RunLog

Pasting the first occurence of the error with a few flanking lines, before and after (the log file is very large),

[2014-09-02 20:17] blue: Timing: validation
[2014-09-02 20:17] blue: ipython: compare_to_rm
[2014-09-03 00:17] bn0106: Resource requests: ; memory: 1.0; cores: 1
[2014-09-03 00:17] bn0106: Configuring 8 jobs to run, using 1 cores each with 1.2g of memory reserved for each job
[2014-09-03 00:16] bn0208: Resource requests: ; memory: 1.0; cores: 1
[2014-09-03 00:16] bn0208: Configuring 8 jobs to run, using 1 cores each with 1.2g of memory reserved for each job
[2014-09-03 00:17] bn0208: Comparing variant calls using bcbio.variation : NA12878_Germline_NGv3bed
[2014-09-03 00:17] bn0208: Picked up _JAVA_OPTIONS: -XX:+UseSerialGC
[2014-09-03 00:17] bn0106: Comparing variant calls using bcbio.variation : NA12878_Germline_NGv3bed
[2014-09-03 00:17] bn0106: Picked up _JAVA_OPTIONS: -XX:+UseSerialGC
[2014-09-03 00:17] bn0106: 2014-09-02 20:17:22,586 [INFO ] MLog clients using log4j logging.
[2014-09-03 00:17] bn0208: 2014-09-02 20:17:03,881 [INFO ] MLog clients using log4j logging.
[2014-09-03 00:17] bn0106: 2014-09-02 20:17:22,939 [INFO ] State :begin :: {:desc "Starting variation analysis"}
[2014-09-03 00:17] bn0208: 2014-09-02 20:17:04,246 [INFO ] State :begin :: {:desc "Starting variation analysis"}
[2014-09-03 00:17] bn0106: 2014-09-02 20:17:22,971 [INFO ] State :clean :: {:desc "Cleaning input VCF: ref"}
[2014-09-03 00:17] bn0208: 2014-09-02 20:17:04,278 [INFO ] State :clean :: {:desc "Cleaning input VCF: ref"}
[2014-09-03 00:17] bn0106: java.lang.IndexOutOfBoundsException
[2014-09-03 00:17] bn0106: 	at clojure.lang.PersistentVector.arrayFor(PersistentVector.java:107)
[2014-09-03 00:17] bn0106: 	at clojure.lang.PersistentVector.nth(PersistentVector.java:111)
[2014-09-03 00:17] bn0106: 	at clojure.lang.RT.nth(RT.java:763)
[2014-09-03 00:17] bn0106: 	at bcbio.variation.normalize$clean_problem_vcf$remove_gap__2384.invoke(normalize.clj:573)
[2014-09-03 00:17] bn0106: 	at bcbio.variation.normalize$clean_problem_vcf$clean_line__2388.invoke(normalize.clj:582)
[2014-09-03 00:17] bn0106: 	at clojure.core$map$fn__4207.invoke(core.clj:2487)
[2014-09-03 00:17] bn0106: 	at clojure.lang.LazySeq.sval(LazySeq.java:42)
[2014-09-03 00:17] bn0106: 	at clojure.lang.LazySeq.seq(LazySeq.java:60)
[2014-09-03 00:17] bn0106: 	at clojure.lang.RT.seq(RT.java:484)
[2014-09-03 00:17] bn0106: 	at clojure.core$seq.invoke(core.clj:133)
[2014-09-03 00:17] bn0106: 	at clojure.core$filter$fn__4226.invoke(core.clj:2523)
[2014-09-03 00:17] bn0106: 	at clojure.lang.LazySeq.sval(LazySeq.java:42)
[2014-09-03 00:17] bn0106: 	at clojure.lang.LazySeq.seq(LazySeq.java:60)
[2014-09-03 00:17] bn0106: 	at clojure.lang.RT.seq(RT.java:484)
[2014-09-03 00:17] bn0106: 	at clojure.core$seq.invoke(core.clj:133)
[2014-09-03 00:17] bn0106: 	at clojure.core$map$fn__4207.invoke(core.clj:2479)
[2014-09-03 00:17] bn0106: 	at clojure.lang.LazySeq.sval(LazySeq.java:42)
[2014-09-03 00:17] bn0106: 	at clojure.lang.LazySeq.seq(LazySeq.java:60)
[2014-09-03 00:17] bn0106: 	at clojure.lang.Cons.next(Cons.java:39)
[2014-09-03 00:17] bn0106: 	at clojure.lang.RT.next(RT.java:598)
[2014-09-03 00:17] bn0106: Uncaught exception occurred
Traceback (most recent call last):
  File "/group/ngs/src/bcbio-nextgen/0.8.1a/rhel6-x64/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 22, in run
    _do_run(cmd, checks, log_stdout)
  File "/group/ngs/src/bcbio-nextgen/0.8.1a/rhel6-x64/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 121, in _do_run
    raise subprocess.CalledProcessError(exitcode, error_msg)
CalledProcessError: Command 'java -Xms750m -Xmx4000m -XX:+UseSerialGC -Djava.io.tmpdir=/gpfs/ngs/oncology/Analysis/external/EXT_001_NA12878/EDGE/NA12878_bcbio_NGv3bed/work/validate/NA12878_Germline_NGv3bed/freebayes/tmp -jar /group/ngs/src/bcbio-nextgen/0.8.1a/rhel6-x64/share/java/bcbio_variation/bcbio.variation-0.1.7-standalone.jar variant-compare /gpfs/ngs/oncology/Analysis/external/EXT_001_NA12878/EDGE/NA12878_bcbio_NGv3bed/work/validate/NA12878_Germline_NGv3bed/freebayes/config/validate.yaml
Picked up _JAVA_OPTIONS: -XX:+UseSerialGC
2014-09-02 20:17:22,586 [INFO ] MLog clients using log4j logging.
