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Waltz error processing read #174

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ionox0 opened this issue Apr 9, 2019 · 0 comments
Open

Waltz error processing read #174

ionox0 opened this issue Apr 9, 2019 · 0 comments

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@ionox0
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ionox0 commented Apr 9, 2019

Appears to be related to repetitive sequences:

u32.cbio.private 2019-04-08 14:26:52,870 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv    INFO:cwltool:[job CountReads.cwl] /ifs/work/bergerm1/Innovation/projects/Ian/06302R_06302S/set_4/Project_06302_R/MB-Grail-2.0.0/out_tmpdirQTXvg7$ /opt/common/CentOS_6/java/jdk1.8.0_31/bin/java \
u32.cbio.private 2019-04-08 14:26:52,871 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv        -server \
u32.cbio.private 2019-04-08 14:26:52,871 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv        -Xms4g \
u32.cbio.private 2019-04-08 14:26:52,871 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv        -Xmx4g \
u32.cbio.private 2019-04-08 14:26:52,871 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv        -cp \
u32.cbio.private 2019-04-08 14:26:52,871 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv        /home/johnsoni/vendor_tools/Waltz-2.0.jar \
u32.cbio.private 2019-04-08 14:26:52,871 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv        org.mskcc.juber.waltz.countreads.CountReads \
u32.cbio.private 2019-04-08 14:26:52,871 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv        /ifs/work/bergerm1/Innovation/projects/Ian/06302R_06302S/set_4/Project_06302_R/MB-Grail-2.0.0/tmpxgEhKL/stg12c4ff7a-69f3-4545-8bf5-1e268855682c/MSK-ML-0067-01-5001853C_cl_aln_srt_MD_IR_FX_BR.bam \
u32.cbio.private 2019-04-08 14:26:52,872 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv        50 \
u32.cbio.private 2019-04-08 14:26:52,872 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv        /ifs/work/bergerm1/Innovation/projects/Ian/06302R_06302S/set_4/Project_06302_R/MB-Grail-2.0.0/tmpxgEhKL/stged056e71-a90f-400e-a181-085a71615eb6/juber-hg19-gene-list.bed \
u32.cbio.private 2019-04-08 14:26:52,872 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv        /ifs/work/bergerm1/Innovation/projects/Ian/06302R_06302S/set_4/Project_06302_R/MB-Grail-2.0.0/tmpxgEhKL/stgfff0f880-9339-4a94-97c5-88d9c48c1105/MSK-ACCESS-v1_0-probe-A.sorted.bed
u32.cbio.private 2019-04-08 14:26:52,872 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv    Scanning MSK-ML-0067-01-5001853C_cl_aln_srt_MD_IR_FX_BR.bam
u32.cbio.private 2019-04-08 14:26:52,872 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv    Scanning entire MSK-ML-0067-01-5001853C_cl_aln_srt_MD_IR_FX_BR.bam
u32.cbio.private 2019-04-08 14:26:52,872 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv    Problem processing record:
u32.cbio.private 2019-04-08 14:26:52,872 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv    A00227:98:HJCFJDMXX:2:1352:31774:13401:TGC+CCA	161	2	24487571	41	5S66I25S	=	24487571	81	TACACACACACACACACACACACACACACACAAACACACGTAGCATGAATCGATTGACCTACTCTGTTCCAACTGTCGATAAACAGATCTATCTAC	>><<>??@@@@@@@@@A@@@@A@@@@@@@@@@*9-@@7:6,B.0)9.8BCD((B-.8?9=590D0@>--9)),D.=,'7*&)),(C'7-/&7-04-	YA:Z:2:24487306:237M2D26M89I301M	BD:Z:BBF;=>==<=<<;<;<;<:;:;:;::9:9:9:E=F:898BBEHHFGGHGFIFHGFEHFFHGDGDDG:FHJIEFHI;IHJIFH?H=LIKNILHKFIF	PG:Z:MarkDuplicates	RG:Z:MSK-ML-0067-01-5001853C	BI:Z:DDF>?@?@?@>?>?>?>?>?=>=>=>=>=>=>I@G=<=<FEHJJIHHJIIIGJIHHJGIKIEJFGK>IIKKIHKL?KILLHJCKANMNNMOKJHJF	NM:i:66	YM:i:2	YO:Z:2:24487567:+:5S66M25S	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@	MQ:i:60	OQ:Z:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,:,FF:::,F,,,:,:FFF,,F,,:F::::,F,FF,,:,,,F,F,,:,,,,,,F,:,,,:,,:,	AS:i:56	XS:i:41	YX:i:19
u32.cbio.private 2019-04-08 14:26:52,873 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv
