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MUSCLE Alignment of Nucleotides Crashes in 64-bit Win7 (Read 14604 times)
Apr 18th, 2012 at 9:23pm

R Smith   Offline
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Posts: 17
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Recently upgraded machine and installed UGENE

When aligning several reference hepatitis B virus genomes (~3000 bases each) using MUSCLE (only defaults), UGENE regularly crashes.

This is NOT occurring with Win XP running as a guest OS inside VMware Workstation 8.x virtual machine with the Win7 as host OS.

NOTE:  Soluto with Application Crash Handling option is set, and has been known to induce crashing, I believe.  Is this an issue?

OS: 64bit Win7 Home Premium SP1
UGENE:  1.10.4
CPU: Intel Core i7 2670QM
RAM: 8 GB
 
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Reply #1 - Apr 19th, 2012 at 10:48am

German   Offline
Full Member

Posts: 118
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We have tried to investigate the problem but we can not reproduce the crash. Could you share with us please the files which you use for aligning?

Also, it would be great if you send us a crash report.

Thanks for your feedback!
 
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Reply #2 - Apr 23rd, 2012 at 5:27pm

R Smith   Offline
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Posts: 17
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Replying to this four days after:  not sure why I am not getting email notifications of replies to this topic.

ANSWER:

For example:

1. Download fron NCBI Nuc DB the following accession number entries:
X02763
AF297621
D00330
AB073858
AB033556

These are all reference standard genomes considered definitive for hepatitis B virus genotypes

2. Create alignment file:
a) Select all of them in Project subwindow
b) right click popup:  Export->Export sequences as alignment

3. Alignment:
  a) Alignment subwindow appears after 2b menu action
  b) right click popup:  Align->MUSCLE (no changes to defaults)

4. CRASH:  does it every time

1.10.4 was updated with full (plugin) install
 
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Reply #3 - Apr 24th, 2012 at 5:37pm

Yuriy Vaskin   Offline
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Posts: 138
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Thanks for the detailed description.
Unfortunately the steps you have described have not caused UGENE to fail on our Win7 64bit machines.

We've improved our crash handler a little bit. Could you please load the latest UGENE snapshot from here (http://ugene.unipro.ru/snapshot.html), launch MUSCLE again and send us a crash report. Now the crash report provides us with more details about what's happened right before the crash. And maybe it will help us to fix the problem.

Thank you!
 
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Reply #4 - Apr 24th, 2012 at 8:16pm

R Smith   Offline
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Posts: 17
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Okay,

I downloaded the latest development package, and it too crashed.

The info generated by UGENE is below and also sent via crash reporter control.

