Hi Jan,
You have an additional problem: the baits file you provide is not found. See
below...
Regards,
Chris
On 08/09/2014 15:17, "Jan Taylor"
<[email protected]<mailto:[email protected]>> 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
The University of Dundee is a registered Scottish Charity, No: SC015096
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