#1 BLAST & HMMER Issues
Dear merlin-Devs,
I started using merlin this week to reconstruct the genome of an organism, but I am bumping into errors and some inconveniences that prevent me from progressing beyond the (re)annotation.
HMMER
First of all I tried running HMMER with the standard parameters, which resulted in error messages like the following being displayed in the console. The progress bar did not fill up, and the remaining time got stuck at "00":
URL null class pt.uminho.sysbio.merlin.core.alignment.hmmer.SubmitHMMER exception. Reprocessing WP_010960311.1 RNA-binding protein [Methylococcus capsulatus]. counter:4 <!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN"> <html><head> <title>301 Moved Permanently</title> </head><body> <h1>Moved Permanently</h1> <p>The document has moved <a href="http://www.ebi.ac.uk/Tools/hmmer/search/phmmer">here</a>.</p> <hr> <address>Apache/2.2.3 (Scientific Linux) Server at hmmer.janelia.org Port 80</address> </body></html>
BLAST
Since I saw no changes in the Homology Data Sheet, I tried switching over to using BLAST (NCBI) instead, keeping the standard parameters except for the time . This time the progress bar filled up slowly and the counter showed a remaining time, albeit a very very long one (+150 hours).
After approximately 60 minutes of runtime the BLAST failed showing the following output in the console:
[Fine] Unable to find class in Plugin "pt.uminho.sysbio.merlin.core": pt.uminho.sysbio.common.bioapis.externalAPI.ncbi.CreateGenomeFile
[Fine] Unable to find class in dependent Plugin "AIBench Workbench": pt.uminho.sysbio.common.bioapis.externalAPI.ncbi.CreateGenomeFile
[Fine] Unable to find class in dependent Plugin "AIBench Core": pt.uminho.sysbio.common.bioapis.externalAPI.ncbi.CreateGenomeFile
[Fine] Found class in parent loader: pt.uminho.sysbio.common.bioapis.externalAPI.ncbi.CreateGenomeFile
[Fine] Found class in Plugin "pt.uminho.sysbio.merlin.core": pt.uminho.sysbio.merlin.core.alignment.SearchAndLoadHomologueSequences
[Fine] Found class in Plugin "pt.uminho.sysbio.merlin.core": pt.uminho.sysbio.merlin.core.alignment.SearchAndLoadHomologueSequences$Source
[Fine] Unable to find class in Plugin "pt.uminho.sysbio.merlin.core": pt.uminho.sysbio.common.local.alignments.core.PairwiseSequenceAlignement$Matrix
[Fine] Unable to find class in dependent Plugin "AIBench Workbench": pt.uminho.sysbio.common.local.alignments.core.PairwiseSequenceAlignement$Matrix
[Fine] Unable to find class in dependent Plugin "AIBench Core": pt.uminho.sysbio.common.local.alignments.core.PairwiseSequenceAlignement$Matrix
[Fine] Found class in parent loader: pt.uminho.sysbio.common.local.alignments.core.PairwiseSequenceAlignement$Matrix
BLOSUM62 size 2777
[Fine] Found class in Plugin "pt.uminho.sysbio.merlin.core": pt.uminho.sysbio.merlin.core.alignment.blast.org.biojava3.ws.alignment.qblast.NCBIQBlastAlignmentProperties
[Fine] Found class in Plugin "pt.uminho.sysbio.merlin.core": pt.uminho.sysbio.merlin.core.alignment.blast.org.biojava3.ws.alignment.qblast.NcbiBlastService
[Fine] Unable to find class in Plugin "pt.uminho.sysbio.merlin.core": org.apache.axis2.AxisFault
[Fine] Unable to find class in dependent Plugin "AIBench Workbench": org.apache.axis2.AxisFault
[Fine] Unable to find class in dependent Plugin "AIBench Core": org.apache.axis2.AxisFault
[Fine] Found class in parent loader: org.apache.axis2.AxisFault
[Fine] Found class in Plugin "pt.uminho.sysbio.merlin.core": pt.uminho.sysbio.merlin.core.alignment.blast.org.biojava3.ws.alignment.RemotePairwiseAlignmentOutputProperties
[Fine] Found class in Plugin "pt.uminho.sysbio.merlin.core": pt.uminho.sysbio.merlin.core.alignment.blast.org.biojava3.ws.alignment.qblast.NCBIQBlastOutputProperties
[Fine] Found class in Plugin "pt.uminho.sysbio.merlin.core": pt.uminho.sysbio.merlin.core.alignment.blast.org.biojava3.ws.alignment.qblast.NCBIQBlastOutputFormat
Start 0
Start 1
Start 2
SubmitBLAST Thread-43 100 started.
SubmitBLAST Thread-44 101 started.
Start 3
SubmitBLAST Thread-45 102 started.
Start 4
Sleeping...65000 mSec RID RJUT392S015
Sleeping...64999 mSec RID RJUSZJ5G015
Sleeping...64999 mSec RID RJUT1K09015
Start 5
SubmitBLAST Thread-46 103 started.
SubmitBLAST Thread-47 104 started.
Start 6
Sleeping...65000 mSec RID RJUT43B6015
Sleeping...65000 mSec RID RJUT6VGT015
SubmitBLAST Thread-48 105 started.
Start 7
SubmitBLAST Thread-49 106 started.
Sleeping...65000 mSec RID RJUT74G8015
Start 8
Sleeping...65000 mSec RID RJUTATWT015
SubmitBLAST Thread-50 107 started.
Start 9
SubmitBLAST Thread-51 108 started.
Sleeping...65000 mSec RID RJUTCCBK014
Start 10
Sleeping...65000 mSec RID RJUTDTZR014
SubmitBLAST Thread-52 109 started.
Start 11
Sleeping...65000 mSec RID RJUTEJ15015
SubmitBLAST Thread-53 110 started.
Start 12
SubmitBLAST Thread-54 111 started.
Sleeping...65000 mSec RID RJUTJ5RR014
Start 13
Sleeping...65000 mSec RID RJUTK7ER014
SubmitBLAST Thread-55 112 started.
Start 14
Sleeping...65000 mSec RID RJUTMXA3015
SubmitBLAST Thread-56 113 started.
Start 15
SubmitBLAST Thread-57 114 started.
Sleeping...65000 mSec RID RJUTNSHC015
Sleeping...65000 mSec RID RJUTPD2U015
SubmitBLAST Thread-58 115 started.