2014-09-02 20:17:22,939 [INFO ] State :begin :: {:desc "Starting variation analysis"}
2014-09-02 20:17:22,971 [INFO ] State :clean :: {:desc "Cleaning input VCF: ref"}
java.lang.IndexOutOfBoundsException
	at clojure.lang.PersistentVector.arrayFor(PersistentVector.java:107)
	at clojure.lang.PersistentVector.nth(PersistentVector.java:111)
	at clojure.lang.RT.nth(RT.java:763)
	at bcbio.variation.normalize$clean_problem_vcf$remove_gap__2384.invoke(normalize.clj:573)
	at bcbio.variation.normalize$clean_problem_vcf$clean_line__2388.invoke(normalize.clj:582)
	at clojure.core$map$fn__4207.invoke(core.clj:2487)
	at clojure.lang.LazySeq.sval(LazySeq.java:42)
	at clojure.lang.LazySeq.seq(LazySeq.java:60)
	at clojure.lang.RT.seq(RT.java:484)
	at clojure.core$seq.invoke(core.clj:133)
	at clojure.core$filter$fn__4226.invoke(core.clj:2523)
	at clojure.lang.LazySeq.sval(LazySeq.java:42)
	at clojure.lang.LazySeq.seq(LazySeq.java:60)
	at clojure.lang.RT.seq(RT.java:484)
	at clojure.core$seq.invoke(core.clj:133)
	at clojure.core$map$fn__4207.invoke(core.clj:2479)
	at clojure.lang.LazySeq.sval(LazySeq.java:42)
	at clojure.lang.LazySeq.seq(LazySeq.java:60)
	at clojure.lang.Cons.next(Cons.java:39)
	at clojure.lang.RT.next(RT.java:598)
	at clojure.core$next.invoke(core.clj:64)
	at clojure.core$dorun.invoke(core.clj:2781)
	at clojure.core$doall.invoke(core.clj:2796)
	at bcbio.variation.normalize$clean_problem_vcf$fn__2390$fn__2391.invoke(normalize.clj:599)
	at bcbio.variation.normalize$clean_problem_vcf$fn__2390.invoke(normalize.clj:595)
	at bcbio.variation.normalize$clean_problem_vcf.doInvoke(normalize.clj:594)
	at clojure.lang.RestFn.invoke(RestFn.java:529)
	at bcbio.variation.combine$gatk_normalize$fn__3284.invoke(combine.clj:180)
	at clojure.core$map$fn__4207.invoke(core.clj:2485)
	at clojure.lang.LazySeq.sval(LazySeq.java:42)
	at clojure.lang.LazySeq.seq(LazySeq.java:60)
	at clojure.lang.RT.seq(RT.java:484)
	at clojure.lang.LazilyPersistentVector.create(LazilyPersistentVector.java:31)
	at clojure.core$vec.invoke(core.clj:354)
	at bcbio.variation.combine$gatk_normalize.invoke(combine.clj:179)
	at bcbio.variation.compare$prepare_vcf_calls$fn__7534.invoke(compare.clj:120)
	at clojure.core$map$fn__4207.invoke(core.clj:2487)
	at clojure.lang.LazySeq.sval(LazySeq.java:42)
	at clojure.lang.LazySeq.seq(LazySeq.java:60)
	at clojure.lang.RT.seq(RT.java:484)
	at clojure.lang.LazilyPersistentVector.create(LazilyPersistentVector.java:31)
	at clojure.core$vec.invoke(core.clj:354)
	at bcbio.variation.compare$prepare_vcf_calls.invoke(compare.clj:121)
	at bcbio.variation.compare$variant_comparison_from_config$iter__7590__7594$fn__7595.invoke(compare.clj:255)
	at clojure.lang.LazySeq.sval(LazySeq.java:42)
	at clojure.lang.LazySeq.seq(LazySeq.java:60)
	at clojure.lang.RT.seq(RT.java:484)
	at clojure.core$seq.invoke(core.clj:133)
	at clojure.core$tree_seq$walk__4647$fn__4648.invoke(core.clj:4475)
	at clojure.lang.LazySeq.sval(LazySeq.java:42)
	at clojure.lang.LazySeq.seq(LazySeq.java:60)
	at clojure.lang.LazySeq.more(LazySeq.java:96)
	at clojure.lang.RT.more(RT.java:607)