u32.cbio.private 2019-04-08 14:26:52,873 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv    java.lang.IllegalArgumentException: Invalid range: [24487571?24487570]
u32.cbio.private 2019-04-08 14:26:52,873 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv    	at com.google.common.collect.Range.<init>(Range.java:363)
u32.cbio.private 2019-04-08 14:26:52,873 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv    	at com.google.common.collect.Range.create(Range.java:153)
u32.cbio.private 2019-04-08 14:26:52,873 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv    	at com.google.common.collect.Range.closed(Range.java:177)
u32.cbio.private 2019-04-08 14:26:52,873 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv    	at org.mskcc.juber.intervals.IntervalNameMap.getIntersecting(IntervalNameMap.java:61)
u32.cbio.private 2019-04-08 14:26:52,873 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv    	at org.mskcc.juber.waltz.countreads.CountReads.scanBam(CountReads.java:109)
u32.cbio.private 2019-04-08 14:26:52,873 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv    	at org.mskcc.juber.waltz.countreads.CountReads.main(CountReads.java:67)
u32.cbio.private 2019-04-08 14:26:52,874 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv    Problem processing record:
u32.cbio.private 2019-04-08 14:26:52,874 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv    A00227:98:HJCFJDMXX:2:1365:29758:4961:TCC+AAT	81	3	13723579	33	9S49I39S	=	13723496	-83	TGTGTGCGCGCATGTGTGTGCATGCATGTGTATGTGCATGTGCGTGTGCGTGTGTGTGCGTGCATGTGTGTGTGTGAGTGTGCATGTGTGTGCATGC	;;;;<B>C>D@B???????D@B?D@B@@@@BC@@@EAC@@@E@@@@@E@A@AAAAAAFAAAFBDAAAAAAAAAA;FFAAAAFBDAA@@@@@E@@<A>	SA:Z:X,14904626,+,5S44M48S,0,2;	YA:Z:3:13723271:308M52I47M62I259M	BD:Z:;:;:KGFGFJKK=;<;<:HHIIGGHH:9:ECG98FFGG98FBB898FBB8989898FBB8FFGH:9:9:9:9::IFI:;:HIJJ<;<<=<JKLIHBB	PG:Z:MarkDuplicates	RG:Z:MSK-ML-0067-01-5001853C	BI:Z:>=>=OKJJIMMLA@@?@?KJJJKIII>=>FFI=<IHHH=<IDF<=<IDF<=<=<=<IDF<IHHH=<>=>=>=>=JGK=>>KJJJ?>?>@?LKKIJDD	NM:i:49	YM:i:1	YO:Z:3:13723597:-:9S49M39S	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@	MQ:i:60	OQ:Z:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF	AS:i:44	XS:i:34	YX:i:27
u32.cbio.private 2019-04-08 14:26:52,874 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv
u32.cbio.private 2019-04-08 14:26:52,874 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv    java.lang.IllegalArgumentException: Invalid range: [13723579?13723578]
u32.cbio.private 2019-04-08 14:26:52,874 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv    	at com.google.common.collect.Range.<init>(Range.java:363)
u32.cbio.private 2019-04-08 14:26:52,874 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv    	at com.google.common.collect.Range.create(Range.java:153)
u32.cbio.private 2019-04-08 14:26:52,874 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv    	at com.google.common.collect.Range.closed(Range.java:177)
u32.cbio.private 2019-04-08 14:26:52,875 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv    	at org.mskcc.juber.intervals.IntervalNameMap.getIntersecting(IntervalNameMap.java:61)
u32.cbio.private 2019-04-08 14:26:52,875 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv    	at org.mskcc.juber.waltz.countreads.CountReads.scanBam(CountReads.java:109)
u32.cbio.private 2019-04-08 14:26:52,875 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv    	at org.mskcc.juber.waltz.countreads.CountReads.main(CountReads.java:67)
u32.cbio.private 2019-04-08 14:26:52,875 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv    Problem processing record:
u32.cbio.private 2019-04-08 14:26:52,875 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv    A00227:98:HJCFJDMXX:2:1247:20473:10614:TAT+TAT	161	5	107963795	60	96I	=	107963795	63	CTTCTTATATGAGATCTTCAGTTCACATTTCTTTTTCTACACAGAGCTCACCAGGAAGCCTAGGAGGCACATAGAGTTTTTCCTGAGGGGTGTTTG	>A>ACAACBCADEDCEFBE@E@BE@@@CBBEEBBBBEEB@@@@EDEEEE@?B?DCCADDBDADCCDCD6??BADCC=@@@@CAC?BCBBA<>:<<;	YA:Z:5:107963602:193M101I294M	BD:Z:BBFIIIJGGGKKHHJLGGIIJIGII9:HG=HEE===GDGD989HEEHHDG8FHHIHGFHHHGHIHEJIG9:HDIGGIG>>?JLKKLIMIIJ=;G>G	PG:Z:MarkDuplicates	RG:Z:MSK-ML-0067-01-5001853C	BI:Z:DDIIJKLHHHJLJJKKIJJKKJIIJ=>IIBIHIAAAHGIE=<=JHHJKFI<IJJJJIIJIKIJJJIKKJ=>IFKJJKJCDDKMONNMOKLNB>IBI	NM:i:96	YM:i:0	YO:Z:N/A:107963795	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@	MQ:i:36	OQ:Z:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFF	AS:i:0	XS:i:0	YX:i:96
u32.cbio.private 2019-04-08 14:26:52,875 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv
u32.cbio.private 2019-04-08 14:26:52,875 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv    java.lang.IllegalArgumentException: Invalid range: [107963795?107963794]
u32.cbio.private 2019-04-08 14:26:52,875 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv    	at com.google.common.collect.Range.<init>(Range.java:363)
u32.cbio.private 2019-04-08 14:26:52,876 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv    	at com.google.common.collect.Range.create(Range.java:153)
u32.cbio.private 2019-04-08 14:26:52,876 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv    	at com.google.common.collect.Range.closed(Range.java:177)
u32.cbio.private 2019-04-08 14:26:52,876 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv    	at org.mskcc.juber.intervals.IntervalNameMap.getIntersecting(IntervalNameMap.java:61)
u32.cbio.private 2019-04-08 14:26:52,876 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv    	at org.mskcc.juber.waltz.countreads.CountReads.scanBam(CountReads.java:109)
u32.cbio.private 2019-04-08 14:26:52,876 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv    	at org.mskcc.juber.waltz.countreads.CountReads.main(CountReads.java:67)
u32.cbio.private 2019-04-08 14:26:52,876 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv    Problem processing record:
u32.cbio.private 2019-04-08 14:26:52,876 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv    A00227:98:HJCFJDMXX:2:1330:9805:21793:TAT+TAT	161	5	107963795	60	96I	=	107963795	63	CTTCTTATATGAGATCTTCAGTTCACATTTCTTTTTCTACACAGAGCTCACCAGGAAGCCTAGGAGGCACATAGAGTTTTTCCTGAGGGGTGTTTG	>A>ACAAC7CA9E);E?BE@E@BE@;@C;BEEBBB;EEB@@@)EDEEEE@?B?DCCADDBDADCCDCD6??BADCC=@@@@CAC?6CBBA<>:-<;	YA:Z:5:107963602:193M101I294M	BD:Z:BBFIIIJGGGKKHHJLGGIIJIGII9:HG=HEE===GDGD989HEEHHDG8FHHIHGFHHHGHIHEJIG9:HDIGGIG>>?JLKKLIMIIJ=;G>G	PG:Z:MarkDuplicates	RG:Z:MSK-ML-0067-01-5001853C	BI:Z:DDIIJKLHHHJLJJKKIJJKKJIIJ=>IIBIHIAAAHGIE=<=JHHJKFI<IJJJJIIJIKIJJJIKKJ=>IFKJJKJCDDKMONNMOKLNB>IBI	NM:i:96	YM:i:0	YO:Z:N/A:107963795	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@	MQ:i:36	OQ:Z:FFFFFFFF:FF:F,:F:FFFFFFFF:FF:FFFFFF:FFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFFFFFF,FF	AS:i:0	XS:i:0	YX:i:96
u32.cbio.private 2019-04-08 14:26:52,877 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv
u32.cbio.private 2019-04-08 14:26:52,877 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv    java.lang.IllegalArgumentException: Invalid range: [107963795?107963794]
u32.cbio.private 2019-04-08 14:26:52,877 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv    	at com.google.common.collect.Range.<init>(Range.java:363)
u32.cbio.private 2019-04-08 14:26:52,877 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv    	at com.google.common.collect.Range.create(Range.java:153)
u32.cbio.private 2019-04-08 14:26:52,877 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv    	at com.google.common.collect.Range.closed(Range.java:177)
u32.cbio.private 2019-04-08 14:26:52,877 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv    	at org.mskcc.juber.intervals.IntervalNameMap.getIntersecting(IntervalNameMap.java:61)
u32.cbio.private 2019-04-08 14:26:52,877 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv    	at org.mskcc.juber.waltz.countreads.CountReads.scanBam(CountReads.java:109)
u32.cbio.private 2019-04-08 14:26:52,877 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv    	at org.mskcc.juber.waltz.countreads.CountReads.main(CountReads.java:67)