Sleeping...65000 mSec RID RJUTR68R01R
Sleeping...64573 mSec RID RJUUDYNS014
Sleeping...64561 mSec RID RJUV0R99014
Sleeping...64559 mSec RID RJUUXW5J015
Sleeping...64549 mSec RID RJUV3CBF014
Sleeping...64545 mSec RID RJUUR71N015
Sleeping...64538 mSec RID RJUUV770015
Sleeping...64537 mSec RID RJUUU31Z015
Sleeping...64525 mSec RID RJUUJUW6015
Sleeping...64513 mSec RID RJUUNVK9015
Sleeping...64510 mSec RID RJUUTZJW015
Sleeping...64396 mSec RID RJUUGAMH014
Sleeping...64386 mSec RID RJUV16X7015
Sleeping...64382 mSec RID RJUUKK15015
[Fine] Found class in Plugin "pt.uminho.sysbio.merlin.core": pt.uminho.sysbio.merlin.core.alignment.blast.ReadBlasttoList
[Fine] Unable to find class in Plugin "pt.uminho.sysbio.merlin.core": org.biojava.bio.seq.db.SequenceDBInstallation
[Fine] Unable to find class in dependent Plugin "AIBench Workbench": org.biojava.bio.seq.db.SequenceDBInstallation
[Fine] Unable to find class in dependent Plugin "AIBench Core": org.biojava.bio.seq.db.SequenceDBInstallation
[Fine] Found class in parent loader: org.biojava.bio.seq.db.SequenceDBInstallation
[Fine] Unable to find class in Plugin "pt.uminho.sysbio.merlin.core": org.biojava.bio.seq.db.SequenceDB
[Fine] Unable to find class in dependent Plugin "AIBench Workbench": org.biojava.bio.seq.db.SequenceDB
[Fine] Unable to find class in dependent Plugin "AIBench Core": org.biojava.bio.seq.db.SequenceDB
[Fine] Found class in parent loader: org.biojava.bio.seq.db.SequenceDB
[Fine] Unable to find class in Plugin "pt.uminho.sysbio.merlin.core": org.biojava.bio.search.SearchContentHandler
[Fine] Unable to find class in dependent Plugin "AIBench Workbench": org.biojava.bio.search.SearchContentHandler
[Fine] Unable to find class in dependent Plugin "AIBench Core": org.biojava.bio.search.SearchContentHandler
[Fine] Found class in parent loader: org.biojava.bio.search.SearchContentHandler
[Fine] Unable to find class in Plugin "pt.uminho.sysbio.merlin.core": org.xml.sax.ContentHandler
[Fine] Unable to find class in dependent Plugin "AIBench Workbench": org.xml.sax.ContentHandler
[Fine] Unable to find class in dependent Plugin "AIBench Core": org.xml.sax.ContentHandler
[Fine] Found class in parent loader: org.xml.sax.ContentHandler
[Fine] Found class in Plugin "pt.uminho.sysbio.merlin.core": pt.uminho.sysbio.merlin.core.alignment.blast.CheckBlastResult
[Fine] Unable to find class in Plugin "pt.uminho.sysbio.merlin.core": org.xml.sax.InputSource
[Fine] Unable to find class in dependent Plugin "AIBench Workbench": org.xml.sax.InputSource
[Fine] Unable to find class in dependent Plugin "AIBench Core": org.xml.sax.InputSource
[Fine] Found class in parent loader: org.xml.sax.InputSource
[Fine] Unable to find class in Plugin "pt.uminho.sysbio.merlin.core": org.biojava.bio.program.sax.BlastLikeSAXParser
[Fine] Unable to find class in dependent Plugin "AIBench Workbench": org.biojava.bio.program.sax.BlastLikeSAXParser
[Fine] Unable to find class in dependent Plugin "AIBench Core": org.biojava.bio.program.sax.BlastLikeSAXParser
[Fine] Found class in parent loader: org.biojava.bio.program.sax.BlastLikeSAXParser
[Fine] Unable to find class in Plugin "pt.uminho.sysbio.merlin.core": org.biojava.bio.program.ssbind.SeqSimilarityAdapter
[Fine] Unable to find class in dependent Plugin "AIBench Workbench": org.biojava.bio.program.ssbind.SeqSimilarityAdapter
[Fine] Unable to find class in dependent Plugin "AIBench Core": org.biojava.bio.program.ssbind.SeqSimilarityAdapter
[Fine] Found class in parent loader: org.biojava.bio.program.ssbind.SeqSimilarityAdapter
[Fine] Unable to find class in Plugin "pt.uminho.sysbio.merlin.core": org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
[Fine] Unable to find class in dependent Plugin "AIBench Workbench": org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
[Fine] Unable to find class in dependent Plugin "AIBench Core": org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
[Fine] Found class in parent loader: org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
[Fine] Unable to find class in Plugin "pt.uminho.sysbio.merlin.core": org.biojava.bio.seq.db.DummySequenceDB
[Fine] Unable to find class in dependent Plugin "AIBench Workbench": org.biojava.bio.seq.db.DummySequenceDB
[Fine] Unable to find class in dependent Plugin "AIBench Core": org.biojava.bio.seq.db.DummySequenceDB
[Fine] Found class in parent loader: org.biojava.bio.seq.db.DummySequenceDB
[Fine] Unable to find class in Plugin "pt.uminho.sysbio.merlin.core": org.biojava.bio.seq.db.DummySequenceDBInstallation
[Fine] Unable to find class in dependent Plugin "AIBench Workbench": org.biojava.bio.seq.db.DummySequenceDBInstallation
[Fine] Unable to find class in dependent Plugin "AIBench Core": org.biojava.bio.seq.db.DummySequenceDBInstallation
[Fine] Found class in parent loader: org.biojava.bio.seq.db.DummySequenceDBInstallation
[Fine] Unable to find class in Plugin "pt.uminho.sysbio.merlin.core": org.biojava.bio.search.SeqSimilaritySearchResult
[Fine] Unable to find class in dependent Plugin "AIBench Workbench": org.biojava.bio.search.SeqSimilaritySearchResult
[Fine] Unable to find class in dependent Plugin "AIBench Core": org.biojava.bio.search.SeqSimilaritySearchResult
[Fine] Found class in parent loader: org.biojava.bio.search.SeqSimilaritySearchResult
[Fine] Unable to find class in Plugin "pt.uminho.sysbio.merlin.core": org.biojava.bio.Annotation
[Fine] Unable to find class in dependent Plugin "AIBench Workbench": org.biojava.bio.Annotation
[Fine] Unable to find class in dependent Plugin "AIBench Core": org.biojava.bio.Annotation
[Fine] Found class in parent loader: org.biojava.bio.Annotation
[Fine] Found class in Plugin "pt.uminho.sysbio.merlin.core": pt.uminho.sysbio.merlin.core.alignment.HomologyDataClient
[Fine] Found class in Plugin "pt.uminho.sysbio.merlin.core": pt.uminho.sysbio.merlin.core.alignment.HomologyDataClient$HomologySearchServer
[Fine] Unable to find class in Plugin "pt.uminho.sysbio.merlin.core": pt.uminho.sysbio.common.bioapis.externalAPI.datatypes.HomologuesData
[Fine] Unable to find class in dependent Plugin "AIBench Workbench": pt.uminho.sysbio.common.bioapis.externalAPI.datatypes.HomologuesData
[Fine] Unable to find class in dependent Plugin "AIBench Core": pt.uminho.sysbio.common.bioapis.externalAPI.datatypes.HomologuesData
[Fine] Found class in parent loader: pt.uminho.sysbio.common.bioapis.externalAPI.datatypes.HomologuesData
[Fine] Unable to find class in Plugin "pt.uminho.sysbio.merlin.core": pt.uminho.sysbio.common.bioapis.externalAPI.uniprot.EntryData
[Fine] Unable to find class in dependent Plugin "AIBench Workbench": pt.uminho.sysbio.common.bioapis.externalAPI.uniprot.EntryData
[Fine] Unable to find class in dependent Plugin "AIBench Core": pt.uminho.sysbio.common.bioapis.externalAPI.uniprot.EntryData
[Fine] Found class in parent loader: pt.uminho.sysbio.common.bioapis.externalAPI.uniprot.EntryData
[Fine] Unable to find class in Plugin "pt.uminho.sysbio.merlin.core": pt.uminho.sysbio.common.bioapis.externalAPI.ncbi.NcbiAPI
[Fine] Unable to find class in dependent Plugin "AIBench Workbench": pt.uminho.sysbio.common.bioapis.externalAPI.ncbi.NcbiAPI
[Fine] Unable to find class in dependent Plugin "AIBench Core": pt.uminho.sysbio.common.bioapis.externalAPI.ncbi.NcbiAPI
[Fine] Found class in parent loader: pt.uminho.sysbio.common.bioapis.externalAPI.ncbi.NcbiAPI
[13:06:28,628] [Thread-44] WARN org.apache.axiom.util.stax.dialect.StAXDialectDetector - Unable to determine dialect of the StAX implementation at jar:file:/Users/clie/Desktop/EFPro2/merlin-unix/lib/jsbml-1.0-a3.jar!/
[Fine] Unable to find class in Plugin "pt.uminho.sysbio.merlin.core": org.biojava.bio.search.SeqSimilaritySearchHit
[Fine] Unable to find class in dependent Plugin "AIBench Workbench": org.biojava.bio.search.SeqSimilaritySearchHit
[Fine] Unable to find class in dependent Plugin "AIBench Core": org.biojava.bio.search.SeqSimilaritySearchHit
[Fine] Found class in parent loader: org.biojava.bio.search.SeqSimilaritySearchHit
