When a Pegasus Lite job fails, pegasus-analyzer shows stderr from both the Kickstart record and the job stderr. See below for an example. This is pretty confusing as stderr for those jobs are used to log all kinds of PegasusLite stuff, and has usually nothing to do with the failure. To make these jobs easier to debug for our users, I think we should add some logic to only show the Kickstart stderr in these cases.

===============================sort_sam_ID0000024===============================

last state: POST_SCRIPT_FAILED
site: execution
submit file: sort_sam_ID0000024.sub
output file: sort_sam_ID0000024.out.003
error file: sort_sam_ID0000024.err.003

------------------------------Task #1 - Summary-------------------------------

site : execution
hostname : workflow.isi.edu
executable : /local-scratch/condor/execute/dir_16894/pegasus.QLJWK6/sort_sam
arguments : SortSam.jar CREATE_INDEX=TRUE MAX_RECORDS_IN_RAM=5000000 TMP_DIR=. I=20141106-042026-IRIS_313-10534_120227_I295_FCD0RG3ACXX_L1_RICwdsRSYHSD14-3-IPAAPEK-142_aligned_reads.sam O=20141106-042026-IRIS_313-10534_120227_I295_FCD0RG3ACXX_L1_RICwdsRSYHSD14-3-IPAAPEK-142_sorted_reads.bam SO=coordinate VALIDATION_STRINGENCY=LENIENT
exitcode : 1
working dir : /local-scratch/condor/execute/dir_16894/pegasus.QLJWK6

--------------Task #1 - sort_sam - ID0000024 - Kickstart stderr---------------

[1m[31mUSAGE: PicardCommandLine[32m<program name>[1m[31m [-h]
[0m[1m[31mAvailable Programs:
[0m[37m--------------------------------------------------------------------------------------
[0m[31mFasta: Tools for manipulating FASTA, or related data.[0m
[32m CreateSequenceDictionary[36mCreates a SAM or BAM file from reference sequence in fasta format[0m
[32m ExtractSequences[36mExtracts intervals from a reference sequence, writing them to a FASTA file[0m
[32m NormalizeFasta[36mNormalizes lines of sequence in a fasta file to be of the same length[0m
[37m--------------------------------------------------------------------------------------
[0m[31mIllumina Tools: Tools for manipulating data specific to Illumina sequencers.[0m
[32m CheckIlluminaDirectory[36mAsserts the validity of the data in the specified Illumina basecalling data[0m
[32m CollectIlluminaBasecallingMetrics[36mGiven an Illumina basecalling and a lane, produces per-lane-barcode basecalling metrics[0m
[32m CollectIlluminaLaneMetrics[36mCollects Illumina lane metrics for the given basecalling analysis directory[0m
[32m CollectIlluminaSummaryMetrics[36mCollects summary metrics according to Illumina specifications.[0m
[32m ExtractIlluminaBarcodes[36mTool to determine the barcode for each read in an Illumina lane[0m
[32m IlluminaBasecallsToFastq[36mGenerate fastq file(s) from data in an Illumina basecalls output directory[0m
[32m IlluminaBasecallsToSam[36mGenerate a SAM or BAM file from data in an Illumina basecalls output directory[0m
[32m MarkIlluminaAdapters[36mReads a SAM or BAM file and rewrites it with new adapter-trimming tags[0m
[37m--------------------------------------------------------------------------------------
[0m[31mInterval Tools: Tools for manipulating Picard interval lists.[0m
[32m BedToIntervalList[36mConverts a BED file to an Picard Interval List.[0m
[32m IntervalListTools[36mGeneral tool for manipulating interval lists[0m
[32m LiftOverIntervalList[36mLifts over an interval list from one reference build to another[0m
