[BARNA-194] Reading gene sequences close to the chromosome border Created:
16/Jul/12 Updated: 09/Oct/15
Status:
Project:
Component/s:
Affects
Version/s:
Fix Version/s:
Reopened
Barna Package
Simulator
Simulator 1.0.2 (API 1.11)
Type:
Reporter:
Resolution:
Labels:
Remaining
Estimate:
Time Spent:
Original
Estimate:
Bug
Priority:
Micha Sammeth
Assignee:
Unresolved
Votes:
git-branch-master, git-branch-sam
Not Specified
Attachments:
Simulator 1.1 (API 1.15)
Major
Micha Sammeth
1
Not Specified
Not Specified
reopen.par
Description
[LIBRARY] Configuration
Mode: RH
PWM: No
RT MIN: 200
RT MAX: 5500
Processing Fragments ********** OK (00:03:57)
34569813 mol: in 34569746, new 67, out 34565024
avg Len 214.94418, maxLen 744
start amplification
[INFO] Loading default PCR distribution
preparing transcript sequences ******* ERROR
[ERROR] Error while preparing sequences: Problems reading sequence Chr3: pos -1, len 100,
check whether chromosomal sequence exists / has the correct size
java.lang.RuntimeException: Problems reading sequence Chr3: pos -1, len 100,
check whether chromosomal sequence exists / has the correct size
at barna.model.Graph.readSequence(Graph.java:585)
at barna.model.Graph.readSequence(Graph.java:473)
at barna.model.Transcript.getSplicedSequence(Transcript.java:459)
at barna.flux.simulator.fragmentation.Fragmenter.getMapTxSeq(Fragmenter.java:375)
at barna.flux.simulator.fragmentation.Fragmenter.process(Fragmenter.java:539)
at barna.flux.simulator.fragmentation.Fragmenter.call(Fragmenter.java:258)
at barna.flux.simulator.SimulationPipeline.call(SimulationPipeline.java:424)
at barna.flux.simulator.SimulationPipeline.call(SimulationPipeline.java:53)
at barna.commons.launcher.Flux.main(Flux.java:212)
Caused by: java.lang.NegativeArraySizeException
at barna.model.Graph.readSequence(Graph.java:507)
at barna.model.Graph.readSequence(Graph.java:473)
at barna.model.Graph.readSequence(Graph.java:529)
... 8 more
FAILED
Comments
Comment by Jenkins [ 17/Jul/12 ]
Integrated in
Barna-All-Nightly-Builds #49
Fix reading across genome border (BARNA-194) (Revision
921f46c66fadea1e92bcfe23de2ae3b6f34c5ba7)
Result = SUCCESS
micha : 921f46c66fadea1e92bcfe23de2ae3b6f34c5ba7
Files :
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barna.model/src/test/java/barna/model/splicegraph/GraphTest.java
barna.model/src/test/java/barna/model/GraphTest.java
barna.model/src/main/java/barna/model/Graph.java
barna.model/src/test/java/barna/model/splicegraph/SplicingGraphTest.java
Comment by Anonymous [ 19/Jul/12 ]
Is there a nightly build I could download with this error fixed?
Comment by Micha Sammeth [ 19/Jul/12 ]
Yes, the fix should already be included in yesterday's nightly build
http://sammeth.net/artifactory/barna-nightly/barna/barna.simulator/1.0.4-20120718010037/
After testing a problematic case that has been provided by some user, we will include the fix in
a simulator release.
Comment by Anonymous [ 19/Jul/12 ]
Hi, I am Arun, the one who posted about this on the flux-wiki forum. I downloaded the nightlybuild and ran it again, it ends up with the same error. But now, it happens after filtering and
during PCR amplification stage. I am creating a new post with this and all another error and 2
other questions that have been bothering me for quite a while now in a new post here:
http://fluxcapacitor.wikidot.com/forum/t-529477/a-comprehensive-error-report-of-what-i-havefound-so-far. It would be great if you could spare some of your time in answering these
questions!
Arun.
Comment by Micha Sammeth [ 26/Jul/12 ]
I am getting the following error with the latest nightly build (I am trying to simulate expression
from a reference genome with many contigs, hence many short chromosomes)
SEQUENCING] getting the reads
Initializing Fragment Index
Indexing ********** OK (00:00:03)
2818814 lines indexed (2818814 fragments, 2630 entries)
sequencing [WARN] skipped line ACCK01000001.1 mgb2gtf gene 148 1200 . + . transcript_id
"CATMIT_00001"; gene_id "CATMIT_00001";
*[ERROR] Error while sequencing : Problems reading BED object ACCK01000003.1 14785
14861 ACCK01000003.1:14115-14861W:CATMIT_00041:5:747:466:746:A/2 0 - . . 0,0,0 1 76
0
java.lang.RuntimeException: Problems reading BED object ACCK01000003.1 14785 14861
ACCK01000003.1:14115-14861W:CATMIT_00041:5:747:466:746:A/2 0 - . . 0,0,0 1 76 0
at barna.model.bed.BEDobject2.readSequence(BEDobject2.java:335)
at barna.flux.simulator.Sequencer.createQSeq(Sequencer.java:600)
at barna.flux.simulator.Sequencer$SequenceWriter.writeRead(Sequencer.java:936)
at barna.flux.simulator.Sequencer$Processor.process(Sequencer.java:771)
at barna.flux.simulator.Sequencer.sequence(Sequencer.java:247)
at barna.flux.simulator.Sequencer.call(Sequencer.java:120)
at barna.flux.simulator.SimulationPipeline.call(SimulationPipeline.java:436)
at barna.flux.simulator.SimulationPipeline.call(SimulationPipeline.java:53)
at barna.commons.launcher.Flux.main(Flux.java:212)
Caused by: java.lang.RuntimeException: Problems reading chromosome ACCK01000003.1
from 14785 to 14780
I managed a work-around wherein I add 100 N nucleotides to the end of each of my
'chromosomes' as buffer and updated the ranges of the GTF file accordingly. Obviously this is
not ideal (I would rather it not sequence past the boundary rather than having to add garbage to
the simulator which I will have to remove later)
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