	at clojure.core$rest.invoke(core.clj:73)
	at clojure.core$flatten.invoke(core.clj:6478)
	at bcbio.variation.compare$variant_comparison_from_config.invoke(compare.clj:254)
	at bcbio.variation.compare$_main.invoke(compare.clj:274)
	at clojure.lang.AFn.applyToHelper(AFn.java:161)
	at clojure.lang.AFn.applyTo(AFn.java:151)
	at clojure.core$apply.invoke(core.clj:617)
	at bcbio.variation.core$_main.doInvoke(core.clj:35)
	at clojure.lang.RestFn.applyTo(RestFn.java:137)
	at bcbio.variation.core.main(Unknown Source)
' returned non-zero exit status 255
[2014-09-03 00:17] bn0106: Unexpected error
Traceback (most recent call last):
  File "/group/ngs/src/bcbio-nextgen/0.8.1a/rhel6-x64/anaconda/lib/python2.7/site-packages/bcbio/distributed/ipythontasks.py", line 38, in _setup_logging
    yield config
  File "/group/ngs/src/bcbio-nextgen/0.8.1a/rhel6-x64/anaconda/lib/python2.7/site-packages/bcbio/distributed/ipythontasks.py", line 217, in compare_to_rm
    return ipython.zip_args(apply(validate.compare_to_rm, *args))
  File "/group/ngs/src/bcbio-nextgen/0.8.1a/rhel6-x64/anaconda/lib/python2.7/site-packages/bcbio/variation/validate.py", line 77, in compare_to_rm
    bcbio_variation_comparison(val_config_file, base_dir, toval_data)
  File "/group/ngs/src/bcbio-nextgen/0.8.1a/rhel6-x64/anaconda/lib/python2.7/site-packages/bcbio/variation/validate.py", line 95, in bcbio_variation_comparison
    do.run(cmd, "Comparing variant calls using bcbio.variation", data)
  File "/group/ngs/src/bcbio-nextgen/0.8.1a/rhel6-x64/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 22, in run
    _do_run(cmd, checks, log_stdout)
  File "/group/ngs/src/bcbio-nextgen/0.8.1a/rhel6-x64/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 121, in _do_run
    raise subprocess.CalledProcessError(exitcode, error_msg)
CalledProcessError: Command 'java -Xms750m -Xmx4000m -XX:+UseSerialGC -Djava.io.tmpdir=/gpfs/ngs/oncology/Analysis/external/EXT_001_NA12878/EDGE/NA12878_bcbio_NGv3bed/work/validate/NA12878_Germline_NGv3bed/freebayes/tmp -jar /group/ngs/src/bcbio-nextgen/0.8.1a/rhel6-x64/share/java/bcbio_variation/bcbio.variation-0.1.7-standalone.jar variant-compare /gpfs/ngs/oncology/Analysis/external/EXT_001_NA12878/EDGE/NA12878_bcbio_NGv3bed/work/validate/NA12878_Germline_NGv3bed/freebayes/config/validate.yaml
Picked up _JAVA_OPTIONS: -XX:+UseSerialGC
2014-09-02 20:17:22,586 [INFO ] MLog clients using log4j logging.
2014-09-02 20:17:22,939 [INFO ] State :begin :: {:desc "Starting variation analysis"}
2014-09-02 20:17:22,971 [INFO ] State :clean :: {:desc "Cleaning input VCF: ref"}
java.lang.IndexOutOfBoundsException
	at clojure.lang.PersistentVector.arrayFor(PersistentVector.java:107)
	at clojure.lang.PersistentVector.nth(PersistentVector.java:111)
	at clojure.lang.RT.nth(RT.java:763)
	at bcbio.variation.normalize$clean_problem_vcf$remove_gap__2384.invoke(normalize.clj:573)
	at bcbio.variation.normalize$clean_problem_vcf$clean_line__2388.invoke(normalize.clj:582)
	at clojure.core$map$fn__4207.invoke(core.clj:2487)
	at clojure.lang.LazySeq.sval(LazySeq.java:42)