[Fine] Found class in Plugin "pt.uminho.sysbio.merlin.core": pt.uminho.sysbio.merlin.core.alignment.LoadSimilarityResultstoDatabase
[Fine] Unable to find class in Plugin "pt.uminho.sysbio.merlin.core": pt.uminho.sysbio.common.database.connector.datatypes.MySQL_Utilities
[Fine] Unable to find class in dependent Plugin "AIBench Workbench": pt.uminho.sysbio.common.database.connector.datatypes.MySQL_Utilities
[Fine] Unable to find class in dependent Plugin "AIBench Core": pt.uminho.sysbio.common.database.connector.datatypes.MySQL_Utilities
[Fine] Found class in parent loader: pt.uminho.sysbio.common.database.connector.datatypes.MySQL_Utilities
Gene WP_041360687 processed. 3 genes left in cue 2
Sleeping...46465 mSec RID RJUUEM7F014
Gene MCA1875 processed. 3 genes left in cue 1
Sleeping...44938 mSec RID RJUUDK02014
Gene WP_041360574 processed. 2 genes left in cue 3
Sleeping...39410 mSec RID RJUUF36X014
Sleeping...64519 mSec RID RJUT392S015
Sleeping...64488 mSec RID RJUU59SS01R
Sleeping...64384 mSec RID RJUSZJ5G015
Sleeping...64225 mSec RID RJUU6GYB01R
Sleeping...64199 mSec RID RJUT1K09015
Sleeping...64150 mSec RID RJUUBZFA014
Sleeping...64142 mSec RID RJUU42EM01R
Sleeping...64129 mSec RID RJUU7XYV01R
Sleeping...64125 mSec RID RJUTXK7601R
Sleeping...64120 mSec RID RJUU1Z9B01R
Sleeping...64116 mSec RID RJUUF36X014
Sleeping...64107 mSec RID RJUTZAWM01R
Sleeping...64100 mSec RID RJUU8DYF014
Gene MCA1295 processed. 2 genes left in cue 7
Sleeping...56514 mSec RID RJUU2TTA01R
Trial EFetchResult 0 for request 499262637,515934268,493947225,652888728,670489027,670486050,651616749,771612656,519002924,652904424,495317369,697080249,521973001,515998971,750570050,349794181,654480474,548426608,752303934,496592263,654488941,518704406,655019492,703298849,675593225,496011686,516224371,746116954,517043950,739101577,654379950,521993498,651608432,501335919,490367712,800967903,490372681,529187213,557401985,739038821,529141056,517748687,737614991,653087317,490365172,504817795,738755624,654374349,494174531,737884167,398208840,738302696,738976616,491015186,584384863,495165531,745784761,759817100,759832715,496244240,812676361,759383595,648220824,544759344,685059490,490857245,648608946,498010260,494079705,737584842,797165657,522054222,749636747,750562165,595640032,755598194,736566303,755308594,343921903,737434928,702351318,491516559,503275723,746334588,490844786,653099396,377816307,727281623,639215863,497410705,635652695,802312619,499825096,739543417,670481560,522170789,518197077,727329158,746292108
Gene MCA1982 processed. 2 genes left in cue 8
Sleeping...42789 mSec RID RJUU3XZN01R
Gene MCA0857 processed. 2 genes left in cue 15
Sleeping...38891 mSec RID RJUUCY3Y014
Sleeping...64578 mSec RID RJUV7VNG014
Sleeping...64566 mSec RID RJUUCY3Y014
Sleeping...64563 mSec RID RJUTNSHC015
Sleeping...64560 mSec RID RJUUDYNS014
Sleeping...64548 mSec RID RJUV6BPN014
Sleeping...64545 mSec RID RJUT6VGT015
Sleeping...64313 mSec RID RJUUF36X014
Sleeping...64313 mSec RID RJUTK7ER014
Sleeping...64295 mSec RID RJUT74G8015
Sleeping...64292 mSec RID RJUTJ5RR014
Sleeping...64292 mSec RID RJUTEJ15015
Sleeping...64280 mSec RID RJUU2TTA01R
Sleeping...64276 mSec RID RJUU3XZN01R
Sleeping...64267 mSec RID RJUTPD2U015
Sleeping...64263 mSec RID RJUTMXA3015
Sleeping...64247 mSec RID RJUTATWT015
Sleeping...64550 mSec RID RJUU3XZN01R
Sleeping...64546 mSec RID RJUUF36X014
Sleeping...64526 mSec RID RJUUV770015
Sleeping...64510 mSec RID RJUUU31Z015
Sleeping...64133 mSec RID RJUUXW5J015
Sleeping...64127 mSec RID RJUUKK15015
Sleeping...64119 mSec RID RJUUGAMH014
Sleeping...64116 mSec RID RJUUJUW6015
Sleeping...64106 mSec RID RJUUTZJW015
Sleeping...63989 mSec RID RJUU2TTA01R
Sleeping...63920 mSec RID RJUUCY3Y014
Sleeping...62187 mSec RID RJUV0R99014
Sleeping...60827 mSec RID RJUSZJ5G015
Sleeping...60814 mSec RID RJUV16X7015
Gene MCA1732 processed. 2 genes left in cue 2
Sleeping...56679 mSec RID RJUUEM7F014
Gene MCA2039 processed. 2 genes left in cue 1
Sleeping...51144 mSec RID RJUUDK02014
Sleeping...64686 mSec RID RJUU3XZN01R
Sleeping...64678 mSec RID RJUU2TTA01R
Sleeping...64667 mSec RID RJUUEM7F014
Sleeping...64654 mSec RID RJUUDK02014
Sleeping...64642 mSec RID RJUUCY3Y014
Sleeping...64577 mSec RID RJUUDYNS014
Gene MCA2273 processed. 2 genes left in cue 10
Sleeping...64579 mSec RID RJUUDK02014
Sleeping...64577 mSec RID RJUUEM7F014
Sleeping...64571 mSec RID RJUSZJ5G015
Timeout for rid waiting exceeded! Skiping RID RJUUV770015
Timeout for rid waiting exceeded! Skiping RID RJUTK7ER014
Timeout for rid waiting exceeded! Skiping RID RJUU6GYB01R
SubmitBLAST Thread-54 111 ended!
Timeout for rid waiting exceeded! Skiping RID RJUUKK15015
Timeout for rid waiting exceeded! Skiping RID RJUTATWT015
Timeout for rid waiting exceeded! Skiping RID RJUU1Z9B01R
SubmitBLAST Thread-49 106 ended!
Timeout for rid waiting exceeded! Skiping RID RJUUGAMH014
Timeout for rid waiting exceeded! Skiping RID RJUT6VGT015
Timeout for rid waiting exceeded! Skiping RID RJUTXK7601R
SubmitBLAST Thread-47 104 ended!
Timeout for rid waiting exceeded! Skiping RID RJUUXW5J015
Timeout for rid waiting exceeded! Skiping RID RJUTMXA3015
Timeout for rid waiting exceeded! Skiping RID RJUU7XYV01R
SubmitBLAST Thread-55 112 ended!
Timeout for rid waiting exceeded! Skiping RID RJUV0R99014
Timeout for rid waiting exceeded! Skiping RID RJUTNSHC015
Timeout for rid waiting exceeded! Skiping RID RJUU8DYF014
SubmitBLAST Thread-56 113 ended!
Timeout for rid waiting exceeded! Skiping RID RJUUJUW6015
Timeout for rid waiting exceeded! Skiping RID RJUT74G8015
Timeout for rid waiting exceeded! Skiping RID RJUTZAWM01R
SubmitBLAST Thread-48 105 ended!
Timeout for rid waiting exceeded! Skiping RID RJUV16X7015
Timeout for rid waiting exceeded! Skiping RID RJUTPD2U015
Timeout for rid waiting exceeded! Skiping RID RJUUBZFA014
SubmitBLAST Thread-57 114 ended!
Timeout for rid waiting exceeded! Skiping RID RJUT43B6015
Timeout for rid waiting exceeded! Skiping RID RJUUTZJW015
Timeout for rid waiting exceeded! Skiping RID RJUTEJ15015
Timeout for rid waiting exceeded! Skiping RID RJUU42EM01R
SubmitBLAST Thread-52 109 ended!
Timeout for rid waiting exceeded! Skiping RID RJUUU31Z015
Timeout for rid waiting exceeded! Skiping RID RJUU59SS01R
SubmitBLAST Thread-53 110 ended!
Timeout for rid waiting exceeded! Skiping RID RJUUNVK9015
Timeout for rid waiting exceeded! Skiping RID RJUU2TTA01R
SubmitBLAST Thread-50 107 ended!
Timeout for rid waiting exceeded! Skiping RID RJUUR71N015
Timeout for rid waiting exceeded! Skiping RID RJUU3XZN01R
SubmitBLAST Thread-51 108 ended!
Timeout for rid waiting exceeded! Skiping RID RJUV3CBF014
Timeout for rid waiting exceeded! Skiping RID RJUUCY3Y014
SubmitBLAST Thread-58 115 ended!
Timeout for rid waiting exceeded! Skiping RID RJUUEM7F014
Timeout for rid waiting exceeded! Skiping RID RJUV7VNG014
SubmitBLAST Thread-45 102 ended!
Timeout for rid waiting exceeded! Skiping RID RJUUDK02014
Timeout for rid waiting exceeded! Skiping RID RJUV6BPN014
SubmitBLAST Thread-44 101 ended!
Timeout for rid waiting exceeded! Skiping RID RJUUDYNS014
Timeout for rid waiting exceeded! Skiping RID RJUV5NZF014
Timeout for rid waiting exceeded! Skiping RID RJUSZJ5G015
Timeout for rid waiting exceeded! Skiping RID RJUTSP07014
SubmitBLAST Thread-43 100 ended!
Timeout for rid waiting exceeded! Skiping RID RJUUF36X014
SubmitBLAST Thread-46 103 ended!
Start 0
Start 1
SubmitBLAST Thread-59 137 started.
Start 2
Sleeping...65000 mSec RID RJVPA3WE014
SubmitBLAST Thread-60 138 started.
Start 3
Sleeping...65000 mSec RID RJVPCXNY015
SubmitBLAST Thread-61 139 started.
Start 4
Sleeping...65000 mSec RID RJVPDM70015
SubmitBLAST Thread-62 140 started.
Sleeping...65000 mSec RID RJVPE36D014
Start 5
SubmitBLAST Thread-63 141 started.
Sleeping...65000 mSec RID RJVPHUW7015
Start 6
SubmitBLAST Thread-64 142 started.
Sleeping...65000 mSec RID RJVPJGM1014
Start 7
SubmitBLAST Thread-65 143 started.
Sleeping...64999 mSec RID RJVPMZXW015
Start 8
SubmitBLAST Thread-66 144 started.
Sleeping...65000 mSec RID RJVPPS6D01R
Start 9
SubmitBLAST Thread-67 145 started.