[32m ScatterIntervalsByNs[36mWrites an interval list based on splitting the reference by Ns[0m
[37m--------------------------------------------------------------------------------------
[0m[31mMetrics: Tools for reporting metrics on various data types.[0m
[32m CalculateHsMetrics[36mCalculates Hybrid Selection-specific metrics for a SAM or BAM file[0m
[32m CollectAlignmentSummaryMetrics[36mProduces from a SAM or BAM a file containing summary alignment metrics[0m
[32m CollectBaseDistributionByCycle[36mProgram to chart the nucleotide distribution per cycle in a SAM or BAM file.[0m
[32m CollectGcBiasMetrics[36mCollects information about GC bias in the reads in the provided SAM or BAM[0m
[32m CollectHiSeqXPfFailMetrics[36mClassify PF-Failing reads in a HiSeqX Illumina Basecalling directory into various categories.[0m
[32m CollectInsertSizeMetrics[36mWrites insert size distribution metrics for a SAM or BAM file[0m
[32m CollectJumpingLibraryMetrics[36mProduces jumping library metrics for the provided SAM/BAMs[0m
[32m CollectMultipleMetrics[36mA"meta-metrics"calculating program that produces multiple metrics for the provided SAM/BAM[0m
[32m CollectOxoGMetrics[36mCollects metrics quantifying the CpCG ->CpCA error rate from the provided SAM/BAM[0m
[32m CollectQualityYieldMetrics[36mCollects a set of metrics that quantify the quality and yield of sequence data from the provided SAM/BAM[0m
[32m CollectRnaSeqMetrics[36mProduces RNA alignment metrics for a SAM or BAM file[0m
[32m CollectRrbsMetrics[36mCollects metrics about bisulfite conversion for RRBS data[0m
[32m CollectTargetedPcrMetrics[36mProduces Targeted PCR-related metrics given the provided SAM/BAM[0m
[32m CollectWgsMetrics[36mWrites whole genome sequencing-related metrics for a SAM or BAM file[0m
[32m EstimateLibraryComplexity[36mEstimates library complexity from the sequence of read pairs[0m
[32m MeanQualityByCycle[36mWrites mean quality by cycle for a SAM or BAM file[0m
[32m QualityScoreDistribution[36mCharts quality score distributions for a SAM or BAM file[0m
[37m--------------------------------------------------------------------------------------
[0m[31mMiscellaneous Tools: A set of miscellaneous tools.[0m
[32m BaitDesigner[36mDesigns baits or oligos for hybrid selection reactions.[0m
[32m FifoBuffer[36mFIFO buffer used to buffer input and output streams with a customizable buffer size[0m
[37m--------------------------------------------------------------------------------------
[0m[31mSAM/BAM: Tools for manipulating SAM, BAM, or related data.[0m
[32m AddCommentsToBam[36mAdds comments to the header of a BAM file[0m
[32m AddOrReplaceReadGroups[36mReplaces read groups in a BAM or SAM file with a single new read group[0m
[32m BamIndexStats[36mGenerates index statistics from a BAM file[0m
[32m BamToBfq[36mCreate BFQ files from a BAM file for use by the Maq aligner.[0m
[32m BuildBamIndex[36mGenerates a BAM index (.bai) file[0m
[32m CalculateReadGroupChecksum[36mCreates a hash code based on the read groups (RG) in the SAM or BAM header.[0m
[32m CheckTerminatorBlock[36mAsserts the provided gzip file's (e.g., BAM) last block is well-formed; RC 100 otherwise[0m
[32m CleanSam[36mCleans the provided SAM/BAM, soft-clipping beyond-end-of-reference alignments and setting MAPQ to 0 for unmapped reads[0m
