Thanks for your replies. The file type is ascii text, readable by gedit
(constructed using R), tab delimited and permissions are set to 775, but
the file is still not found.
Jan
On Mon, Sep 8, 2014 at 3:37 PM, Nils Homer <[email protected]>
wrote:
> It looks like the file located at "/home/jan-local/data/baitStranded.txt"
> is not readable by the program. Can you confirm you can read the file with
> an editor?
>
> N
>
> On Mon, Sep 8, 2014 at 10:17 AM, Jan Taylor <[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
>>
>>
>>
>> ------------------------------------------------------------------------------
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>>
>
------------------------------------------------------------------------------
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When you want reliability, choose Perforce.
Perforce version control. Predictably reliable.
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