Start 10
Sleeping...65000 mSec RID RJVPS2NH01R
SubmitBLAST Thread-68 146 started.
Start 11
SubmitBLAST Thread-69 147 started.
Sleeping...65000 mSec RID RJVPUHE401R
Sleeping...65000 mSec RID RJVPVP0101R
Start 12
SubmitBLAST Thread-70 148 started.
Sleeping...65000 mSec RID RJVPW2GK01R
Start 13
SubmitBLAST Thread-71 149 started.
Sleeping...65000 mSec RID RJVPXKZF01R
Start 14
SubmitBLAST Thread-72 150 started.
Start 15
SubmitBLAST Thread-73 151 started.
Sleeping...65000 mSec RID RJVPYB0201R
Sleeping...65000 mSec RID RJVPZRNY01R
SubmitBLAST Thread-74 152 started.
Sleeping...65000 mSec RID RJVR4C8X015
Sleeping...64531 mSec RID RJVSSK76015
Sleeping...64528 mSec RID RJVSB8TG01R
Sleeping...64517 mSec RID RJVSGPZW014
Sleeping...64516 mSec RID RJVS9HC201R
Sleeping...64505 mSec RID RJVSFTAA01R
Sleeping...64505 mSec RID RJVSV1Y6015
Sleeping...63992 mSec RID RJVS84Y801R
Sleeping...63978 mSec RID RJVSDCH301R
Sleeping...63976 mSec RID RJVSHXYW014
Sleeping...63968 mSec RID RJVSRSXX015
Sleeping...63961 mSec RID RJVSUGPE015
Sleeping...63959 mSec RID RJVSPSRZ014
Sleeping...63954 mSec RID RJVSMCP7014
Sleeping...63942 mSec RID RJVSJMDH014
Sleeping...63934 mSec RID RJVSKX64014
Sleeping...63928 mSec RID RJVSC1S001R
Sleeping...64694 mSec RID RJVRNZUG014
Sleeping...64667 mSec RID RJVRFUVX015
Sleeping...64642 mSec RID RJVRVGUA015
Sleeping...64635 mSec RID RJVRYZ8X015
Sleeping...64620 mSec RID RJVPCXNY015
Sleeping...64617 mSec RID RJVS3DUR015
Sleeping...64607 mSec RID RJVRZFX7015
Sleeping...64605 mSec RID RJVRWBDW015
Sleeping...64601 mSec RID RJVS1DKF015
Sleeping...64592 mSec RID RJVRXD60015
Sleeping...64584 mSec RID RJVS25D001R
Sleeping...64110 mSec RID RJVPA3WE014
Sleeping...64095 mSec RID RJVPDM70015
Sleeping...64091 mSec RID RJVRU4G8014
Sleeping...64089 mSec RID RJVRH691015
Sleeping...64077 mSec RID RJVS5XV501R
Sleeping...64674 mSec RID RJVPUHE401R
Sleeping...64671 mSec RID RJVPW2GK01R
Sleeping...64659 mSec RID RJVPPS6D01R
Sleeping...64656 mSec RID RJVS9HC201R
Sleeping...64647 mSec RID RJVPMZXW015
Sleeping...64640 mSec RID RJVPVP0101R
Sleeping...64634 mSec RID RJVPE36D014
Sleeping...64629 mSec RID RJVSB8TG01R
Sleeping...64623 mSec RID RJVPS2NH01R
Sleeping...64487 mSec RID RJVPHUW7015
Sleeping...64341 mSec RID RJVPXKZF01R
Sleeping...64340 mSec RID RJVPYB0201R
Sleeping...64329 mSec RID RJVPZRNY01R
Sleeping...64327 mSec RID RJVS84Y801R
Sleeping...64297 mSec RID RJVR4C8X015
Sleeping...64299 mSec RID RJVPJGM1014
Sleeping...64594 mSec RID RJVSFTAA01R
Sleeping...64562 mSec RID RJVSHXYW014
Sleeping...64542 mSec RID RJVSKX64014
Sleeping...64535 mSec RID RJVSMCP7014
Sleeping...64520 mSec RID RJVSDCH301R
Sleeping...64527 mSec RID RJVSC1S001R
Sleeping...64523 mSec RID RJVPDM70015
Sleeping...64513 mSec RID RJVSJMDH014
Sleeping...64512 mSec RID RJVSRSXX015
Sleeping...64493 mSec RID RJVSUGPE015
Sleeping...64485 mSec RID RJVPA3WE014
Sleeping...64488 mSec RID RJVSSK76015
Sleeping...64474 mSec RID RJVSV1Y6015
Sleeping...64463 mSec RID RJVSPSRZ014
Sleeping...64445 mSec RID RJVSGPZW014
Sleeping...64444 mSec RID RJVPCXNY015
Sleeping...64546 mSec RID RJVS84Y801R
Sleeping...64536 mSec RID RJVSB8TG01R
Sleeping...64372 mSec RID RJVS9HC201R
Sleeping...64672 mSec RID RJVPDM70015
Sleeping...64635 mSec RID RJVPA3WE014
Sleeping...64629 mSec RID RJVPCXNY015
Timeout for rid waiting exceeded! Skiping RID RJVSGPZW014
Timeout for rid waiting exceeded! Skiping RID RJVPMZXW015
Timeout for rid waiting exceeded! Skiping RID RJVRU4G8014
SubmitBLAST Thread-65 143 ended!
Timeout for rid waiting exceeded! Skiping RID RJVSFTAA01R
Timeout for rid waiting exceeded! Skiping RID RJVPJGM1014
Timeout for rid waiting exceeded! Skiping RID RJVRNZUG014
SubmitBLAST Thread-64 142 ended!
Timeout for rid waiting exceeded! Skiping RID RJVSV1Y6015
Timeout for rid waiting exceeded! Skiping RID RJVR4C8X015
Timeout for rid waiting exceeded! Skiping RID RJVS5XV501R
SubmitBLAST Thread-74 152 ended!
Timeout for rid waiting exceeded! Skiping RID RJVSSK76015
Timeout for rid waiting exceeded! Skiping RID RJVPYB0201R
Timeout for rid waiting exceeded! Skiping RID RJVS25D001R
SubmitBLAST Thread-72 150 ended!
Timeout for rid waiting exceeded! Skiping RID RJVSJMDH014
Timeout for rid waiting exceeded! Skiping RID RJVPS2NH01R
Timeout for rid waiting exceeded! Skiping RID RJVRWBDW015
SubmitBLAST Thread-67 145 ended!
Timeout for rid waiting exceeded! Skiping RID RJVSKX64014
Timeout for rid waiting exceeded! Skiping RID RJVPUHE401R
Timeout for rid waiting exceeded! Skiping RID RJVRXD60015
SubmitBLAST Thread-68 146 ended!
Timeout for rid waiting exceeded! Skiping RID RJVSPSRZ014
Timeout for rid waiting exceeded! Skiping RID RJVPW2GK01R
Timeout for rid waiting exceeded! Skiping RID RJVRZFX7015
SubmitBLAST Thread-70 148 ended!
Timeout for rid waiting exceeded! Skiping RID RJVSDCH301R
Timeout for rid waiting exceeded! Skiping RID RJVPHUW7015
Timeout for rid waiting exceeded! Skiping RID RJVRH691015
SubmitBLAST Thread-63 141 ended!
Timeout for rid waiting exceeded! Skiping RID RJVSUGPE015
Timeout for rid waiting exceeded! Skiping RID RJVPZRNY01R
Timeout for rid waiting exceeded! Skiping RID RJVS3DUR015
SubmitBLAST Thread-73 151 ended!
Timeout for rid waiting exceeded! Skiping RID RJVSRSXX015
Timeout for rid waiting exceeded! Skiping RID RJVPXKZF01R
Timeout for rid waiting exceeded! Skiping RID RJVS1DKF015
SubmitBLAST Thread-71 149 ended!
Timeout for rid waiting exceeded! Skiping RID RJVSC1S001R
Timeout for rid waiting exceeded! Skiping RID RJVPE36D014
Timeout for rid waiting exceeded! Skiping RID RJVRFUVX015
SubmitBLAST Thread-62 140 ended!
Timeout for rid waiting exceeded! Skiping RID RJVSMCP7014
Timeout for rid waiting exceeded! Skiping RID RJVPVP0101R
Timeout for rid waiting exceeded! Skiping RID RJVRYZ8X015
SubmitBLAST Thread-69 147 ended!
Timeout for rid waiting exceeded! Skiping RID RJVSHXYW014
Timeout for rid waiting exceeded! Skiping RID RJVPPS6D01R
Timeout for rid waiting exceeded! Skiping RID RJVRVGUA015
SubmitBLAST Thread-66 144 ended!
Timeout for rid waiting exceeded! Skiping RID RJVS84Y801R
Timeout for rid waiting exceeded! Skiping RID RJVSWJ2J015
Timeout for rid waiting exceeded! Skiping RID RJVPA3WE014
Timeout for rid waiting exceeded! Skiping RID RJVR54YM015
SubmitBLAST Thread-59 137 ended!