===========================


Exception with code c0000005 - Access violation::143ce5f

Operation system: Windows x86

UGENE version: 1.11.0-dev

ActiveWindow: None

Log:
[16:06:18.834] [Input/Output] DbiPool: decreasing reference count. Url: Z:/service.web.proteomics/Projects/UgeneDownloadedData/ugene_tmp/p10260/session_
0.ugenedb, ref-count: 1
[16:06:18.834] [Input/Output] DbiPool: Opening DBI. Url: Z:/service.web.proteomics/Projects/UgeneDownloadedData/ugene_tmp/p10260/session_
0.ugenedb, factory: SQLiteDbi
[16:06:18.834] [Input/Output] DbiPool: decreasing reference count. Url: Z:/service.web.proteomics/Projects/UgeneDownloadedData/ugene_tmp/p10260/session_
0.ugenedb, ref-count: 1
[16:06:18.834] [Input/Output] DbiPool: Opening DBI. Url: Z:/service.web.proteomics/Projects/UgeneDownloadedData/ugene_tmp/p10260/session_
0.ugenedb, factory: SQLiteDbi
[16:06:18.834] [Input/Output] DbiPool: decreasing reference count. Url: Z:/service.web.proteomics/Projects/UgeneDownloadedData/ugene_tmp/p10260/session_
0.ugenedb, ref-count: 1
[16:06:18.834] [Input/Output] DbiPool: Opening DBI. Url: Z:/service.web.proteomics/Projects/UgeneDownloadedData/ugene_tmp/p10260/session_
0.ugenedb, factory: SQLiteDbi
[16:06:18.834] [Input/Output] DbiPool: decreasing reference count. Url: Z:/service.web.proteomics/Projects/UgeneDownloadedData/ugene_tmp/p10260/session_
0.ugenedb, ref-count: 1
[16:06:18.834] [Input/Output] DbiPool: Opening DBI. Url: Z:/service.web.proteomics/Projects/UgeneDownloadedData/ugene_tmp/p10260/session_
0.ugenedb, factory: SQLiteDbi
[16:06:18.834] [Input/Output] DbiPool: decreasing reference count. Url: Z:/service.web.proteomics/Projects/UgeneDownloadedData/ugene_tmp/p10260/session_
0.ugenedb, ref-count: 1
[16:06:18.834] [Input/Output] DbiPool: Opening DBI. Url: Z:/service.web.proteomics/Projects/UgeneDownloadedData/ugene_tmp/p10260/session_
0.ugenedb, factory: SQLiteDbi
[16:06:18.834] [Input/Output] DbiPool: decreasing reference count. Url: Z:/service.web.proteomics/Projects/UgeneDownloadedData/ugene_tmp/p10260/session_
0.ugenedb, ref-count: 1
[16:06:18.834] [Input/Output] DbiPool: Opening DBI. Url: Z:/service.web.proteomics/Projects/UgeneDownloadedData/ugene_tmp/p10260/session_
0.ugenedb, factory: SQLiteDbi
[16:06:18.834] [Input/Output] DbiPool: decreasing reference count. Url: Z:/service.web.proteomics/Projects/UgeneDownloadedData/ugene_tmp/p10260/session_
0.ugenedb, ref-count: 1
[16:06:18.835] [Tasks] Registering new task: Export sequence to document
[16:06:18.849] [Tasks] promoting task {Export sequence to document} to 'Prepared'
[16:06:18.849] [Tasks] promoting task {Export alignment to 'RefStandards.aln'} to 'Prepared'
[16:06:18.849] [Tasks] promoting task {Export sequence to document} to 'Running'
[16:06:18.849] [Tasks] acquiring resource: 'Threads':1, state: 1/1000
[16:06:18.849] [Tasks] promoting task {Export alignment to 'RefStandards.aln'} to 'Running'
[16:06:18.881] [Tasks] releasing resource: 'Threads':1, state: 0/1000
[16:06:18.882] [Tasks] promoting task {Export alignment to 'RefStandards.aln'} to 'Finished'
[16:06:18.882] [Tasks] promoting task {Adding document to project: Z:/service.web.abiyotek/UGENE/RefStandards.aln} to 'Prepared'
[16:06:18.882] [Tasks] promoting task {Adding document to project: Z:/service.web.abiyotek/UGENE/RefStandards.aln} to 'Running'
[16:06:18.882] [Core Services] Adding document to the project: Z:/service.web.abiyotek/UGENE/RefStandards.aln
[16:06:18.882] [Tasks] promoting task {Adding document to project: Z:/service.web.abiyotek/UGENE/RefStandards.aln} to 'Finished'
