Chromosome names are ususally matched using exact string matching. "20"
does not match "chr20".
- tom blackwell -
On Mon, 8 Sep 2014, Jan Taylor wrote:
> Hi,
>
> Have searched for help and seen numerous posts but my error not resolved.
>
> My interval_list file is:
>
> @HD VN:1.0 GO:none SO:coordinate
> @SQ SN:chrM LN:16571
> @SQ SN:chr1 LN:249250621
> @SQ SN:chr2 LN:243199373
> @SQ SN:chr3 LN:198022430
> @SQ SN:chr4 LN:191154276
> @SQ SN:chr5 LN:180915260
> @SQ SN:chr6 LN:171115067
> @SQ SN:chr7 LN:159138663
> @SQ SN:chr8 LN:146364022
> @SQ SN:chr9 LN:141213431
> @SQ SN:chr10 LN:135534747
> @SQ SN:chr11 LN:135006516
> @SQ SN:chr12 LN:133851895
> @SQ SN:chr13 LN:115169878
> @SQ SN:chr14 LN:107349540
> @SQ SN:chr15 LN:102531392
> @SQ SN:chr16 LN:90354753
> @SQ SN:chr17 LN:81195210
> @SQ SN:chr18 LN:78077248
> @SQ SN:chr19 LN:59128983
> @SQ SN:chr20 LN:63025520
> @SQ SN:chr21 LN:48129895
> @SQ SN:chr22 LN:51304566
> @SQ SN:chrX LN:155270560
> @SQ SN:chrY LN:59373566
> 20 31022180 31022372 + ASXL1_25
> 20 31022265 31022446 + ASXL1_26
> 20 31022388 31022586 + ASXL1_27
> <snip>
>
> The command I enter is:
>
> java -Xmx2G -jar /usr/picard/CalculateHsMetrics.jar
> BAIT_INTERVALS=/home/jan-local/data/baitStranded.txt,
> TARGET_INTERVALS=/home/jan-local/data/baitStranded.txt I=3448-11_S44.bam
> O=3448HSmetrics.out
>
> [Mon Sep 08 14:50:29 BST 2014] picard.analysis.directed.CalculateHsMetrics
> BAIT_INTERVALS=[/home/jan-local/data/baitStranded.txt,]
> TARGET_INTERVALS=[/home/jan-local/data/baitStranded.txt]
> INPUT=3448-11_S44.bam OUTPUT=3448HSmetrics.out
> REFERENCE_SEQUENCE=/usr/references/hg19.fa
> METRIC_ACCUMULATION_LEVEL=[ALL_READS] VERBOSITY=INFO QUIET=false
> VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000
> CREATE_INDEX=false CREATE_MD5_FILE=false
> Java HotSpot(TM) 64-Bit Server VM warning: You have loaded library
> /usr/picard/libIntelDeflater.so which might have disabled stack guard. The
> VM will try to fix the stack guard now.
> It's highly recommended that you fix the library with 'execstack -c
> <libfile>', or link it with '-z noexecstack'.
> [Mon Sep 08 14:50:29 BST 2014] Executing as jan-local@limm-lnx1019 on Linux
> 2.6.32-431.23.3.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM
> 1.7.0_67-b01; Picard version:
> 1.119(d44cdb51745f5e8075c826430a39d8a61f1dd832_1408991805) IntelDeflater
> WARNING 2014-09-08 14:50:29 IntervalList Ignoring interval for
> unknown reference: 20:31022180-31022372
> WARNING 2014-09-08 14:50:29 IntervalList Ignoring interval for
> unknown reference: 20:31022265-31022446
> <snip>
> [Mon Sep 08 14:50:29 BST 2014] picard.analysis.directed.CalculateHsMetrics
> done. Elapsed time: 0.00 minutes.
> Runtime.totalMemory()=503316480
> To get help, see http://picard.sourceforge.net/index.shtml#GettingHelp
> Exception in thread "main" htsjdk.samtools.SAMException: Cannot read
> non-existent file: /home/jan-local/data/baitStranded.txt,
> at htsjdk.samtools.util.IOUtil.assertFileIsReadable(IOUtil.java:280)
> at
> picard.analysis.directed.CalculateHsMetrics.getProbeIntervals(CalculateHsMetrics.java:63)
> at
> picard.analysis.directed.CollectTargetedMetrics.doWork(CollectTargetedMetrics.java:93)
> at
> picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:183)
> at
> picard.analysis.directed.CalculateHsMetrics.main(CalculateHsMetrics.java:82)
>
>
>
> Any help would be appreciated. I have checked that headers are tab
> delimited. No intervals are detected.
>
> Sorry for repeating an often asked question
>
> JanT
>
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