[32m CompareSAMs[36mCompares two input SAM or BAM files[0m
[32m DownsampleSam[36mDown-sample a SAM or BAM file to retain a random subset of the reads[0m
[32m FastqToSam[36mConverts a fastq file to an unaligned BAM or SAM file[0m
[32m FilterSamReads[36mCreates a new SAM or BAM file by including or excluding aligned reads[0m
[32m FixMateInformation[36mEnsure that all mate-pair information is in sync between each read and its mate pair[0m
[32m GatherBamFiles[36mConcatenates one or more BAM files together as efficiently as possible[0m
[32m MarkDuplicates[36mExamines aligned records in the supplied SAM or BAM file to locate duplicate molecules.[0m
[32m MarkDuplicatesWithMateCigar[36mExamines aligned records in the supplied SAM or BAM file to locate duplicate molecules.[0m
[32m MergeBamAlignment[36mMerges alignment data from a SAM or BAM with data in an unmapped BAM file[0m
[32m MergeSamFiles[36mMerges multiple SAM or BAM files into one file[0m
[32m ReorderSam[36mReorders reads in a SAM or BAM file to match ordering in reference[0m
[32m ReplaceSamHeader[36mReplace the SAMFileHeader in a SAM file with the given header[0m
[32m RevertOriginalBaseQualitiesAndAddMateCigar[36mReverts the original base qualities and adds the mate cigar tag to read-group BAMs[0m
[32m RevertSam[36mReverts SAM or BAM files to a previous state[0m
[32m SamFormatConverter[36mConvert a BAM file to a SAM file, or a SAM to a BAM[0m
[32m SamToFastq[36mConverts a SAM/BAM into a FASTQ[0m
[32m SortSam[36mSorts a SAM or BAM file[0m
[32m SplitSamByLibrary[36mSplits a SAM or BAM file into individual files by library[0m
[32m ValidateSamFile[36mValidates a SAM or BAM file[0m
[32m ViewSam[36mPrints a SAM or BAM file to the screen[0m
[37m--------------------------------------------------------------------------------------
[0m[31mVCF/BCF: Tools for manipulating VCF, BCF, or related data.[0m
[32m FilterVcf[36mHard filters a VCF.[0m
[32m GatherVcfs[36mGathers multiple VCF files from a scatter operation into a single VCF file[0m
[32m GenotypeConcordance[36mCalculates the concordance between genotype data for two samples in two different VCFs[0m
[32m MakeSitesOnlyVcf[36mCreates a VCF bereft of genotype information from an input VCF or BCF[0m
[32m MergeVcfs[36mMerges multiple VCF or BCF files into one VCF file or BCF[0m
[32m RenameSampleInVcf[36mRename a sample within a VCF or BCF.[0m
[32m SortVcf[36mSorts one or more VCF files[0m
[32m SplitVcfs[36mSplits an input VCF or BCF file into two VCF or BCF files[0m
[32m UpdateVcfSequenceDictionary[36mTakes a VCF and a second file that contains a sequence dictionary and updates the VCF with the new sequence dictionary.[0m
[32m VcfFormatConverter[36mConverts a VCF file to a BCF file, or BCF to VCF[0m
[32m VcfToIntervalList[36mConverts a VCF or BCF file to a Picard Interval List.[0m
[37m--------------------------------------------------------------------------------------
[0m
'SortSam.jar'is not a valid command. See PicardCommandLine --help for more information.

-------------------Task #1 - sort_sam - ID0000024 - stderr--------------------

2014-11-05 22:41:58: PegasusLite: version 4.4.0
2014-11-05 22:41:58: Expanded $SSH_PRIVATE_KEY_isi_workflow to /local-scratch/condor/execute/dir_16894/workflow
2014-11-05 22:41:58: Checking /var/lib/condor/execute/dir_16894 for potential use as work space...
