MantisBT - MEGA |
| View Issue Details |
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| ID | Project | Category | View Status | Date Submitted | Last Update |
| 0001158 | MEGA | Alignment Explorer | public | 2019-03-19 18:26 | 2019-03-21 13:11 |
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| Reporter | guest | |
| Assigned To | gstecher | |
| Priority | normal | Severity | minor | Reproducibility | have not tried |
| Status | resolved | Resolution | won't fix | |
| Platform | PC | OS | Linux | OS Version | other |
| Product Version | MEGA-CC 11 (command line version) | |
| Target Version | | Fixed in Version | | |
| First Name | Tom |
| Last Name | Caldwell |
| Email | tcaldwel@uci.edu |
| Confirm Email | tcaldwel@uci.edu |
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| Summary | 0001158: error in TClustalThread.SetSeqArray: Out of memory |
| Description | I am trying to run multiple sequence alignment with a very large data sets containing 100,000 to 1,000,000 sequences using the megacc program on a high performing computing cluster associated with my school. Cluster runs on linux OS. My alignments get aborted about 5 minutes after starting, and they are giving me an error message that reads: "error in TClustalThread.SetSeqArray: Out of memory". The issue may be an internal one regarding the module itself, not a problem with the cpu memory usage (see image "cpu memory usage.jpg"). |
| Steps To Reproduce | For my data set (P02c.fas, too large to be uploaded into this error report but it contains ~ 1.6 million sequences), I am using ClustalW alignment (clustal_align_NC.mao). I set my output to P02_align. I run this command using the following script:
megacc -a clustal_align_NC.mao -d P02c.fas -o P02_align
After I submit this job on the high-throughput scheduler, the job is in qw (waiting) for a minute or two before the run begins.
Run lasts about 5 minutes before the error occurs.
This worked in the past with a different dataset, but it only contained ~ 5,000 sequences. I don't know if this is a problem with the size of the input or software bug, but it definitely isn't a problem with the HPCC. |
| Additional Information | See "error_report.txt" for the error message I received when running this script.
Size of input file is ~ 527MB |
| Tags | No tags attached. |
| Relationships | |
| Attached Files |  mega bug report.zip (198,878) 2019-03-19 18:26
https://megasoftware.net/mantis_bt/ |
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| Issue History |
| Date Modified | Username | Field | Change |
| 2019-03-19 18:26 | guest | New Issue | |
| 2019-03-19 18:26 | guest | File Added: mega bug report.zip | |
| 2019-03-21 13:11 | gstecher | Note Added: 0004211 | |
| 2019-03-21 13:11 | gstecher | Status | new => resolved |
| 2019-03-21 13:11 | gstecher | Resolution | open => won't fix |
| 2019-03-21 13:11 | gstecher | Assigned To | => gstecher |