTHOMCL1973.phylip_raxml_tree1.singleTreeBest-scoring ML tree written to: /root/exp_SciPhy2/exp/raxml/235/RAxML_bestTree.ORTHOMCL1973.phylip_raxml_tree1.singleTreeOverall execution time: 11.196178 secs or 0.003110 hours or 0.000130 daysraxmlHPC -s ORTHOMCL1973.phylip -n ORTHOMCL1973.phylip_tree2.raxml -c 4 -f d -m PROTGAMMARTREV -b 234534251 -N 100 -p 1IMPORTANT WARNING: Sequences 1 and 6 are exactly identicalIMPORTANT WARNING: Sequences 2 and 7 are exactly identicalIMPORTANT WARNING: Sequences 3 and 8 are exactly identicalIMPORTANT WARNING: Sequences 4 and 9 are exactly identicalIMPORTANT WARNING: Sequences 5 and 10 are exactly identicalIMPORTANT WARNINGFound 5 sequences that are exactly identical to other sequences in the alignment.Normally they should be excluded from the analysis.An alignment file with sequence duplicates removed has alreadybeen printed to file ORTHOMCL1973.phylip.reducedYou are using RAxML version 7.2.2 released by Alexandros Stamatakis in August 2009Alignment has 103 distinct alignment patternsProportion of gaps and completely undetermined characters in this alignment: 0.111565RAxML rapid hill-climbing modeUsing 1 distinct models/data partitions with joint branch length optimizationExecuting 100 non-parametric bootstrap inferencesAll free model parameters will be estimated by RAxMLGAMMA model of rate heteorgeneity, ML estimate of alpha-parameterGAMMA Model parameters will be estimated up to an accuracy of 0.1000000000 Log Likelihood unitsPartition: 0Alignment Patterns: 103Name: No Name ProvidedDataType: AASubstitution Matrix: RTREVFixed Base Frequencies:RAxML was called as follows:/usr/local/bin/raxmlHPC -s ORTHOMCL1973.phylip -n ORTHOMCL1973.phylip_tree2.raxml -c 4 -f d -m PROTGAMMARTREV -b 234534251 -N 100 -p 1 Bootstrap[0]: Time 4.143687 bootstrap likelihood -882.654430, best rearrangement setting 5Bootstrap[1]: Time 5.133301 bootstrap likelihood -957.877291, best rearrangement setting 5Bootstrap[2]: Time 4.236653 bootstrap likelihood -986.439382, best rearrangement setting 5Bootstrap[3]: Time 4.094587 bootstrap likelihood -860.336704, best rearrangement setting 5Bootstrap[4]: Time 7.187790 bootstrap likelihood -957.691359, best rearrangement setting 5Bootstrap[5]: Time 6.555075 bootstrap likelihood -959.199566, best rearrangement setting 5Bootstrap[6]: Time 4.495686 bootstrap likelihood -882.008126, best rearrangement setting 5Bootstrap[7]: Time 3.960355 bootstrap likelihood -923.743045, best rearrangement setting 5Bootstrap[8]: Time 6.066996 bootstrap likelihood -947.289235, best rearrangement setting 5Bootstrap[9]: Time 3.672821 bootstrap likelihood -900.505985, best rearrangement setting 5Bootstrap[10]: Time 3.981279 bootstrap likelihood -860.710107, best rearrangement setting 5Bootstrap[11]: Time 7.284058 bootstrap likelihood -970.016325, best rearrangement setting 5Bootstrap[12]: Time 3.789841 bootstrap likelihood -875.734303, best rearrangement setting 5Bootstrap[13]: Time 4.067762 bootstrap likelihood -871.904211, best rearrangement setting 5Bootstrap[14]: Time 4.894045 bootstrap likelihood -941.869530, best rearrangement setting 5Bootstrap[15]: Time 3.943835 bootstrap likelihood -987.751847, best rearrangement setting 5Bootstrap[16]: Time 4.607584 bootstrap likelihood -900.838384, best rearrangement setting 5Bootstrap[17]: Time 5.096721 bootstrap likelihood -877.888666, best