Timeout for rid waiting exceeded! Skiping RID RJVSB8TG01R
Timeout for rid waiting exceeded! Skiping RID RJVT2YVJ015
Timeout for rid waiting exceeded! Skiping RID RJVPDM70015
Timeout for rid waiting exceeded! Skiping RID RJVR8CV7014
SubmitBLAST Thread-61 139 ended!
Timeout for rid waiting exceeded! Skiping RID RJVS9HC201R
Timeout for rid waiting exceeded! Skiping RID RJVT1CNF01R
Timeout for rid waiting exceeded! Skiping RID RJVPCXNY015
Timeout for rid waiting exceeded! Skiping RID RJVR7VED014
SubmitBLAST Thread-60 138 ended!
Start 0
Start 1
SubmitBLAST Thread-75 172 started.
Start 2
Sleeping...65000 mSec RID RJWJKCU4015
SubmitBLAST Thread-76 173 started.
Start 3
Sleeping...65000 mSec RID RJWJN5C4015
SubmitBLAST Thread-77 174 started.
Start 4
SubmitBLAST Thread-78 175 started.
Sleeping...65000 mSec RID RJWJRD7V015
Sleeping...65000 mSec RID RJWJS8NM014
Start 5
SubmitBLAST Thread-79 176 started.
Sleeping...65000 mSec RID RJWJT5BD01R
Start 6
SubmitBLAST Thread-80 177 started.
Sleeping...65000 mSec RID RJWJXMXM01R
Start 7
SubmitBLAST Thread-81 178 started.
Sleeping...64999 mSec RID RJWJYGA801R
Start 8
SubmitBLAST Thread-82 179 started.
Sleeping...65000 mSec RID RJWK1YND01R
Start 9
SubmitBLAST Thread-83 180 started.
Sleeping...65000 mSec RID RJWK2P7V014
Start 10
SubmitBLAST Thread-84 181 started.
Sleeping...65000 mSec RID RJWK92WM014
Start 11
SubmitBLAST Thread-85 182 started.
Sleeping...65000 mSec RID RJWKK0SE014
Start 12
SubmitBLAST Thread-86 183 started.
Sleeping...65000 mSec RID RJWKSMSA015
Start 13
SubmitBLAST Thread-87 184 started.
Start 14
SubmitBLAST Thread-88 185 started.
Sleeping...65000 mSec RID RJWKVZ7U014
Sleeping...65000 mSec RID RJWKXAG401R
Start 15
SubmitBLAST Thread-89 186 started.
Sleeping...65000 mSec RID RJWKYUPN01R
SubmitBLAST Thread-90 187 started.
Sleeping...65000 mSec RID RJWM0Z4H01R
[Fine] Unable to find class in Plugin "pt.uminho.sysbio.merlin.core": pt.uminho.sysbio.merlin.utilities.Pair
[Fine] Unable to find class in dependent Plugin "AIBench Workbench": pt.uminho.sysbio.merlin.utilities.Pair
[Fine] Unable to find class in dependent Plugin "AIBench Core": pt.uminho.sysbio.merlin.utilities.Pair
[Fine] Found class in parent loader: pt.uminho.sysbio.merlin.utilities.Pair
[Fine] Unable to find class in Plugin "pt.uminho.sysbio.merlin.core": pt.uminho.sysbio.merlin.utilities.PairComparator
[Fine] Unable to find class in dependent Plugin "AIBench Workbench": pt.uminho.sysbio.merlin.utilities.PairComparator
[Fine] Unable to find class in dependent Plugin "AIBench Core": pt.uminho.sysbio.merlin.utilities.PairComparator
[Fine] Found class in parent loader: pt.uminho.sysbio.merlin.utilities.PairComparator
[Fine] Found class in Plugin "pt.uminho.sysbio.merlin.core": pt.uminho.sysbio.merlin.core.utilities.ComboBoxColumn$3
Sleeping...64583 mSec RID RJWN16DB014
Sleeping...64572 mSec RID RJWN4J5601R
Sleeping...64537 mSec RID RJWN7P5201R
Sleeping...64532 mSec RID RJWMX9TH014
Sleeping...64383 mSec RID RJWNSXEX01R
Sleeping...64367 mSec RID RJWMYTGS014
Sleeping...64362 mSec RID RJWN8AN4014
Sleeping...64359 mSec RID RJWNP9SM01R
Sleeping...64358 mSec RID RJWNVTB501R
Sleeping...64355 mSec RID RJWNXWRE01R
Sleeping...64344 mSec RID RJWN071T014
Sleeping...64321 mSec RID RJWNR0C601R
Sleeping...64321 mSec RID RJWNW2B101R
Sleeping...64310 mSec RID RJWNM2W401R
Sleeping...64308 mSec RID RJWNKFGB01R
Sleeping...64300 mSec RID RJWNTK1X01R
Sleeping...64605 mSec RID RJWMKSHS014
Sleeping...64602 mSec RID RJWMGAES014
Sleeping...64596 mSec RID RJWMJVNG014
Sleeping...64583 mSec RID RJWMR4AH014
Sleeping...64573 mSec RID RJWM978K015
Sleeping...64559 mSec RID RJWJRD7V015
Sleeping...64562 mSec RID RJWMN6JE014
Sleeping...64541 mSec RID RJWJN5C4015
Sleeping...64538 mSec RID RJWMC8NV01R
Sleeping...64532 mSec RID RJWMA2AH015
Sleeping...64533 mSec RID RJWMVECF014
Sleeping...64517 mSec RID RJWMD4RV014
Sleeping...64514 mSec RID RJWMFW80014
Sleeping...64512 mSec RID RJWMT7G8014
Sleeping...64506 mSec RID RJWMWD0P014
Sleeping...64488 mSec RID RJWJKCU4015
Sleeping...64543 mSec RID RJWKVZ7U014
Sleeping...64524 mSec RID RJWMX9TH014
Sleeping...64519 mSec RID RJWKK0SE014
Sleeping...64518 mSec RID RJWKYUPN01R
Sleeping...64505 mSec RID RJWM0Z4H01R
Sleeping...64497 mSec RID RJWJT5BD01R
Sleeping...64498 mSec RID RJWK2P7V014
Sleeping...64485 mSec RID RJWKSMSA015
Sleeping...64477 mSec RID RJWK1YND01R
Sleeping...64453 mSec RID RJWJXMXM01R
Sleeping...64462 mSec RID RJWKXAG401R
Sleeping...64448 mSec RID RJWK92WM014
Sleeping...63632 mSec RID RJWJYGA801R
Sleeping...63621 mSec RID RJWMYTGS014
Sleeping...63614 mSec RID RJWN071T014
Sleeping...63556 mSec RID RJWJS8NM014
Sleeping...64627 mSec RID RJWN7P5201R
Sleeping...64428 mSec RID RJWJKCU4015
Sleeping...61454 mSec RID RJWN4J5601R
Sleeping...58186 mSec RID RJWN16DB014
Submit Blast Exception BLAST Failed
Reprocessing: RJWMJVNG014
Counter: 1
REPROCESS WHY!!!!!!!!!!!!!!!! Submit Blast Exception BLAST Failed Reprocessing: RJWMD4RV014 Counter: 1 REPROCESS WHY!!!!!!!!!!!!!!!! Submit Blast Exception BLAST Failed Reprocessing: RJWMR4AH014 Counter: 1 REPROCESS WHY!!!!!!!!!!!!!!!! Submit Blast Exception BLAST Failed Reprocessing: RJWMT7G8014 Counter: 1 REPROCESS WHY!!!!!!!!!!!!!!!! Submit Blast Exception BLAST Failed Reprocessing: RJWMWD0P014 Counter: 1 REPROCESS WHY!!!!!!!!!!!!!!!! Submit Blast Exception BLAST Failed Reprocessing: RJWMGAES014 Counter: 1 REPROCESS WHY!!!!!!!!!!!!!!!! Submit Blast Exception BLAST Failed Reprocessing: RJWMFW80014 Counter: 1 REPROCESS WHY!!!!!!!!!!!!!!!! Submit Blast Exception BLAST Failed Reprocessing: RJWP4VM3014 Counter: 1 REPROCESS WHY!!!!!!!!!!!!!!!! Submit Blast Exception BLAST Failed Reprocessing: RJWMVECF014 Counter: 1 REPROCESS WHY!!!!!!!!!!!!!!!! Submit Blast Exception BLAST Failed Reprocessing: RJWMN6JE014 Counter: 1 REPROCESS WHY!!!!!!!!!!!!!!!! Submit Blast Exception BLAST Failed Reprocessing: RJWNZ2UD014 Counter: 1 REPROCESS WHY!!!!!!!!!!!!!!!! Submit Blast Exception BLAST Failed Reprocessing: RJWMKSHS014 Counter: 1 REPROCESS WHY!!!!!!!!!!!!!!!! Sleeping...65000 mSec RID RJWM5ZGX014 Sleeping...65000 mSec RID RJWM3HP8014 Sleeping...65000 mSec RID RJWM0Z4H01R Sleeping...65000 mSec RID RJWJYGA801R NCBI QBlast refused this request because: <!--<ul class="msg"><li class="error"><p> REPROCESS WHY!!!!!!!!!!!!!!!! REPROCESS WHY!!!!!!!!!!!!!!!! REPROCESS WHY!!!!!!!!!!!!!!!! REPROCESS WHY!!!!!!!!!!!!!!!! REPROCESS WHY!!!!!!!!!!!!!!!! REPROCESS WHY!!!!!!!!!!!!!!!! REPROCESS WHY!!!!!!!!!!!!!!!! NCBI QBlast refused this request because: <!