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  • GenoMax
    Senior Member
    • Feb 2008
    • 7142
    #16
    @cmccabe: Can you run the command without the R option and see if it works? You will not get certain stats (AT/GC dropout metrics) but let us see if you can get the command to work otherwise.

    $ picard-tools -v or --version (does that print the version number you are using)?

    Comment

    • cmccabe
      Senior Member
      • Jul 2012
      • 355
      #17
      Here are the results of the 3 things:

      Code:
      dnascopev@ubuntu:/media/C2F8EFBFF8EFAFB9$ picard-tools --version
picard-tools
Copyright 2010 The Broad Institute
      java -jar
      Code:
       java -jar picard-tools CalculateHsMetrics BI=xgen_probes_sort.bed TI=xgen_targets_sort.bed I=IonXpress_009_150603.bam O=IonXpress_009_150603_epilepsy70.CalculateHSmetrics REFERENCE_SEQUENCE=/home/dnascopev/Desktop/hg19_fasta/hg19.fasta
Unable to access jarfile picard-tools
      without R=
      Code:
      dnascopev@ubuntu:/media/C2F8EFBFF8EFAFB9$ picard-tools CalculateHsMetrics BI=xgen_probes_sort.bed TI=xgen_targets_sort.bed I=IonXpress_009_150603.bam O=IonXpress_009_150603_epilepsy70.CalculateHSmetrics
[Mon Jun 22 14:04:14 CDT 2015] net.sf.picard.analysis.directed.CalculateHsMetrics BAIT_INTERVALS=xgen_probes_sort.bed TARGET_INTERVALS=xgen_targets_sort.bed INPUT=IonXpress_009_150603.bam OUTPUT=IonXpress_009_150603_epilepsy70.CalculateHSmetrics    TMP_DIR=/tmp/dnascopev VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Mon Jun 22 14:04:14 CDT 2015] net.sf.picard.analysis.directed.CalculateHsMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=61079552
Exception in thread "main" java.lang.IllegalStateException: Interval list file must contain header. 
	at net.sf.picard.util.IntervalList.fromReader(IntervalList.java:176)
	at net.sf.picard.util.IntervalList.fromFile(IntervalList.java:152)
	at net.sf.picard.analysis.directed.HsMetricsCalculator.<init>(HsMetricsCalculator.java:83)
	at net.sf.picard.analysis.directed.CalculateHsMetrics.doWork(CalculateHsMetrics.java:83)
	at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:158)
	at net.sf.picard.analysis.directed.CalculateHsMetrics.main(CalculateHsMetrics.java:68
      Thank you .

      Comment

      • GenoMax
        Senior Member
        • Feb 2008
        • 7142
        #18
        So we now have a new error to work on

        "Interval list file must contain header"

        Can you post a few lines from your bed file?

        Comment

        • cmccabe
          Senior Member
          • Jul 2012
          • 355
          #19
          BI=
          Code:
          chr1	133573	133692
chr1	659937	660056
chr1	809529	809649
          TI=
          Code:
          chr1	955542	955763
chr1	957570	957852
chr1	976034	976270
          The bed files are sorted using
          Code:
           sort -k1,1 -k2,2g -o out.bed in.bed
          , should I not sort them for picard? Thank you .

          Comment

          • skbrimer
            Member
            • Mar 2014
            • 55
            #20
            would you put the out of
            Code:
            ls /usr/bin/picard-tools

            Comment

            • GenoMax
              Senior Member
              • Feb 2008
              • 7142
              #21
              With a disclaimer that we are in a "blind leading the blind" situation here

              See this: https://github.com/dnanexus/dnanexus...xample_targets

              Looks like you need to modify your interval files to include sam headers. More info here: https://www.broadinstitute.org/gatk/...rticle?id=1204

              Comment

              • cmccabe
                Senior Member
                • Jul 2012
                • 355
                #22
                Code:
                 dnascopev@ubuntu:/media/C2F8EFBFF8EFAFB9$ ls /usr/bin/picard-tools
/usr/bin/picard-tools
                I will read the posts as well and try to modify the files. Thank you .