[16:06:18.882] [Tasks] promoting task {Load document: 'RefStandards.aln'} to 'Prepared'
[16:06:18.882] [Core Services] Starting load document from Z:/service.web.abiyotek/UGENE/RefStandards.aln, document format CLUSTALW
[16:06:18.882] [Core Services] resource 'Project Document::Z:/service.web.abiyotek/UGENE/RefStandards.aln' is used by 'Load 'RefStandards.aln''
[16:06:18.882] [Tasks] promoting task {Load 'RefStandards.aln'} to 'Prepared'
[16:06:18.882] [Core Services] load document:Memory resource 0
[16:06:18.882] [Tasks] promoting task {Read document: 'RefStandards.aln'} to 'Prepared'
[16:06:18.882] [Tasks] promoting task {Load document: 'RefStandards.aln'} to 'Running'
[16:06:18.882] [Tasks] promoting task {Load 'RefStandards.aln'} to 'Running'
[16:06:18.882] [Tasks] acquiring resource: 'Threads':1, state: 1/1000
[16:06:18.882] [Tasks] promoting task {Read document: 'RefStandards.aln'} to 'Running'
[16:06:18.892] [Tasks] releasing resource: 'Threads':1, state: 0/1000
[16:06:18.892] [Tasks] promoting task {Read document: 'RefStandards.aln'} to 'Finished'
[16:06:18.892] [Core Services] resource 'Project Document::Z:/service.web.abiyotek/UGENE/RefStandards.aln' is released by 'Load 'RefStandards.aln''
[16:06:18.892] [Tasks] promoting task {Load 'RefStandards.aln'} to 'Finished'
[16:06:18.922] [Tasks] promoting task {Open view} to 'Prepared'
[16:06:18.928] [Tasks] promoting task {Open new 'Alignment editor'} to 'Prepared'
[16:06:18.928] [Tasks] promoting task {Open view} to 'Running'
[16:06:18.928] [Tasks] promoting task {Open new 'Alignment editor'} to 'Running'
[16:06:18.982] [Tasks] promoting task {Open new 'Alignment editor'} to 'Finished'
[16:06:18.982] [Tasks] promoting task {Open view} to 'Finished'
[16:06:18.982] [Tasks] promoting task {Load document: 'RefStandards.aln'} to 'Finished'
[16:06:19.067] [Tasks] promoting task {Export sequence to document} to 'Finished'
[16:06:19.067] [Tasks] Unregistering task: Export sequence to document
[16:06:19.067] [Tasks] Deleting task: Export alignment to 'RefStandards.aln'
[16:06:19.067] [Tasks] Deleting task: Adding document to project: Z:/service.web.abiyotek/UGENE/RefStandards.aln
[16:06:19.067] [Tasks] Deleting task: Read document: 'RefStandards.aln'
[16:06:19.067] [Tasks] Deleting task: Load 'RefStandards.aln'
[16:06:19.067] [Tasks] Deleting task: Open new 'Alignment editor'
[16:06:19.067] [Tasks] Deleting task: Open view
[16:06:19.067] [Tasks] Deleting task: Load document: 'RefStandards.aln'
[16:06:19.067] [Tasks] Deleting task: Export sequence to document
[16:06:31.626] [Tasks] Registering new task: MUSCLE align 'RefStandards.aln'
[16:06:31.667] [Tasks] promoting task {MUSCLE align 'RefStandards.aln'} to 'Prepared'
[16:06:31.667] [Tasks] Starting {MUSCLE align 'RefStandards.aln'} task
[16:06:31.668] [Tasks] promoting task {Workflow wrapper 'MUSCLE align 'RefStandards.aln''} to 'Prepared'
[16:06:31.669] [Tasks] promoting task {Run workflow: align} to 'Prepared'
[16:06:31.669] [Tasks] promoting task {Save document} to 'Prepared'
[16:06:31.669] [Tasks] promoting task {MUSCLE align 'RefStandards.aln'} to 'Running'
[16:06:31.669] [Tasks] promoting task {Workflow wrapper 'MUSCLE align 'RefStandards.aln''} to 'Running'
[16:06:31.669] [Tasks] promoting task {Run workflow: align} to 'Running'
[16:06:31.669] [Tasks] acquiring resource: 'Threads':1, state: 1/1000
[16:06:31.669] [Tasks] promoting task {Save document} to 'Running'
[16:06:31.672] [Core Services] Saving document C:/Users/mitch/AppData/Local/Temp/c10260.fasta

