CollectMultipleMetrics IllegalArgumentException in 1.134

[jeremiahsavage]

I can run 1.133 on a particular BAM without error.

$ java -d64 -jar picard-tools-1.133/picard.jar CollectMultipleMetrics INPUT=2817851434.bam OUTPUT=2817851434.bam.metrics VALIDATION_STRINGENCY=LENIENT
[Wed Jun 17 16:58:19 UTC 2015] picard.analysis.CollectMultipleMetrics INPUT=2817851434.bam OUTPUT=2817851434.bam.metrics VALIDATION_STRINGENCY=LENIENT    ASSUME_SORTED=true STOP_AFTER=0 PROGRAM=[CollectAlignmentSummaryMetrics, CollectInsertSizeMetrics, QualityScoreDistribution, MeanQualityByCycle, CollectBaseDistributionByCycle] VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Wed Jun 17 16:58:19 UTC 2015] Executing as ubuntu@frontend001 on Linux 3.13.0-53-generic amd64; OpenJDK 64-Bit Server VM 1.7.0_79-b14; Picard version: 1.133(95818b6e611725775e29d3b4acbaa23747eb3e94_1433169311) IntelDeflater
INFO    2015-06-17 16:58:23 SinglePassSamProgram    Processed     1,000,000 records.  Elapsed time: 00:00:04s.  Time for last 1,000,000:    4s.  Last read position: chr2:121,708,696
.
.
.

However, with 1.134, I get

$ java -d64 -jar picard-tools-1.134/picard.jar CollectMultipleMetrics INPUT=2817851434.bam OUTPUT=2817851434.bam.metrics VALIDATION_STRINGENCY=LENIENT
[Wed Jun 17 16:57:46 UTC 2015] picard.analysis.CollectMultipleMetrics INPUT=2817851434.bam OUTPUT=2817851434.bam.metrics VALIDATION_STRINGENCY=LENIENT    ASSUME_SORTED=true STOP_AFTER=0 PROGRAM=[CollectAlignmentSummaryMetrics, CollectInsertSizeMetrics, QualityScoreDistribution, MeanQualityByCycle, CollectBaseDistributionByCycle, CollectGcBiasMetrics] VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Wed Jun 17 16:57:46 UTC 2015] Executing as ubuntu@frontend001 on Linux 3.13.0-53-generic amd64; OpenJDK 64-Bit Server VM 1.7.0_79-b14; Picard version: 1.134(a7a08c474e4d99346eec7a9956a8fe71943b5d80_1434033355) IntelDeflater
[Wed Jun 17 16:57:46 UTC 2015] picard.analysis.CollectMultipleMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2058354688
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" java.lang.IllegalArgumentException: Cannot check readability of null file.
    at htsjdk.samtools.util.IOUtil.assertFileIsReadable(IOUtil.java:306)
    at picard.analysis.CollectGcBiasMetrics.setup(CollectGcBiasMetrics.java:126)
    at picard.analysis.SinglePassSamProgram.makeItSo(SinglePassSamProgram.java:98)
    at picard.analysis.CollectMultipleMetrics.doWork(CollectMultipleMetrics.java:199)
    at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:206)
    at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
    at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)

[nh13]

I think it is because you are not specifying REFERENCE_SEQUENCE on the command line.

@vdauwera @kbergin we should add custom command line validation for when CollectGcBiasMetrics are computed within CollectMultipleMetrics.

[tfenne]

I might also suggest not making CollectGcBiasMetrics a default operation for CollectMultipleMetrics. This bit me too during an upgrade. It's the only default tool that isn't designed to work on any BAM, but is specific to WGS.

[yfarjoun]

Shouldn't be related to picard-private issues.

I like the suggestion by Tim to make the CollectGcBiasMetrics non-default.

Jeremiyah, currently, as a workaround, you'll need to either provide a
Reference_sequence as mentioned, or remove the CollectGcBiasMetrics from
the list of programs.

On Wed, Jun 17, 2015 at 9:25 PM, kbergin notifications@github.com wrote:

this is related to broadinstitute/picard-private#315
https://github.com/broadinstitute/picard-private/pull/315 and #221
#221 for reference..

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#225 (comment)
.

[jeremiahsavage]

I ran 134 with REFERENCE_SEQUENCE and that is a fine workaround. Thanks Nils and Yossi.

[yfarjoun]

can this be fixed properly?

1. remove CollectGcBiasMetrics from default list
2. improve argument validation as per Nils.

[kbergin]

Yes, to both parts. I worked on fixing it today with Nils and Louis's help, should be able to finish it up tomorrow!

On Jun 17, 2015, at 8:37 PM, Yossi Farjoun notifications@github.com wrote:

can this be fixed properly?

remove CollectGcBiasMetrics from default list
improve argument validation as per Nils.
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[yfarjoun]

Fantastic!

On Thu, Jun 18, 2015 at 3:46 AM, kbergin notifications@github.com wrote:

Yes, to both parts. I worked on fixing it today with Nils and Louis's
help, should be able to finish it up tomorrow!

On Jun 17, 2015, at 8:37 PM, Yossi Farjoun notifications@github.com
wrote:

can this be fixed properly?

remove CollectGcBiasMetrics from default list
improve argument validation as per Nils.
—
Reply to this email directly or view it on GitHub.

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#225 (comment)
.

[yfarjoun]

I think this issue can be closed.

[kbergin]

I think so too, we addressed this.