                EDIT:

                Interval format for Picard
                Code:
                @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
                So using my bed, I need to convert
                Code:
                chr1	133573	133692
chr1	659937	660056
chr1	809529	809649
                to
                Code:
                @SQ 	SN:chr1	LN:133573-133692
@SQ	SN:chr1	LN:659937-660056
@SQ	SN:chr1	LN:809529-809649
                Last edited by cmccabe; 06-22-2015, 12:06 PM.

                Comment

                • GenoMax
                  Senior Member
                  • Feb 2008
                  • 7142
                  #23
                  That is incorrect.

                  First example you pasted are lengths of entire chromosomes in the reference. They need to remain as they are in your reference at the top of the file.

                  Code:
                  @SQ	SN:chr1	LN:249250621
@SQ	SN:chr2	LN:243199373
............ (and so on)
@SQ	SN:chr22	LN:51304566
@SQ	SN:chrX	LN:155270560
@SQ	SN:chrY	LN:59373566
@SQ	SN:chrMT	LN:16569
(your interval data starts here : this line will not be included in your file)
chr1	14362	14829	+	1:14363-14829:WASH5P
chr1	14969	15038	+	1:14970-15038:WASH5P
chr1	15795	15947	+	1:15796-15947:WASH5P

                  Comment

                  • cmccabe
                    Senior Member
                    • Jul 2012
                    • 355
                    #24
                    I think I understand.

                    In both the BI= and TI= files:
                    Code:
                    @SQ	SN:chr1	LN:249250621
@SQ	SN:chr2	LN:243199373
............ (and so on)
@SQ	SN:chr22	LN:51304566
@SQ	SN:chrX	LN:155270560
@SQ	SN:chrY	LN:59373566
@SQ	SN:chrMT	LN:16569
                    Then use a script/tool to create the intervals for each (based on the bed file):
                    Code:
                    chr1	14362	14829	+	1:14363-14829:WASH5P
chr1	14969	15038	+	1:14970-15038:WASH5P
chr1	15795	15947	+	1:15796-15947:WASH5P
                    Is this more or less right and is there a script or tool that will help? Thank you .

                    Comment

                    • GenoMax
                      Senior Member
                      • Feb 2008
                      • 7142
                      #25
                      Start by grabbing the headers from your BAM file

                      Code:
                      $ samtools view -H IonXpress_009_150603.bam > header.sam

$ cat header.sam your_file.bed > new_file.bed
                      See if the new bed file works with picard before extensively modifying your bed file.
                      Last edited by GenoMax; 06-22-2015, 04:06 PM.

                      Comment

                      • cmccabe
                        Senior Member
                        • Jul 2012
                        • 355
                        #26
                        I created new bed files witth sam hearders and tried Picard again, below is the error and some samples lines of each of the bed files. Thank you .