--<ul class="msg"><li class="error"><p> REPROCESS WHY!!!!!!!!!!!!!!!! NCBI QBlast refused this request because: <!--<ul class="msg"><li class="error"><p> REPROCESS WHY!!!!!!!!!!!!!!!! NCBI QBlast refused this request because: <!--<ul class="msg"><li class="error"><p> REPROCESS WHY!!!!!!!!!!!!!!!! NCBI QBlast refused this request because: <!--<ul class="msg"><li class="error"><p> REPROCESS WHY!!!!!!!!!!!!!!!! Sleeping...63660 mSec RID RJWMX9TH014 NCBI QBlast refused this request because: <!--<ul class="msg"><li class="error"><p> REPROCESS WHY!!!!!!!!!!!!!!!! REPROCESS WHY!!!!!!!!!!!!!!!! NCBI QBlast refused this request because: <!--<ul class="msg"><li class="error"><p> REPROCESS WHY!!!!!!!!!!!!!!!! REPROCESS WHY!!!!!!!!!!!!!!!! Sleeping...64516 mSec RID RJWZ8XSH01R Sleeping...64399 mSec RID RJWZ8NAC01R Sleeping...64608 mSec RID RJWN8AN4014 Sleeping...64586 mSec RID RJWNXWRE01R Sleeping...65000 mSec RID RJWK2P7V014 Sleeping...65000 mSec RID RJWKSMSA015 Sleeping...65000 mSec RID RJWKVZ7U014 Sleeping...65000 mSec RID RJWKK0SE014 Sleeping...65000 mSec RID RJWKXAG401R Sleeping...65000 mSec RID RJWKYUPN01R Sleeping...64516 mSec RID RJWJKCU4015 Timeout for rid waiting exceeded! Skiping RID RJWN7P5201R Timeout for rid waiting exceeded! Skiping RID RJWJXMXM01R Timeout for rid waiting exceeded! Skiping RID RJWMC8NV01R SubmitBLAST Thread-80 177 ended! Timeout for rid waiting exceeded! Skiping RID RJWN16DB014 Timeout for rid waiting exceeded! Skiping RID RJWJS8NM014 Timeout for rid waiting exceeded! Skiping RID RJWM978K015 SubmitBLAST Thread-78 175 ended! Timeout for rid waiting exceeded! Skiping RID RJWN4J5601R Timeout for rid waiting exceeded! Skiping RID RJWJT5BD01R Timeout for rid waiting exceeded! Skiping RID RJWMA2AH015 SubmitBLAST Thread-79 176 ended! Timeout for rid waiting exceeded! Skiping RID RJWNKFGB01R Timeout for rid waiting exceeded! Skiping RID RJWK1YND01R Sleeping...65000 mSec RID RJX10XZV015 Timeout for rid waiting exceeded! Skiping RID RJWNP9SM01R Timeout for rid waiting exceeded! Skiping RID RJWK92WM014 Sleeping...65000 mSec RID RJX14R1Z015 Sleeping...64658 mSec RID RJWNM2W401R Sleeping...64601 mSec RID RJWNSXEX01R Sleeping...64643 mSec RID RJWNTK1X01R Sleeping...64641 mSec RID RJWNR0C601R Sleeping...64649 mSec RID RJWNVTB501R Sleeping...64663 mSec RID RJWNW2B101R Timeout for rid waiting exceeded! Skiping RID RJWN071T014 Timeout for rid waiting exceeded! Skiping RID RJWMYTGS014 Sleeping...65000 mSec RID RJWNXWRE01R Sleeping...65000 mSec RID RJWN8AN4014 Sleeping...64522 mSec RID RJX10XZV015 Sleeping...64676 mSec RID RJX14R1Z015 Timeout for rid waiting exceeded! Skiping RID RJWK2P7V014 Timeout for rid waiting exceeded! Skiping RID RJWNM2W401R Sleeping...64619 mSec RID RJWZBGTY015 Timeout for rid waiting exceeded! Skiping RID RJWKSMSA015 Timeout for rid waiting exceeded! Skiping RID RJWMX9TH014 Timeout for rid waiting exceeded! Skiping RID RJWNYSP501R Timeout for rid waiting exceeded! Skiping RID RJWJKCU4015 Timeout for rid waiting exceeded! Skiping RID RJWM162W01R SubmitBLAST Thread-75 172 ended! Timeout for rid waiting exceeded! Skiping RID RJWNSXEX01R Sleeping...64650 mSec RID RJX07NTC01R Timeout for rid waiting exceeded! Skiping RID RJWKVZ7U014 Timeout for rid waiting exceeded! Skiping RID RJWNTK1X01R Sleeping...64642 mSec RID RJX0CHAX01R Timeout for rid waiting exceeded! Skiping RID RJWKK0SE014 Timeout for rid waiting exceeded! Skiping RID RJWNR0C601R Sleeping...64654 mSec RID RJX0N97K01R Timeout for rid waiting exceeded! Skiping RID RJWKXAG401R Timeout for rid waiting exceeded! Skiping RID RJWNVTB501R Sleeping...64652 mSec RID RJX0CVYV014 Timeout for rid waiting exceeded! Skiping RID RJWKYUPN01R Timeout for rid waiting exceeded! Skiping RID RJWNW2B101R Sleeping...64671 mSec RID RJX15JXZ014 Timeout for rid waiting exceeded! Skiping RID RJWM0Z4H01R Timeout for rid waiting exceeded! Skiping RID RJWJYGA801R Sleeping...62578 mSec RID RJX14R1Z015 Sleeping...62014 mSec RID RJX10XZV015 Sleeping...64215 mSec RID RJX10XZV015 Sleeping...64259 mSec RID RJX14R1Z015 Timeout for rid waiting exceeded! Skiping RID RJWJRD7V015 Timeout for rid waiting exceeded! Skiping RID RJWM5ZGX014 Timeout for rid waiting exceeded! Skiping RID RJWZ8NAC01R SubmitBLAST Thread-77 174 ended! Timeout for rid waiting exceeded! Skiping RID RJWJN5C4015 Timeout for rid waiting exceeded! Skiping RID RJWM3HP8014 Timeout for rid waiting exceeded! Skiping RID RJWZ8XSH01R SubmitBLAST Thread-76 173 ended! Sleeping...64337 mSec RID RJX10XZV015 Sleeping...64232 mSec RID RJX14R1Z015 Timeout for rid waiting exceeded! Skiping RID RJWNXWRE01R Timeout for rid waiting exceeded! Skiping RID RJWZGTYU01R SubmitBLAST Thread-90 187 ended! Timeout for rid waiting exceeded! Skiping RID RJWN8AN4014 Timeout for rid waiting exceeded! Skiping RID RJWZGC6V01R SubmitBLAST Thread-81 178 ended! Timeout for rid waiting exceeded! Skiping RID RJWZBGTY015 SubmitBLAST Thread-83 180 ended! Timeout for rid waiting exceeded! Skiping RID RJX07NTC01R SubmitBLAST Thread-86 183 ended! Timeout for rid waiting exceeded! Skiping RID RJX0CHAX01R SubmitBLAST Thread-87 184 ended! Timeout for rid waiting exceeded! Skiping RID RJX0N97K01R SubmitBLAST Thread-85 182 ended! Timeout for rid waiting exceeded! Skiping RID RJX0CVYV014 SubmitBLAST Thread-88 185 ended! Timeout for rid waiting exceeded! Skiping RID RJX15JXZ014 SubmitBLAST Thread-89 186 ended! Timeout for rid waiting exceeded! Skiping RID RJX10XZV015 SubmitBLAST Thread-82 179 ended! Timeout for rid waiting exceeded! Skiping RID RJX14R1Z015 SubmitBLAST Thread-84 181 ended! NCBI QBlast refused this request because: <!--<ul class="msg"><li class="error"><p> NCBI QBlast refused this request because: <!--<ul class="msg"><li class="error"><p> NCBI QBlast refused this request because: <!--<ul class="msg"><li class="error"><p> NCBI QBlast refused this request because: <!--<ul class="msg"><li class="error"><p> NCBI QBlast refused this request because: <!--<ul class="msg"><li class="error"><p> NCBI QBlast refused this request because: <!--<ul class="msg"><li class="error"><p> NCBI QBlast refused this request because: <!--<ul class="msg"><li class="error"><p> NCBI QBlast refused this request because: <!--<ul class="msg"><li class="error"><p> NCBI QBlast refused this request because: <!--<ul class="msg"><li class="error"><p> NCBI QBlast refused this request because: <!--<ul class="msg"><li class="error"><p> NCBI QBlast refused this request because: <!