Details
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Type:
Task
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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:None
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Story Points:1
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Epic Link:
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Sprint:Fall 1 - Sep 5
Description
Relates to error: IGBF-3420
Error:
Exception in thread "main" java.lang.RuntimeException: Postion is too high (more than 64792705)
at org.biojava.nbio.genome.parsers.twobit.TwoBitParser.setCurrentSequencePosition(TwoBitParser.java:191)
at org.biojava.nbio.genome.parsers.twobit.TwoBitParser.loadFragment(TwoBitParser.java:332)
at org.lorainelab.findjunctions.FindJunctions.main(FindJunctions.java:249)
Issue: Looked at the bam file which looks fine but there are reads that expand upon the chromosome. They have been soft clipped but find_junctions isn't taking that into consideration and won't process the file entirely to create the .FJ.bed.gz file.
Visualize the error in IGB.
Attachments
Issue Links
Activity
Next step: Create ticket to modify junction code so that it accepts soft clipping issue and the junction file can be complete.
I have added a test bam file with the problematic reads (SL40ch10_64782127_64792705.bam as well as its index) from Malintka-R1-0hr-25C-self.bam.
Code:
samtools view -b Malintka-R1-0hr-25C-self.bam SL4.0ch10:64782127-64792705 > SL40ch10_64782127_64792705.bam samtools index SL40ch10_64782127_64792705.bam
To test the SL40ch10_64782127_64792705.bam with find junctions run:
java -jar find-junctions-1.0.0-jar-with-dependencies.jar -u -f 5 -b S_lycopersicum_Sep_2019.2bit -o SL40ch10_64782127_64792705.FJ.bed SL40ch10_64782127_64792705.bam
The S_lycopersicum_Sep_2019.2bit file can be found here.
The find-junctions-1.0.0-jar-with-dependencies.jar can be found here.
Files used to visualize error:
- Proof nothing wrong with bam file: Malintka-R1-0hr-25C-self.bam
- Needed to view bam in IGB: Malintka-R1-0hr-25C-self.bam.bai
- Error file: Malintka-R1-0hr-25C-self.FJ.bed.gz
- Control file: Nagcarlang-R2-8hr-37C-self.FJ.bed.gz
Directory: /projects/tomato_genome/fnb/dataprocessing/30-804059537-KP/S_lycopersicum_Sep_2019/results/star_salmon
Visualization of the Junction Error in IGB:
Issue was seen at end of chromosome 10 SL4. You can see in the red track that a lot of data is missing for the junction file, while in the green the junction file is normal and was processed correctly.
End of chromosome 10:
I have created a new ticket, IGBF-3435 to address the edge case in FindJunctions.