                        Code:
                        dnascopev@ubuntu:/media/C2F8EFBFF8EFAFB9$ picard-tools CalculateHsMetrics BI=xgen_probes_sam_sort.bed TI=xgen_targets_sam_sort.bed I=IonXpress_009_150603.bam O=IonXpress_009_150603_all_IDT.CalculateHSmetrics
[Tue Jun 23 09:07:03 CDT 2015] net.sf.picard.analysis.directed.CalculateHsMetrics BAIT_INTERVALS=xgen_probes_sam_sort.bed TARGET_INTERVALS=xgen_targets_sam_sort.bed INPUT=IonXpress_009_150603.bam OUTPUT=IonXpress_009_150603_all_IDT.CalculateHSmetrics    TMP_DIR=/tmp/dnascopev VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Tue Jun 23 09:07:04 CDT 2015] net.sf.picard.analysis.directed.CalculateHsMetrics done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=89980928
Exception in thread "main" net.sf.picard.PicardException: Invalid interval record contains 3 fields: chr1	133573	133692
	at net.sf.picard.util.IntervalList.fromReader(IntervalList.java:192)
	at net.sf.picard.util.IntervalList.fromFile(IntervalList.java:152)
	at net.sf.picard.analysis.directed.HsMetricsCalculator.<init>(HsMetricsCalculator.java:83)
	at net.sf.picard.analysis.directed.CalculateHsMetrics.doWork(CalculateHsMetrics.java:83)
	at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:158)
	at net.sf.picard.analysis.directed.CalculateHsMetrics.main(CalculateHsMetrics.java:68)
                        BI=
                        Code:
                        @HD	VN:1.4	GO:none	SO:coordinate
@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
@SQ	SN:chrM	LN:16569
@RG	ID:8AH6U.IonXpress_009	PL:IONTORRENT	PU:Unspecified/P1.1.17/IonXpress_009	FO:TACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACG	DT:2015-06-03T14:03:02-0700	SM:E1	PG:tmap	KS:TCAGTGAGCGGAACGAT	CN:TorrentServer/Proton
@RG	ID:8AH6U.IonXpress_009.1	PL:IONTORRENT	PU:Unspecified/P1.1.17/IonXpress_009	FO:TACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACG	DT:2015-06-03T13:27:05-0700	SM:E1	PG:tmap	KS:TCAGTGAGCGGAACGAT	CN:TorrentServer/Proton
@RG	ID:8AH6U.IonXpress_009.10	PL:IONTORRENT	PU:Unspecified/P1.1.17/IonXpress_009	FO:TACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACG	DT:2015-06-03T11:44:53-0700	SM:E1	PG:tmap	KS:TCAGTGAGCGGAACGAT	CN:TorrentServer/Proton
@RG	ID:8AH6U.IonXpress_009.11	PL:IONTORRENT	PU:Unspecified/P1.1.17/IonXpress_009	FO:TACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACG	DT:2015-06-03T11:39:13-0700	SM:E1	PG:tmap	KS:TCAGTGAGCGGAACGAT	CN:TorrentServer/Proton
@RG	ID:8AH6U.IonXpress_009.12	PL:IONTORRENT	PU:Unspecified/P1.1.17/IonXpress_009	FO:TACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACG	DT:2015-06-03T11:33:41-0700	SM:E1	PG:tmap	KS:TCAGTGAGCGGAACGAT	CN:TorrentServer/Proton
@RG	ID:8AH6U.IonXpress_009.13	PL:IONTORRENT	PU:Unspecified/P1.1.17/IonXpress_009	FO:TACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACG	DT:2015-06-03T11:49:17-0700	SM:E1	PG:tmap	KS:TCAGTGAGCGGAACGAT	CN:TorrentServer/Proton
                        TI=
                        Code:
                        @HD	VN:1.4	GO:none	SO:coordinate
@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
@SQ	SN:chrM	LN:16569
@RG	ID:8AH6U.IonXpress_009	PL:IONTORRENT	PU:Unspecified/P1.1.17/IonXpress_009	FO:TACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACG	DT:2015-06-03T14:03:02-0700	SM:E1	PG:tmap	KS:TCAGTGAGCGGAACGAT	CN:TorrentServer/Proton
@RG	ID:8AH6U.IonXpress_009.1	PL:IONTORRENT	PU:Unspecified/P1.1.17/IonXpress_009	FO:TACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACG	DT:2015-06-03T13:27:05-0700	SM:E1	PG:tmap	KS:TCAGTGAGCGGAACGAT	CN:TorrentServer/Proton
@RG	ID:8AH6U.IonXpress_009.10	PL:IONTORRENT	PU:Unspecified/P1.1.17/IonXpress_009

                        Comment

                        • GenoMax
                          Senior Member
                          • Feb 2008
                          • 7142
                          #27
                          Looks like picard is expecting the bed file to have a fourth field (+/- strand?) where your data starts. If you have that information then add it and try again.

                          Comment

                          • skbrimer
                            Member
                            • Mar 2014
                            • 55
                            #28
                            While I could be wrong, I feel the error is in how the program is being invoked. I'm not sure with the older versions as I have only worked with the newest 1.134 so if I am wrong maybe GenoMax can correct me since he has clearly had a lot of experience with this program. I think if you can find on your setup where the files are installed and call them with the absolute path I think it will work.

                            Here is an example of what I mean on my machine.
                            Code:
                            sean@LEN320:~$ java -jar picard-tools-1.134/picard.jar CalculateHsMeterics
                            I think if you can run your code this way it will accept your reference file and compute what you are after.

                            Most likely I think you will find the files in usr/share/picard-tools, I think that is where apt-get puts things.

                            Comment

                            • cmccabe
                              Senior Member
                              • Jul 2012
                              • 355
                              #29
                              Modified the bed files to be 5 column (chr, start, end, stand, chr:start-end) and am closer. I will try invoking another way as well. Thank you .