u32.cbio.private 2019-04-08 14:26:52,878 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv    Problem processing record:
u32.cbio.private 2019-04-08 14:26:52,878 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv    A00227:98:HJCFJDMXX:2:2227:7518:20149:TAT+TAT	97	5	107963795	60	96I	=	107963795	63	CTTCTTATATGAGATCTTCAGTTCACATTTCTTTTTCTACACAGAGCTCACCAGGAAGCCTAGGAGGCACATAGAGTTTTTCCTGAGGGGTGTTTG	>A>BDBBCBCA<FEDFFCFA?@CFAAADCCFFCCCCF1CAAAA>EFEFE@@C@EDDBEECEBEDDEDE)@@BA<CD:AAA;DBD@CDCBB=>8==<	YA:Z:5:107963602:193M101I294M	BD:Z:BBFIIIIGGGJKHHJLFFIIJIGIH9:HG=HEE=<<GDGD989HEEHHDG8FHHIHGFHHHGHIHEIIG9:HDIFGIG>>?JLKKLIMIIJ=;G>G	PG:Z:MarkDuplicates	RG:Z:MSK-ML-0067-01-5001853C	BI:Z:DDIIJKLHHGJLJJKKIJIJKJIIJ=>IIBIGHAAAHGIE=<=JHHJKFI<IJJJJIIJIKIJJJIKKJ=>IFKJJKJCDDKMONNMOKLNC>IBI	NM:i:96	YM:i:0	YO:Z:N/A:107963795	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@	MQ:i:36	OQ:Z:FFFFFFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFF,FFFFF:FFFFFFFFFFFFFFFFFFFFFFFF,FFFF:FF:FFF:FFFFFFFFFFF:FFF	AS:i:0	XS:i:0	YX:i:96
u32.cbio.private 2019-04-08 14:26:52,881 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv
u32.cbio.private 2019-04-08 14:26:52,881 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv    java.lang.IllegalArgumentException: Invalid range: [107963795?107963794]
u32.cbio.private 2019-04-08 14:26:52,882 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv    	at com.google.common.collect.Range.<init>(Range.java:363)
u32.cbio.private 2019-04-08 14:26:52,882 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv    	at com.google.common.collect.Range.create(Range.java:153)
u32.cbio.private 2019-04-08 14:26:52,882 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv    	at com.google.common.collect.Range.closed(Range.java:177)
u32.cbio.private 2019-04-08 14:26:52,882 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv    	at org.mskcc.juber.intervals.IntervalNameMap.getIntersecting(IntervalNameMap.java:61)
u32.cbio.private 2019-04-08 14:26:52,882 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv    	at org.mskcc.juber.waltz.countreads.CountReads.scanBam(CountReads.java:109)
u32.cbio.private 2019-04-08 14:26:52,882 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv    	at org.mskcc.juber.waltz.countreads.CountReads.main(CountReads.java:67)
u32.cbio.private 2019-04-08 14:26:52,882 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv    Finished processing in 899 seconds.
u32.cbio.private 2019-04-08 14:26:52,883 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv    [job CountReads.cwl] completed success
u32.cbio.private 2019-04-08 14:26:52,883 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv    INFO:cwltool:[job CountReads.cwl] completed success
u32.cbio.private 2019-04-08 14:26:52,883 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv    DEBUG:toil.fileStore:LOG-TO-MASTER: Job h/k/jobqP_v0S/g/tmpGPS6jm.tmp used 36.74% (11.1 GB [11952664576B] used, 30.3 GB [32531021824B] requested) at the end of its run.
u32.cbio.private 2019-04-08 14:26:52,883 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv    DEBUG:toil.worker:The jobGraph has multiple predecessors, we must return to the leader.
u32.cbio.private 2019-04-08 14:26:52,883 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv    INFO:toil.worker:Worker log can be found at /home/johnsoni/Projects/Ian/06302R_06302S/set_4/Project_06302_R/MB-Grail-2.0.0/tmp/toil-ba1866f0-1880-441d-9f70-e389dc90881b-c9948558b80baa6b28363dfb0000001b/tmpqU3S6g. Set --cleanWorkDir to retain this log
u32.cbio.private 2019-04-08 14:26:52,883 Thread-323 DEBUG toil.statsAndLogging: 'file:///home/johnsoni/pipeline_2.0.0/ACCESS-Pipeline/cwl_tools/waltz/CountReads.cwl' 1/N/jobcPXKgv    INFO:toil.worker:Finished running the chain of jobs on this node, we ran for a total of 902.780110 seconds
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