cp: cannot stat `/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/PRJNA395963_ERa/ERaflox_F_Met4/fastq/tophat2/ERaflox_F_Met4_primary_unique.bam': No such file or directory
[Tue Apr 30 04:25:37 EDT 2019] picard.analysis.CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=FIRST_READ_TRANSCRIPTION_STRAND INPUT=ERaflox_F_Met4_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/ERaflox_F_Met4_metrics    MINIMUM_LENGTH=500 RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Tue Apr 30 04:25:41 EDT 2019] Executing as kkarri@scc-ka1.scc.bu.edu on Linux 2.6.32-754.6.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_192-b01; Picard version: 1.123(286a232caea2fdc8fdd88574c09c460b46386fff_1413818736) IntelDeflater
[Tue Apr 30 04:25:41 EDT 2019] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=2058354688
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" htsjdk.samtools.SAMException: Cannot read non-existent file: /scratch/5781692.1.linga/ERaflox_F_Met4_primary_unique.bam
	at htsjdk.samtools.util.IOUtil.assertFileIsReadable(IOUtil.java:278)
	at picard.analysis.SinglePassSamProgram.makeItSo(SinglePassSamProgram.java:64)
	at picard.analysis.SinglePassSamProgram.doWork(SinglePassSamProgram.java:53)
	at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:185)
	at picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:125)
	at picard.analysis.CollectRnaSeqMetrics.main(CollectRnaSeqMetrics.java:97)
cp: cannot create directory `/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/CAR_Project_Data/PRJNA395963_ERa/ERaflox_F_Met4/fastq/tophat2': No such file or directory