                              Code:
                              dnascopev@ubuntu:/media/C2F8EFBFF8EFAFB9$ picard-tools CalculateHsMetrics BI=sam_sort_5column_xgen_probes.bed TI=sam_sort_5column_xgen_targets.bed I=IonXpress_009_150603.bam O=IonXpress_009_150603_all_IDT.CalculateHSmetrics
[Tue Jun 23 14:07:49 CDT 2015] net.sf.picard.analysis.directed.CalculateHsMetrics BAIT_INTERVALS=sam_sort_5column_xgen_probes.bed TARGET_INTERVALS=sam_sort_5column_xgen_targets.bed INPUT=IonXpress_009_150603.bam OUTPUT=IonXpress_009_150603_all_IDT.CalculateHSmetrics    TMP_DIR=/tmp/dnascopev VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Tue Jun 23 14:07:50 CDT 2015] net.sf.picard.analysis.directed.CalculateHsMetrics done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=138412032
[B]Exception in thread "main" java.lang.IllegalArgumentException: Program record with group id bc already exists in SAMFileHeader![/B]
	at net.sf.samtools.SAMFileHeader.addProgramRecord(SAMFileHeader.java:197)
	at net.sf.samtools.SAMTextHeaderCodec.parsePGLine(SAMTextHeaderCodec.java:150)
	at net.sf.samtools.SAMTextHeaderCodec.decode(SAMTextHeaderCodec.java:90)
	at net.sf.picard.util.IntervalList.fromReader(IntervalList.java:181)
	at net.sf.picard.util.IntervalList.fromFile(IntervalList.java:152)
	at net.sf.picard.analysis.directed.HsMetricsCalculator.<init>(HsMetricsCalculator.java:83)
	at net.sf.picard.analysis.directed.CalculateHsMetrics.doWork(CalculateHsMetrics.java:83)
	at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:158)
	at net.sf.picard.analysis.directed.CalculateHsMetrics.main(CalculateHsMetrics.java:68
                              BI=
                              Code:
                              @HD	VN:1.4	GO:none	SO:coordinate
@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
@SQ	SN:chrM	LN:16569
@RG	ID:8AH6U.IonXpress_009	PL:IONTORRENT	PU:Unspecified/P1.1.17/IonXpress_009	FO:TACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACG	DT:2015-06-03T14:03:02-0700	SM:E1	PG:tmap	KS:TCAGTGAGCGGAACGAT	CN:TorrentServer/Proton
@RG	ID:8AH6U.IonXpress_009.1	PL:IONTORRENT	PU:Unspecified/P1.1.17/IonXpress_009	FO:TACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACG	DT:2015-06-03T13:27:05-0700	SM:E1	PG:tmap	KS:TCAGTGAGCGGAACGAT	CN:TorrentServer/Proton
@RG	ID:8AH6U.IonXpress_009.10	PL:IONTORRENT	PU:Unspecified/P1.1.17/IonXpress_009
                              TI=
                              Code:
                              @HD	VN:1.4	GO:none	SO:coordinate
@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
@SQ	SN:chrM	LN:16569
@RG	ID:8AH6U.IonXpress_009	PL:IONTORRENT	PU:Unspecified/P1.1.17/IonXpress_009	FO:TACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACG	DT:2015-06-03T14:03:02-0700	SM:E1	PG:tmap	KS:TCAGTGAGCGGAACGAT	CN:TorrentServer/Proton
@RG	ID:8AH6U.IonXpress_009.1	PL:IONTORRENT	PU:Unspecified/P1.1.17/IonXpress_009	FO:TACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACG	DT:2015-06-03T13:27:05-0700	SM:E1	PG:tmap	KS:TCAGTGAGCGGAACGAT	CN:TorrentServer/Proton
@RG	ID:8AH6U.IonXpress_009.10	PL:IONTORRENT	PU:Unspecified/P1.1.17/IonXpress_009

                              Comment

                              • cmccabe
                                Senior Member
                                • Jul 2012
                                • 355
                                #30
                                I am going to repost with some cleaner data that makes more sense (hopefully). Thank you .

                                Comment

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