2014-11-05 22:41:58: Work dir is /var/lib/condor/execute/dir_16894/pegasus.QLJWK6 - 4324395904 kB available
2014-11-05 22:41:58: The job contained a Pegasus worker package
2014-11-05 22:41:58,370 INFO: Reading URL pairs from stdin
2014-11-05 22:41:58,370 INFO: PATH=/var/lib/condor/execute/dir_16894/pegasus.QLJWK6/pegasus-4.4.0/bin:/ccg/software/irods/3.2/bin:/usr/bin:/bin
2014-11-05 22:41:58,370 INFO: LD_LIBRARY_PATH=
2014-11-05 22:41:58,372 INFO: 3 transfers loaded
2014-11-05 22:41:58,372 INFO: Sorting the tranfers based on transfer type and source/destination
2014-11-05 22:41:58,372 INFO: --------------------------------------------------------------------------------
2014-11-05 22:41:58,373 INFO: Starting transfers - attempt 1
2014-11-05 22:41:58,373 INFO: Using 3 threads for this round of transfers
2014-11-05 22:42:00,376 INFO: Trying to detect availability/location of tool: wget
2014-11-05 22:42:00,387 INFO: Tool found: wget Version: 1.12 Path: /usr/bin/wget
2014-11-05 22:42:00,387 INFO: /usr/bin/wget -q --no-check-certificate -O '/var/lib/condor/execute/dir_16894/pegasus.QLJWK6/20141106-042026-IRIS_313-10534_120227_I295_FCD0RG3ACXX_L1_RICwdsRSYHSD14-3-IPAAPEK-142_aligned_reads.sam' 'http://workflow.isi.edu/scratch/rynge/irri/scratch/wf-20141106-042026/20141106-042026-IRIS_313-10534_120227_I295_FCD0RG3ACXX_L1_RICwdsRSYHSD14-3-IPAAPEK-142_aligned_reads.sam'
2014-11-05 22:42:02,378 INFO: /usr/bin/wget -q --no-check-certificate -O '/var/lib/condor/execute/dir_16894/pegasus.QLJWK6/sort_sam' 'http://workflow.isi.edu/scratch/rynge/irri/scratch/wf-20141106-042026/sort_sam'
2014-11-05 22:42:02,386 INFO: /usr/bin/wget -q --no-check-certificate -O '/var/lib/condor/execute/dir_16894/pegasus.QLJWK6/software.tar.gz' 'http://workflow.isi.edu/scratch/rynge/irri/scratch/wf-20141106-042026/software.tar.gz'
2014-11-05 22:42:08,258 INFO: --------------------------------------------------------------------------------
2014-11-05 22:42:08,258 INFO: Stats: 3.1 GB transferred in 10 seconds. Rate: 319.9 MB/s (2.5 Gb/s)
2014-11-05 22:42:08,258 INFO: NOTE: stats do not include third party gsiftp/srm transfers
2014-11-05 22:42:08,258 INFO: All transfers completed successfully.
2014-11-05 22:42:11,369 INFO: Reading URL pairs from stdin
2014-11-05 22:42:11,369 INFO: PATH=/var/lib/condor/execute/dir_16894/pegasus.QLJWK6/pegasus-4.4.0/bin:/ccg/software/irods/3.2/bin:/usr/bin:/bin
2014-11-05 22:42:11,369 INFO: LD_LIBRARY_PATH=
2014-11-05 22:42:11,370 INFO: 2 transfers loaded
2014-11-05 22:42:11,371 INFO: Sorting the tranfers based on transfer type and source/destination
2014-11-05 22:42:11,371 INFO: --------------------------------------------------------------------------------
2014-11-05 22:42:11,371 INFO: Starting transfers - attempt 1
2014-11-05 22:42:11,371 INFO: Using 2 threads for this round of transfers