--<ul class="msg"><li class="error"><p> NCBI QBlast refused this request because: <!--<ul class="msg"><li class="error"><p> NCBI QBlast refused this request because: <!--<ul class="msg"><li class="error"><p> Start 0 Start 1 SubmitBLAST Thread-93 216 started. Start 2 SubmitBLAST Thread-94 217 started. Sleeping...65000 mSec RID RJY2DFNU015 Start 3 Sleeping...65000 mSec RID RJY2FNBA015 SubmitBLAST Thread-95 218 started. Start 4 Sleeping...65000 mSec RID RJY2KD9J01R SubmitBLAST Thread-96 219 started. SubmitBLAST Thread-97 220 started. Sleeping...65000 mSec RID RJY2MBHD01R Start 5 Sleeping...65000 mSec RID RJY2NKPZ01R Start 6 SubmitBLAST Thread-98 221 started. Sleeping...65000 mSec RID RJY2PUJY01R Start 7 SubmitBLAST Thread-99 222 started. Sleeping...65000 mSec RID RJY2RDTR01R Start 8 SubmitBLAST Thread-100 223 started. Sleeping...65000 mSec RID RJY2SJ6701R Start 9 SubmitBLAST Thread-101 224 started. Sleeping...65000 mSec RID RJY2TGNN01R Start 10 SubmitBLAST Thread-102 225 started. Start 11 SubmitBLAST Thread-103 226 started. Sleeping...65000 mSec RID RJY2UVB101R Start 12 Sleeping...65000 mSec RID RJY2VAYU01R SubmitBLAST Thread-104 227 started. Start 13 Sleeping...65000 mSec RID RJY2ZNK7014 SubmitBLAST Thread-105 228 started. Start 14 SubmitBLAST Thread-106 229 started. Sleeping...65000 mSec RID RJY30P8Z014 Start 15 Sleeping...65000 mSec RID RJY31BK7014 SubmitBLAST Thread-107 230 started. SubmitBLAST Thread-108 231 started. Sleeping...65000 mSec RID RJY32NNU014 Sleeping...65000 mSec RID RJY337Z8014 Sleeping...64609 mSec RID RJY655VJ015 Sleeping...64599 mSec RID RJY47XGF014 Sleeping...64582 mSec RID RJY4A449015 Sleeping...64579 mSec RID RJY670BP014 Sleeping...64572 mSec RID RJY682ZW014 Sleeping...64562 mSec RID RJY4BVEE014 Sleeping...64545 mSec RID RJY62WZR015 Sleeping...64535 mSec RID RJY63EVK015 Sleeping...64516 mSec RID RJY647JP015 Sleeping...64506 mSec RID RJY4FJH4015 Sleeping...64502 mSec RID RJY53WEG015 Sleeping...64499 mSec RID RJY60958015 Sleeping...64496 mSec RID RJY4Z0UP015 Sleeping...64490 mSec RID RJY5XD68015 Sleeping...64481 mSec RID RJY4G3EU014 Sleeping...64476 mSec RID RJY4D7F0014 Sleeping...64600 mSec RID RJY2KD9J01R Sleeping...64601 mSec RID RJY3SKSJ01R Sleeping...64594 mSec RID RJY41YJD014 Sleeping...64583 mSec RID RJY3RXMV01R Sleeping...64582 mSec RID RJY43D0Y014 Sleeping...64572 mSec RID RJY3WK0J014 Sleeping...64558 mSec RID RJY2FNBA015 Sleeping...64555 mSec RID RJY2DFNU015 Sleeping...64531 mSec RID RJY39MYT015 Sleeping...64528 mSec RID RJY380ZB015 Sleeping...64528 mSec RID RJY3D41E015 Sleeping...64513 mSec RID RJY3PBPX01R Sleeping...64504 mSec RID RJY3EN1A015 Sleeping...64493 mSec RID RJY3MVNH015 Sleeping...64483 mSec RID RJY3APYD015 Sleeping...64475 mSec RID RJY3J9CX015 Sleeping...64703 mSec RID RJY2VAYU01R Sleeping...64696 mSec RID RJY337Z8014 Sleeping...64676 mSec RID RJY2MBHD01R Sleeping...64670 mSec RID RJY2NKPZ01R Sleeping...64674 mSec RID RJY2SJ6701R Sleeping...64673 mSec RID RJY2UVB101R Sleeping...64667 mSec RID RJY30P8Z014 Sleeping...64654 mSec RID RJY31BK7014 Sleeping...64650 mSec RID RJY32NNU014 Sleeping...64641 mSec RID RJY2RDTR01R Sleeping...64631 mSec RID RJY2PUJY01R Sleeping...64629 mSec RID RJY47XGF014 Sleeping...64608 mSec RID RJY4A449015 Sleeping...64601 mSec RID RJY4BVEE014 Sleeping...64601 mSec RID RJY2ZNK7014 Sleeping...64578 mSec RID RJY2TGNN01R Sleeping...64690 mSec RID RJY2DFNU015 Sleeping...64682 mSec RID RJY670BP014 Sleeping...64665 mSec RID RJY2FNBA015 Sleeping...64647 mSec RID RJY63EVK015 Sleeping...64641 mSec RID RJY647JP015 Sleeping...64636 mSec RID RJY62WZR015 Sleeping...64550 mSec RID RJY682ZW014 Sleeping...64531 mSec RID RJY2KD9J01R Sleeping...64530 mSec RID RJY5XD68015 Sleeping...64525 mSec RID RJY53WEG015 Sleeping...64513 mSec RID RJY4D7F0014 Sleeping...64516 mSec RID RJY4G3EU014 Sleeping...64474 mSec RID RJY655VJ015 Sleeping...64453 mSec RID RJY60958015 Sleeping...64435 mSec RID RJY4Z0UP015 Sleeping...64413 mSec RID RJY4FJH4015 Sleeping...64595 mSec RID RJY4BVEE014 Sleeping...64596 mSec RID RJY47XGF014 Sleeping...64549 mSec RID RJY4A449015 Sleeping...64588 mSec RID RJY2KD9J01R Sleeping...64576 mSec RID RJY2DFNU015 Sleeping...64570 mSec RID RJY2FNBA015 Timeout for rid waiting exceeded! Skiping RID RJY4G3EU014 Timeout for rid waiting exceeded! Skiping RID RJY2PUJY01R Timeout for rid waiting exceeded! Skiping RID RJY3APYD015 SubmitBLAST Thread-98 221 ended! Timeout for rid waiting exceeded! Skiping RID RJY670BP014 Timeout for rid waiting exceeded! Skiping RID RJY32NNU014 Timeout for rid waiting exceeded! Skiping RID RJY41YJD014 SubmitBLAST Thread-107 230 ended! Timeout for rid waiting exceeded! Skiping RID RJY4FJH4015 Timeout for rid waiting exceeded! Skiping RID RJY2NKPZ01R Timeout for rid waiting exceeded! Skiping RID RJY39MYT015 SubmitBLAST Thread-97 220 ended! Timeout for rid waiting exceeded! Skiping RID RJY5XD68015 Timeout for rid waiting exceeded! Skiping RID RJY2TGNN01R Timeout for rid waiting exceeded! Skiping RID RJY3J9CX015 SubmitBLAST Thread-101 224 ended! Timeout for rid waiting exceeded! Skiping RID RJY4Z0UP015 Timeout for rid waiting exceeded! Skiping RID RJY2RDTR01R Timeout for rid waiting exceeded! Skiping RID RJY3D41E015 SubmitBLAST Thread-99 222 ended! Timeout for rid waiting exceeded! Skiping RID RJY53WEG015 Timeout for rid waiting exceeded! Skiping RID RJY2SJ6701R Timeout for rid waiting exceeded! Skiping RID RJY3EN1A015 SubmitBLAST Thread-100 223 ended! Timeout for rid waiting exceeded! Skiping RID RJY60958015 Timeout for rid waiting exceeded! Skiping RID RJY2UVB101R Timeout for rid waiting exceeded! Skiping RID RJY3MVNH015 SubmitBLAST Thread-102 225 ended! Timeout for rid waiting exceeded! Skiping RID RJY4D7F0014 Timeout for rid waiting exceeded! Skiping RID RJY2MBHD01R Timeout for rid waiting exceeded! Skiping RID RJY380ZB015 SubmitBLAST Thread-96 219 ended! Timeout for rid waiting exceeded! Skiping RID RJY655VJ015 Timeout for rid waiting exceeded! Skiping RID RJY31BK7014 Timeout for rid waiting exceeded! Skiping RID RJY3WK0J014 SubmitBLAST Thread-106 229 ended! Timeout for rid waiting exceeded! Skiping RID RJY682ZW014 Timeout for rid waiting exceeded! Skiping RID RJY337Z8014 Timeout for rid waiting exceeded! Skiping RID RJY43D0Y014 SubmitBLAST Thread-108 231 ended! Timeout for rid waiting exceeded! Skiping RID RJY647JP015 Timeout for rid waiting exceeded! Skiping RID RJY30P8Z014 Timeout for rid waiting