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 <nho...@broadinstitute.org
<mailto:nho...@broadinstitute.org>> 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
<jantaylor1...@gmail.com <mailto:jantaylor1...@gmail.com>> 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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Manually upgrade your production database.
When you want reliability, choose Perforce.
Perforce version control. Predictably reliable.
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