I do not understand the eroor recieved from picard just trying to index a bam. Why does the output path get duplicated? It also seems to happen in mark as duplicates. Thank you 
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.Code:
cmccabe@DTV-A5211QLM:~/Desktop/NGS$ java -jar /home/cmccabe/Desktop/NGS/picard-tools-1.139/picard.jar BuildBamIndex \ > INPUT=home/cmccabe/Desktop/NGS/picard-tools-1.139/dedup_sorted_mapped_unmatched_adapter_removed_quality_trimmed_NA12878-NextSeq-S1_R1_and_R2.bam [Wed Nov 04 09:32:11 CST 2015] picard.sam.BuildBamIndex INPUT=home/cmccabe/Desktop/NGS/picard-tools-1.139/dedup_sorted_mapped_unmatched_adapter_removed_quality_trimmed_NA12878-NextSeq-S1_R1_and_R2.bam VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Wed Nov 04 09:32:11 CST 2015] Executing as cmccabe@DTV-A5211QLM on Linux 3.19.0-31-generic amd64; OpenJDK 64-Bit Server VM 1.7.0_85-b01; Picard version: 1.139(8ceee52414e8ab9d13e350ff9cd86d48825dd64d_1442240108) IntelDeflater [Wed Nov 04 09:32:11 CST 2015] picard.sam.BuildBamIndex done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=883425280 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Exception in thread "main" htsjdk.samtools.SAMException: [B]Cannot write file: /home/cmccabe/Desktop/NGS/home/cmccabe/Desktop/NGS/picard-tools-1.139/dedup_sorted_mapped_unmatched_adapter_removed_quality_trimmed_NA12878-NextSeq-S1_R1_and_R2.bai. Neither file nor parent directory exist.[/B] at htsjdk.samtools.util.IOUtil.assertFileIsWritable(IOUtil.java:371) at picard.sam.BuildBamIndex.doWork(BuildBamIndex.java:113) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:206) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95) at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)
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