exceeded! Skiping RID RJY3SKSJ01R SubmitBLAST Thread-105 228 ended! Timeout for rid waiting exceeded! Skiping RID RJY63EVK015 Timeout for rid waiting exceeded! Skiping RID RJY2ZNK7014 Timeout for rid waiting exceeded! Skiping RID RJY3RXMV01R SubmitBLAST Thread-104 227 ended! Timeout for rid waiting exceeded! Skiping RID RJY62WZR015 Timeout for rid waiting exceeded! Skiping RID RJY2VAYU01R Timeout for rid waiting exceeded! Skiping RID RJY3PBPX01R SubmitBLAST Thread-103 226 ended! Timeout for rid waiting exceeded! Skiping RID RJY47XGF014 Timeout for rid waiting exceeded! Skiping RID RJY69ZU1014 Timeout for rid waiting exceeded! Skiping RID RJY2DFNU015 Timeout for rid waiting exceeded! Skiping RID RJY34XJN014 SubmitBLAST Thread-93 216 ended! Timeout for rid waiting exceeded! Skiping RID RJY4BVEE014 Timeout for rid waiting exceeded! Skiping RID RJY6EDHU014 Timeout for rid waiting exceeded! Skiping RID RJY2KD9J01R Timeout for rid waiting exceeded! Skiping RID RJY374C3014 SubmitBLAST Thread-95 218 ended! Timeout for rid waiting exceeded! Skiping RID RJY4A449015 Timeout for rid waiting exceeded! Skiping RID RJY6DGPA014 Timeout for rid waiting exceeded! Skiping RID RJY2FNBA015 Timeout for rid waiting exceeded! Skiping RID RJY35SC1014 SubmitBLAST Thread-94 217 ended! NCBI QBlast refused this request because: <!--<ul class="msg"><li class="error"><p> NCBI QBlast refused this request because: <!--<ul class="msg"><li class="error"><p> NCBI QBlast refused this request because: <!--<ul class="msg"><li class="error"><p> NCBI QBlast refused this request because: <!--<ul class="msg"><li class="error"><p> NCBI QBlast refused this request because: <!--<ul class="msg"><li class="error"><p> NCBI QBlast refused this request because: <!--<ul class="msg"><li class="error"><p> NCBI QBlast refused this request because: <!--<ul class="msg"><li class="error"><p> NCBI QBlast refused this request because: <!--<ul class="msg"><li class="error"><p> NCBI QBlast refused this request because: <!--<ul class="msg"><li class="error"><p> NCBI QBlast refused this request because: <!--<ul class="msg"><li class="error"><p> Message: BLAST unsigned exception. java.lang.Exception: BLAST unsigned exception. at pt.uminho.sysbio.merlin.core.alignment.blast.org.biojava3.ws.alignment.qblast.NcbiBlastService.sendActualAlignementRequest(NcbiBlastService.java:325) at pt.uminho.sysbio.merlin.core.alignment.blast.org.biojava3.ws.alignment.qblast.NcbiBlastService.sendAlignmentRequest(NcbiBlastService.java:365) at pt.uminho.sysbio.merlin.core.alignment.SearchAndLoadHomologueSequences.processQuery(SearchAndLoadHomologueSequences.java:571) at pt.uminho.sysbio.merlin.core.alignment.SearchAndLoadHomologueSequences.processQuery(SearchAndLoadHomologueSequences.java:643) at pt.uminho.sysbio.merlin.core.alignment.SearchAndLoadHomologueSequences.processQuery(SearchAndLoadHomologueSequences.java:643) at pt.uminho.sysbio.merlin.core.alignment.SearchAndLoadHomologueSequences.processQuery(SearchAndLoadHomologueSequences.java:643) at pt.uminho.sysbio.merlin.core.alignment.SearchAndLoadHomologueSequences.processQuery(SearchAndLoadHomologueSequences.java:643) at pt.uminho.sysbio.merlin.core.alignment.SearchAndLoadHomologueSequences.processQuery(SearchAndLoadHomologueSequences.java:643) at pt.uminho.sysbio.merlin.core.alignment.SearchAndLoadHomologueSequences.processQuery(SearchAndLoadHomologueSequences.java:643) at pt.uminho.sysbio.merlin.core.alignment.SearchAndLoadHomologueSequences.processQuery(SearchAndLoadHomologueSequences.java:643) at pt.uminho.sysbio.merlin.core.alignment.SearchAndLoadHomologueSequences.processQuery(SearchAndLoadHomologueSequences.java:643) at pt.uminho.sysbio.merlin.core.alignment.SearchAndLoadHomologueSequences.processQuery(SearchAndLoadHomologueSequences.java:643) at pt.uminho.sysbio.merlin.core.alignment.SearchAndLoadHomologueSequences.blastSingleSequenceNcbi(SearchAndLoadHomologueSequences.java:388) at pt.uminho.sysbio.merlin.core.alignment.SearchAndLoadHomologueSequences.blastProcessGenesListNcbi(SearchAndLoadHomologueSequences.java:1013) at pt.uminho.sysbio.merlin.core.alignment.SearchAndLoadHomologueSequences.blastSequencesNCBI(SearchAndLoadHomologueSequences.java:725) at pt.uminho.sysbio.merlin.core.operations.NcbiBlastSimilaritySearch.selectProject(NcbiBlastSimilaritySearch.java:229) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:606) at es.uvigo.ei.aibench.core.operation.execution.SimpleIncomingEndPoint$1.call(SimpleIncomingEndPoint.java:104) at java.util.concurrent.FutureTask.run(FutureTask.java:262) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) at java.lang.Thread.run(Thread.java:745) Search and load homolgue sequences. BLAST Failed for sequence: %3EWP_041360975.1 molecular chaperone DnaK [Methylococcus capsulatus]%0D%0AMSSAVPRYIVGIDLGTTHTVVSYADGGDPSRIEPLFLEQLVAPGQVAGRPLLPSVRYHPATGELAEADTALPWPVEETAPGCRPVIGEFARQLGSRSRGRLVASAKSWLCHTGVDRTADILPWGAPDEVPKVSPVEASASFLRHVRCAWNHRFPAHPLETQDVIVTIPASFDDAARALTVEAARRAGLANVRLLEEPQAACYDFLWTYRGRLAETLEGVNLLLVCDVGGGTTDFTLIRVDAGGSEPELERIAVGNHLMLGGDNIDLTLAHRLEPRLTGAERSLSATDLILLAEQCRRAKETLLAEQGPESVTVTLLGKGGGLIGGARSVELSRHEVLEVVLDGFFPRVGADAVPERRSGVVEFGLPYAADPAITRHAAAFLIRHRNDAGGAAPDALLLNGGVFHSPVIAGRMAEVVGSWCGRTPVMLRNPRPDQAVAFGAVAFGLSRRGLAVRRIGGGSARAYYLLVGDANERSRRGVCILPRGAAEGQEWTVERRNFLLSVGRPVRFHVFSSTVDSGHAPGDLAVLDEAGFGELPPLAVALQAQEQGDVEVRLAARLTAIGTLQLQCVAVGDPEQRWDLELQLRGGGPRPTASASLHPRAAEAQEHIGLIFGKKTRQFGPKAVKTLRNDLEKILGKREDWDTALCRELYAALLEGAPHRRRSADHERLWLSLAGYCLRPGFGAPLDDWRVGQVWNLYSQGLQFVNEAQNWSEWWIVWRRIAGGLRAEAQQRLFADVAGFIDPVRARRGNAEALAKKRAFEDMVRLAASLERLSAGDKTMLGGWLVQRLDKAPDSAELWWALGRVGARAPFHGSAHNLVAREVVEDWVELALQRDWKRQGFVAFAATLLARLTGDRERDLDATLRNRVAEKLVASSAPEIWLELVTEVRGLDASDEKRIFGEGLPPGLRLVDSAWGA%3E BLOSUM80 size 145 PAM70 size 4 Setting e-value to 200000 for <35mer sequences. PAM30 size 2 Setting e-value to 200000.0 for 10-15mer or shorter sequences. [Fine] Found class in Plugin "pt.uminho.sysbio.merlin.core": es.uvigo.ei.aibench.workbench.Workbench [14:16:39,720] [Thread-18] ERROR es.uvigo.ei.aibench.workbench.Workbench - Errors have ocurred while processsing 196 query(ies).
I hope this little report helps you to improve the software! I would certainly like to use this for my studies, as it seems to be a very promising software to begin with!
My System specs are:
1. MacBook Pro OS X Yosemite
2. Processor 2,6 Ghz Intel Core i5
3. Memory 8 GB 1600 MHZ DDR3
Let me know if you need any more information.
Cheers,
Christian