Details
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Type:
Bug
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:
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Story Points:0.25
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Epic Link:
Description
The sequence of the Lotmaria passim genome cannot be loaded.
I discovered this when I tried to run ProtAnnot on an annotation from this genome. ProtAnnot just seemed to hang half open.
When I try to load the sequence for the first chromosome, I get an error message saying
Couldn't locate partial sequence.
This is the same error message I encountered in issue IGBF-1356.
The task here is to determine if the IGBF-1356 issue is the cause here.
>>If fixing that issue will fix this, increase the priority level for that issue because there is at least one genome currently affected by it.
>>If that is not the root cause here, find out what is and create a jira issue to address it.
Either way, it would also be good to check a few other genomes to see which/how many are affected.
Attachments
Issue Links
- relates to
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IGBF-2583 Investigate ProtAnnot fail to load Lotmaria passim genes
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- Closed
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Activity
| Field | Original Value | New Value |
|---|---|---|
| Link | This issue relates to IGBF-1356 [ IGBF-1356 ] |
| Link | This issue relates to IGBF-1361 [ IGBF-1361 ] |
| Assignee | Ann Loraine [ aloraine ] | Ivory Blakley [ ieclabau ] |
IGB name of genome assembly:
L_passim_Apr_2014
Link to genome assembly directory in IGBQuickload.org:
http://igbquickload.org/quickload/L_passim_Apr_2014/
In that quickload directory, there is only one sequence file:
C_mellificae_Apr_2014.2bit
I expected to find a file called:
L_passim_Apr_2014.2bit
or
L_passim_Apr_2014.fa
I don't think IGB requires the name of the sequence file to follow any particular convention.
---I was mistaken, see comment below.
In the html header, it links to this page,
https://www.ncbi.nlm.nih.gov/bioproject/PRJNA78249
which says:
"This organism, ... was originally identified as Crithidia mellificae strain SF ... and was reclassified and renamed Lotmaria passim strain SF in 2015 ..."
| Assignee | Ivory Blakley [ ieclabau ] | Ann Loraine [ aloraine ] |
IGB expects genome sequence file to use convention G_species_[optional suffixes_]MMM_YYYY
To fix: rename sequence file in Quickload (igbquickload.org) and backup Quickload (scidas-hosted)
I was surprised to learn the name mattered.
But the documentation does already say that here:
https://wiki.transvar.org/display/igbman/Sharing+data+for+a+custom+genome+not+already+part+of+IGB+QuickLoad
In the instructions for making the sequence file for a new genome in quickload:
"The second argument (G_species_MMM_YYYY.2bit) should have the same name as your genome version and use the .2bit file extension."
| Summary | Cannot load sequence from Lotmaria genome | Fix IGB Quickload directory L_passim_Apr_2014/ |
Nowlan & David added this. Will ask NF for clarification.
| Rank | Ranked higher |
| Fix Version/s | 9.0.2 Minor Release [ 10600 ] | |
| Story Points | 0.25 | |
| Labels | Advanced |
| Rank | Ranked higher |
The current name in IGB is correct: L_passim_Apr_2014
Crithidia mellificae, strain SF was renamed to Lotmaria passim, strain SF.
To avoid confusion amongst users, a user asked David and I to update the name while also providing synonyms to the previous name (Crithidia). We updated the synonyms file to reflect the name change, but left all of the annotation/sequence files as Crithidia.
ProtAnnot (and IGB?) appear to be failing to recognize the 2bit file as having sequence data for the genome.
| Summary | Fix IGB Quickload directory L_passim_Apr_2014/ | Fix genome sequence loading for Quickload L_passim_Apr_2014 |
| Rank | Ranked higher |
| Fix Version/s | 9.0.2 Minor Release [ 10600 ] |
| Rank | Ranked higher |
| Assignee | Ann Loraine [ aloraine ] |
Someone renamed the .2bit file to L_passim_Apr_2014.2bit in the quickload and scidas. I can load the sequence file for Lotmaria passim in IGB 9.0.2.
When loading protannot, I am getting the following error and nothing is loading in ProtAnnot:
15:04:11.079 INFO c.a.igb.view.load.GeneralLoadUtils - All residues in range are already loaded on sequence Contig_2
ERROR: Sequence string passed to DNAUtils.translate() is empty
15:04:11.081 ERROR c.a.genometry.thread.CThreadWorker - com.affymetrix.genometry.span.SimpleSeqSpan cannot be cast to com.affymetrix.genometry.MutableSeqSpan
java.lang.ClassCastException: com.affymetrix.genometry.span.SimpleSeqSpan cannot be cast to com.affymetrix.genometry.MutableSeqSpan
at com.affymetrix.genometry.util.SeqUtils.transformLeafSymmetry(SeqUtils.java:709) ~[na:na]
at com.affymetrix.genometry.util.SeqUtils.transformSymmetry(SeqUtils.java:592) ~[na:na]
at com.affymetrix.genometry.util.SeqUtils.transformSymmetry(SeqUtils.java:526) ~[na:na]
at org.lorainelab.igb.protannot.model.ProtannotParser.processCDS(ProtannotParser.java:575) ~[na:na]
at org.lorainelab.igb.protannot.model.ProtannotParser.processMRNA(ProtannotParser.java:528) ~[na:na]
at org.lorainelab.igb.protannot.model.ProtannotParser.processDNASeq(ProtannotParser.java:402) ~[na:na]
at org.lorainelab.igb.protannot.model.ProtannotParser.parse(ProtannotParser.java:235) ~[na:na]
at org.lorainelab.igb.protannot.ProtAnnotAction.load(ProtAnnotAction.java:731) ~[na:na]
at org.lorainelab.igb.protannot.ProtAnnotAction$2.runInBackground(ProtAnnotAction.java:262) ~[na:na]
at com.affymetrix.genometry.thread.CThreadWorker.doInBackground(CThreadWorker.java:73) ~[na:na]
at javax.swing.SwingWorker$1.call(SwingWorker.java:295) [na:1.8.0_192]
at java.util.concurrent.FutureTask.run(FutureTask.java:266) [na:1.8.0_192]
at javax.swing.SwingWorker.run(SwingWorker.java:334) [na:1.8.0_192]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) [na:1.8.0_192]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) [na:1.8.0_192]
at java.lang.Thread.run(Thread.java:748) [na:1.8.0_192]
| Workflow | Loraine Lab Workflow [ 18056 ] | Fall 2019 Workflow Update [ 18885 ] |
| Workflow | Fall 2019 Workflow Update [ 18885 ] | Revised Fall 2019 Workflow Update [ 21012 ] |
| Status | Open [ 1 ] | To-Do [ 10305 ] |
Is this now fixed?
| Epic Link | IGBF-1765 [ 17855 ] |
Able to load the sequence for L_passim_Apr_2014 in Master 9.1.6 on Mac.
There is a separate issue regarding ProtAnnot failing to load gene models. I have created a new issue IGBF-2583.
Closing issue.
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
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