rearrangement setting 5Bootstrap[18]: Time 4.146373 bootstrap likelihood -881.790985, best rearrangement setting 5Bootstrap[19]: Time 3.812691 bootstrap likelihood -880.538359, best rearrangement setting 5Bootstrap[20]: Time 4.415615 bootstrap likelihood -909.573517, best rearrangement setting 5Bootstrap[21]: Time 4.427632 bootstrap likelihood -939.691223, best rearrangement setting 5Bootstrap[22]: Time 7.376673 bootstrap likelihood -926.206609, best rearrangement setting 5Bootstrap[23]: Time 4.878849 bootstrap likelihood -898.478888, best rearrangement setting 5Bootstrap[24]: Time 6.070067 bootstrap likelihood -952.972581, best rearrangement setting 5Bootstrap[25]: Time 4.428009 bootstrap likelihood -918.578575, best rearrangement setting 5Bootstrap[26]: Time 3.948235 bootstrap likelihood -935.653495, best rearrangement setting 5Bootstrap[27]: Time 7.447685 bootstrap likelihood -986.572438, best rearrangement setting 5Bootstrap[28]: Time 3.240585 bootstrap likelihood -812.427383, best rearrangement setting 5Bootstrap[29]: Time 4.928260 bootstrap likelihood -971.845948, best rearrangement setting 5Bootstrap[30]: Time 4.601605 bootstrap likelihood -924.754140, best rearrangement setting 5Bootstrap[31]: Time 8.225795 bootstrap likelihood -902.590772, best rearrangement setting 5Bootstrap[32]: Time 4.057088 bootstrap likelihood -872.765163, best rearrangement setting 5Bootstrap[33]: Time 4.557380 bootstrap likelihood -929.018459, best rearrangement setting 5Bootstrap[34]: Time 6.323910 bootstrap likelihood -901.658507, best rearrangement setting 5Bootstrap[35]: Time 3.854612 bootstrap likelihood -894.800184, best rearrangement setting 5Bootstrap[36]: Time 3.787907 bootstrap likelihood -869.886966, best rearrangement setting 5Bootstrap[37]: Time 7.022416 bootstrap likelihood -919.755267, best rearrangement setting 5Bootstrap[38]: Time 5.139051 bootstrap likelihood -958.005878, best rearrangement setting 5Bootstrap[39]: Time 5.080359 bootstrap likelihood -950.062106, best rearrangement setting 5Bootstrap[40]: Time 3.849614 bootstrap likelihood -933.079705, best rearrangement setting 5Bootstrap[41]: Time 4.002797 bootstrap likelihood -834.930440, best rearrangement setting 5Bootstrap[42]: Time 6.884094 bootstrap likelihood -953.206977, best rearrangement setting 5Bootstrap[43]: Time 4.365375 bootstrap likelihood -900.339674, best rearrangement setting 5Bootstrap[44]: Time 4.410182 bootstrap likelihood -880.283200, best rearrangement setting 5Bootstrap[45]: Time 6.500712 bootstrap likelihood -884.832566, best rearrangement setting 5Bootstrap[46]: Time 6.060143 bootstrap likelihood -881.675870, best rearrangement setting 5Bootstrap[47]: Time 5.214060 bootstrap likelihood -997.971852, best rearrangement setting 5Bootstrap[48]: Time 5.101423 bootstrap likelihood -888.393941, best rearrangement setting 5Bootstrap[49]: Time 6.685374 bootstrap likelihood -950.848556, best rearrangement setting 5Bootstrap[50]: Time 4.641665 bootstrap likelihood -967.313808, best rearrangement setting 5Bootstrap[51]: Time 4.422669 bootstrap likelihood -969.188269, best rearrangement setting 5Bootstrap[52]: Time 3.829065 bootstrap likelihood -888.899685, best rearrangement setting 5Bootstrap[53]: Time 4.394840 bootstrap likelihood -923.657665, best rearrangement setting 5Bootstrap[54]: Time 4.220646 bootstrap likelihood -888.762539, best