To follow this point a bit further, on more than one occasion I've solved a
bug like this by copy/pasting the known good file name (e..g the one you
used w/ gedit) into the command line or vice versa. Sometimes subtle typos
or bad paths get in there.
On Tue, Sep 9, 2014 at 8:29 AM, Bob Handsaker <[email protected]>
wrote:
> Does the file name really end in ".txt,", as specified on your sample
> command line ?
> -Bob
>
>
> On 9/9/14, 3:49 AM, Jan Taylor wrote:
>
> 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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>>>
>>>
>>
>
>
> ------------------------------------------------------------------------------
> Want excitement?
> Manually upgrade your production database.
> When you want reliability, choose Perforce.
> Perforce version control. Predictably
> reliable.http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
>
>
>
> _______________________________________________
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>
>
>
>
> ------------------------------------------------------------------------------
> Want excitement?
> Manually upgrade your production database.
> When you want reliability, choose Perforce.
> Perforce version control. Predictably reliable.
>
> http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
> _______________________________________________
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>
>
------------------------------------------------------------------------------
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When you want reliability, choose Perforce.
Perforce version control. Predictably reliable.
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