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[ADAM-666] Clean up key not found error in partitioner code. #667

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fnothaft commented May 1, 2015

Resolves #666. Checks sequence dictionary when partitioning keys and throws an IllegalArgumentException with the violating key and a list of known contigs.

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AmplabJenkins May 1, 2015

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/693/
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AmplabJenkins commented May 1, 2015

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/693/
Test PASSed.

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Jaeki May 1, 2015

Thank you for your work. I will try to run again after pulling this. BTW. I used the same data that you've used in your paper.( https://github.com/fnothaft/docs/blob/master/adam/sigmod-15/adam.pdf ), NA12878 high coverage.

Jaeki commented May 1, 2015

Thank you for your work. I will try to run again after pulling this. BTW. I used the same data that you've used in your paper.( https://github.com/fnothaft/docs/blob/master/adam/sigmod-15/adam.pdf ), NA12878 high coverage.

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massie May 1, 2015

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Thanks, Frank!

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massie commented May 1, 2015

Thanks, Frank!

massie added a commit that referenced this pull request May 1, 2015

Merge pull request #667 from fnothaft/knf-logging
[ADAM-666] Clean up key not found error in partitioner code.

@massie massie merged commit b2ca494 into bigdatagenomics:master May 1, 2015

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Jaeki May 4, 2015

Hi, Frank.
I got the following error. Which data is wrong among reference and reads?

15/05/04 09:05:26 INFO TaskSetManager: Lost task 64.1 in stage 3.0 (TID 176) on executor swat3-39: java.lang.IllegalArgumentException (requirement failed: Received key (ReferenceRegion(9,129957604,129957605,Independent)) that did not map to a known contig. Contigs are:
chr11
chr5
chr22
chr8
chr19
chrY
chr1
chr15
chr12
chr18
chr20
chr2
chr13
chr7
chr14
chr3
chrM
chr17
chr4
chr6
chr9
chrX
chr10
chr21
chr16) [duplicate 1]
15/05/04 09:05:26 INFO TaskSetManager: Lost task 36.1 in stage 3.0 (TID 169) on executor swat3-40: java.lang.IllegalArgumentException (requirement failed: Received key (ReferenceRegion(hs37d5,10134550,10134551,Independent)) that did not map to a known contig. Contigs are:
chr11
chr5
chr22
chr8
chr19
chrY
chr1
chr15
chr12
chr18
chr20
chr2
chr13
chr7
chr14
chr3
chrM
chr17
chr4
chr6
chr9
chrX
chr10
chr21
chr16) [duplicate 1]

Jaeki commented May 4, 2015

Hi, Frank.
I got the following error. Which data is wrong among reference and reads?

15/05/04 09:05:26 INFO TaskSetManager: Lost task 64.1 in stage 3.0 (TID 176) on executor swat3-39: java.lang.IllegalArgumentException (requirement failed: Received key (ReferenceRegion(9,129957604,129957605,Independent)) that did not map to a known contig. Contigs are:
chr11
chr5
chr22
chr8
chr19
chrY
chr1
chr15
chr12
chr18
chr20
chr2
chr13
chr7
chr14
chr3
chrM
chr17
chr4
chr6
chr9
chrX
chr10
chr21
chr16) [duplicate 1]
15/05/04 09:05:26 INFO TaskSetManager: Lost task 36.1 in stage 3.0 (TID 169) on executor swat3-40: java.lang.IllegalArgumentException (requirement failed: Received key (ReferenceRegion(hs37d5,10134550,10134551,Independent)) that did not map to a known contig. Contigs are:
chr11
chr5
chr22
chr8
chr19
chrY
chr1
chr15
chr12
chr18
chr20
chr2
chr13
chr7
chr14
chr3
chrM
chr17
chr4
chr6
chr9
chrX
chr10
chr21
chr16) [duplicate 1]

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fnothaft May 4, 2015

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@Jaeki The names of your reference contigs and aligned file contigs are different. E.g., your reads are aligned to a chromosome 9 assembly called "9" while your reference contains a chromosome 9 assembly called "chr9".

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fnothaft commented May 4, 2015

@Jaeki The names of your reference contigs and aligned file contigs are different. E.g., your reads are aligned to a chromosome 9 assembly called "9" while your reference contains a chromosome 9 assembly called "chr9".

@fnothaft fnothaft deleted the fnothaft:knf-logging branch May 4, 2015

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