[16:06:31.672] [Tasks] releasing resource: 'Threads':1, state: 0/1000
[16:06:31.672] [Tasks] promoting task {Save document} to 'Finished'
[16:06:31.675] [Core Services] Starting UGENE workflow: C:/Program Files/Unipro UGENE/ugene.exe --task=data:cmdline/align.uwl --log-no-task-progress --ugene-output-progress-state --lang=en --ugene-output-error --ini-file="C:/Users/mitch/AppData/Roaming/Unipro/UGENE.ini" --mode=0 --max-iterations=8 --stable=1 --in=C:/Users/mitch/AppData/Local/Temp/c10260.fasta --out=C:/Users/mitch/AppData/Local/Temp/K10260.fasta --format=fasta --log-level-details

Task tree:
MUSCLE align 'RefStandards.aln'      (Running)      49
-Workflow wrapper 'MUSCLE align 'RefStandards.aln''      (Running)      49
--Run workflow: align      (Running)      49
---Workflow process      (New)      -1

OS-Version: 6.1.7601 (Service Pack 1) 0x300-0x1
0x143ce5f: (U2Lang.dll) ?prepare:RunCmdlineWorkflowTask:U2::UAEXXZ + 0x90f
0x329ac0: (U2Private.dll) ?append:?$QList:PAVPluginRef:U2::::QAEXABQAVPluginRef:U2:::Z + 0x60
0x32d728: (U2Private.dll) ?addToPriorityQueue:TaskSchedulerImpl:U2::AAE_NPAVTask:2:PAVTaskInfo:2::Z + 0x158
0x32d91d: (U2Private.dll) ?processNewSubtasks:TaskSchedulerImpl:U2::AAEXXZ + 0xbd
0x32dc1e: (U2Private.dll) ?update:TaskSchedulerImpl:U2::AAEXXZ + 0x2e
0x32e238: (U2Private.dll) ?qt_metacall:TaskSchedulerImpl:U2::UAEHW4Call:QMetaObject::HPAPAX:Z + 0x48
0x32e238: (U2Private.dll) ?qt_metacall:TaskSchedulerImpl:U2::UAEHW4Call:QMetaObject::HPAPAX:Z + 0x48
 
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Reply #5 - Jun 21st, 2012 at 9:48pm

Mat   Offline
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Posts: 1
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Hi all,

I have a similar problem -sorry no solution here- but since some weeks I cannot use the muscle aligning option any more.
I am trying to align 4813 sequences of ca.700bps which works fine with Kalign, but not with the muscle option any more. The info I get is:

[INFO][16:36] Starting {MUSCLE align '4813er-Kalign.fa'} task
[INFO][16:36] Saving document C:/Users/mgeiger/AppData/Local/Temp/gp5172.fasta
[INFO][16:36] process:6796>UGENE started
[INFO][16:36] process:6796>Reading MSA from C:/Users/mgeiger/AppData/Local/Temp/gp5172.fasta [FASTA]
[INFO][16:36] process:6796>MUSCLE alignment started
[ERROR][16:40] Task {MUSCLE align '4813er-Kalign.fa'} finished with error: Subtask {Workflow wrapper 'MUSCLE align '4813er-Kalign.fa''} is failed: Subtask {Run workflow: align} is failed: Subtask {Read document: 'lg5172.fasta'} is failed: Document is empty.
[ERROR][16:40] No URL provided!

I really would need the "sort by similarity" option of muscle to create sub-alignments. Is there any size limit for fasta files?

Any help would be highly appreciated.

OS: Windows 7 Enterprise 32bit / UGENE 1.10 or 1.11 no difference.

Thank you!

 
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Reply #6 - Jun 22nd, 2012 at 6:00pm

Konstantin Okonechnikov   Offline
Global Moderator

Posts: 173
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Does this happen only to this specific dataset or MUSCLE doesn't work with any data?

This looks like a known issue with running MUSCLE in a separate process, however it should be fixed already.

 
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