rearrangement setting 5Bootstrap[55]: Time 4.827842 bootstrap likelihood -955.542644, best rearrangement setting 5Bootstrap[56]: Time 4.412741 bootstrap likelihood -919.669892, best rearrangement setting 5Bootstrap[57]: Time 6.836956 bootstrap likelihood -909.568328, best rearrangement setting 5Bootstrap[58]: Time 4.191340 bootstrap likelihood -912.601449, best rearrangement setting 5Bootstrap[59]: Time 6.551357 bootstrap likelihood -1000.692107, best rearrangement setting 5Bootstrap[60]: Time 6.710285 bootstrap likelihood -954.570765, best rearrangement setting 5Bootstrap[61]: Time 6.919121 bootstrap likelihood -973.299791, best rearrangement setting 5Bootstrap[62]: Time 4.882708 bootstrap likelihood -952.977251, best rearrangement setting 5Bootstrap[63]: Time 4.215316 bootstrap likelihood -912.177606, best rearrangement setting 5Bootstrap[64]: Time 4.816869 bootstrap likelihood -883.409272, best rearrangement setting 5Bootstrap[65]: Time 6.539172 bootstrap likelihood -933.777655, best rearrangement setting 5Bootstrap[66]: Time 3.669448 bootstrap likelihood -888.725950, best rearrangement setting 5Bootstrap[67]: Time 4.673647 bootstrap likelihood -913.083740, best rearrangement setting 5Bootstrap[68]: Time 5.416815 bootstrap likelihood -968.172804, best rearrangement setting 5Bootstrap[69]: Time 6.510670 bootstrap likelihood -896.150828, best rearrangement setting 5Bootstrap[70]: Time 7.401931 bootstrap likelihood -889.933766, best rearrangement setting 5Bootstrap[71]: Time 4.334268 bootstrap likelihood -924.481733, best rearrangement setting 5Bootstrap[72]: Time 5.878819 bootstrap likelihood -925.053507, best rearrangement setting 5Bootstrap[73]: Time 4.254023 bootstrap likelihood -897.488926, best rearrangement setting 5Bootstrap[74]: Time 6.893060 bootstrap likelihood -956.786310, best rearrangement setting 5Bootstrap[75]: Time 4.121044 bootstrap likelihood -902.303930, best rearrangement setting 5Bootstrap[76]: Time 6.073197 bootstrap likelihood -890.181046, best rearrangement setting 5Bootstrap[77]: Time 3.600885 bootstrap likelihood -975.252795, best rearrangement setting 5Bootstrap[78]: Time 6.296647 bootstrap likelihood -964.925750, best rearrangement setting 5Bootstrap[79]: Time 5.095760 bootstrap likelihood -878.472804, best rearrangement setting 5Bootstrap[80]: Time 4.772661 bootstrap likelihood -948.993057, best rearrangement setting 5Bootstrap[81]: Time 4.307154 bootstrap likelihood -937.825568, best rearrangement setting 5Bootstrap[82]: Time 7.498208 bootstrap likelihood -894.147717, best rearrangement setting 5Bootstrap[83]: Time 4.173288 bootstrap likelihood -928.766163, best rearrangement setting 5Bootstrap[84]: Time 6.629044 bootstrap likelihood -918.689270, best rearrangement setting 5Bootstrap[85]: Time 6.110813 bootstrap likelihood -915.460466, best rearrangement setting 5Bootstrap[86]: Time 7.230430 bootstrap likelihood -934.588062, best rearrangement setting 5Bootstrap[87]: Time 4.140006 bootstrap likelihood -948.665279, best rearrangement setting 5Bootstrap[88]: Time 6.260682 bootstrap likelihood -897.920763, best rearrangement setting 5Bootstrap[89]: Time 6.770371 bootstrap likelihood -894.697570, best rearrangement setting 5Bootstrap[90]: Time 6.459816 bootstrap likelihood -902.838959, best rearrangement setting 5Bootstrap[91]: Time 4.362496 bootstrap likelihood -849.318935, best rearrangement setting 5Bootstrap[92]: Time 4.624116 bootstrap likelihood -983.624119, best rearrangement setting 5Bootstrap[93]: Time 6.817315 bootstrap likelihood -884.268171, best rearrangement setting 5Bootstrap[94]: Time 6.394809 bootstrap likelihood -917.925196, best rearrangement setting 5Bootstrap[95]: Time 3.812187 bootstrap likelihood -916.863812, best rearrangement setting 5Bootstrap[96]: Time 4.042018 bootstrap likelihood -886.461984, best rearrangement setting 5Bootstrap[97]: Time 4.074061 bootstrap likelihood -930.660544, best rearrangement setting 5Bootstrap[98]: Time 4.403471 bootstrap likelihood -883.403091, best rearrangement setting 5Bootstrap[99]: Time 3.700914 bootstrap likelihood -902.686012, best rearrangement setting 5Overall Time for 100 Bootstraps 527.781239Average Time per Bootstrap 5.277812All 100 bootstrapped trees written to: /root/exp_SciPhy2/exp/raxml/235/RAxML_bootstrap.ORTHOMCL1973.phylip_tree2.raxmlraxmlHPC -f b -m PROTGAMMARTREV -c 4 -s ORTHOMCL1973.phylip -z RAxML_bootstrap.ORTHOMCL1973.phylip_tree2.raxml -t RAxML_bestTree.ORTHOMCL1973.phylip_raxml_tree1.singleTree -n ORTHOMCL1973.phylip_tree3.BS_TREE -p 1Found a total of 10 taxa in first tree of tree collection RAxML_bootstrap.ORTHOMCL1973.phylip_tree2.raxmlExpecting all remaining trees in collection to have the same taxon setYou are using RAxML version 7.2.2 released by Alexandros Stamatakis in August 2009RAxML Bipartition Computation: Drawing support values from trees in file RAxML_bootstrap.ORTHOMCL1973.phylip_tree2.raxml onto tree in file RAxML_bestTree.ORTHOMCL1973.phylip_raxml_tree1.singleTreeRAxML was called as follows:/usr/local/bin/raxmlHPC -f b -m PROTGAMMARTREV -c 4 -s ORTHOMCL1973.phylip -z RAxML_bootstrap.ORTHOMCL1973.phylip_tree2.raxml -t RAxML_bestTree.ORTHOMCL1973.phylip_raxml_tree1.singleTree -n ORTHOMCL1973.phylip_tree3.BS_TREE -p 1 Found 100 trees in File RAxML_bootstrap.ORTHOMCL1973.phylip_tree2.raxmlTime for Computation of Bipartitions 0.467121Tree with bipartitions written to file: /root/exp_SciPhy2/exp/raxml/235/RAxML_bipartitions.ORTHOMCL1973.phylip_tree3.BS_TREETree with bipartitions as branch labels written to file: /root/exp_SciPhy2/exp/raxml/235/RAxML_bipartitionsBranchLabels.ORTHOMCL1973.phylip_tree3.BS_TREEExecution information file written to : /root/exp_SciPhy2/exp/raxml/235/RAxML_info.ORTHOMCL1973.phylip_tree3.BS_TREE",starttime:"2015-10-08 01:08:44.585+00",endtime:"2015-10-08 01:17:50.87+00",status:"FINISHED",extractor:"./extractor.cmd"});

It does not seem to me that the problem is caused by the size of the Document.

For example, when I divide the string (field called tout) in different parts and assign it to a variable in NoSQLManager, the error does not occur.

Maybe the problem is caused by a character contained in the string, but I am not sure.

Can somebody help me with this problem?

Best regards



 Comments   
Comment by Kelsey Schubert [ 20/Nov/15 ]

Hi rnlaigner,

Thanks for your report. Please note that SERVER project is for reporting bugs or feature suggestions for the MongoDB server.
For MongoDB-related support discussion please post on the mongodb-users group
or Stack Overflow with the mongodb tag.
A question like this involving more discussion would be best posted on the mongodb-users group.

Kind Regards,
Thomas

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