2014-11-05 22:42:13,374 INFO: /usr/bin/ssh -i /local-scratch/condor/execute/dir_16894/workflow -q -o StrictHostKeyChecking=no rynge@workflow.isi.edu '/bin/mkdir -p /local-scratch/http/rynge/irri/scratch/wf-20141106-042026'
2014-11-05 22:42:13,473 INFO: /usr/bin/scp -q -B -o StrictHostKeyChecking=no -i /local-scratch/condor/execute/dir_16894/workflow '/var/lib/condor/execute/dir_16894/pegasus.QLJWK6/20141106-042026-IRIS_313-10534_120227_I295_FCD0RG3ACXX_L1_RICwdsRSYHSD14-3-IPAAPEK-142_sorted_reads.bai' 'rynge@workflow.isi.edu:/local-scratch/http/rynge/irri/scratch/wf-20141106-042026/20141106-042026-IRIS_313-10534_120227_I295_FCD0RG3ACXX_L1_RICwdsRSYHSD14-3-IPAAPEK-142_sorted_reads.bai'
/var/lib/condor/execute/dir_16894/pegasus.QLJWK6/20141106-042026-IRIS_313-10534_120227_I295_FCD0RG3ACXX_L1_RICwdsRSYHSD14-3-IPAAPEK-142_sorted_reads.bai: No such file or directory
2014-11-05 22:42:13,565 ERROR: Command '/usr/bin/scp -q -B -o StrictHostKeyChecking=no -i /local-scratch/condor/execute/dir_16894/workflow '/var/lib/condor/execute/dir_16894/pegasus.QLJWK6/20141106-042026-IRIS_313-10534_120227_I295_FCD0RG3ACXX_L1_RICwdsRSYHSD14-3-IPAAPEK-142_sorted_reads.bai' 'rynge@workflow.isi.edu:/local-scratch/http/rynge/irri/scratch/wf-20141106-042026/20141106-042026-IRIS_313-10534_120227_I295_FCD0RG3ACXX_L1_RICwdsRSYHSD14-3-IPAAPEK-142_sorted_reads.bai'' failed with error code 1
2014-11-05 22:42:13,565 INFO: /usr/bin/scp -q -B -o StrictHostKeyChecking=no -i /local-scratch/condor/execute/dir_16894/workflow '/var/lib/condor/execute/dir_16894/pegasus.QLJWK6/20141106-042026-IRIS_313-10534_120227_I295_FCD0RG3ACXX_L1_RICwdsRSYHSD14-3-IPAAPEK-142_sorted_reads.bam' 'rynge@workflow.isi.edu:/local-scratch/http/rynge/irri/scratch/wf-20141106-042026/20141106-042026-IRIS_313-10534_120227_I295_FCD0RG3ACXX_L1_RICwdsRSYHSD14-3-IPAAPEK-142_sorted_reads.bam'
/var/lib/condor/execute/dir_16894/pegasus.QLJWK6/20141106-042026-IRIS_313-10534_120227_I295_FCD0RG3ACXX_L1_RICwdsRSYHSD14-3-IPAAPEK-142_sorted_reads.bam: No such file or directory
2014-11-05 22:42:13,658 ERROR: Command '/usr/bin/scp -q -B -o StrictHostKeyChecking=no -i /local-scratch/condor/execute/dir_16894/workflow '/var/lib/condor/execute/dir_16894/pegasus.QLJWK6/20141106-042026-IRIS_313-10534_120227_I295_FCD0RG3ACXX_L1_RICwdsRSYHSD14-3-IPAAPEK-142_sorted_reads.bam' 'rynge@workflow.isi.edu:/local-scratch/http/rynge/irri/scratch/wf-20141106-042026/20141106-042026-IRIS_313-10534_120227_I295_FCD0RG3ACXX_L1_RICwdsRSYHSD14-3-IPAAPEK-142_sorted_reads.bam'' failed with error code 1
2014-11-05 22:42:25,386 INFO: --------------------------------------------------------------------------------
2014-11-05 22:42:25,386 INFO: Starting transfers - attempt 2
2014-11-05 22:42:25,387 INFO: Using 1 threads for this round of transfers
2014-11-05 22:42:27,389 INFO: /usr/bin/scp -q -B -o StrictHostKeyChecking=no -i /local-scratch/condor/execute/dir_16894/workflow '/var/lib/condor/execute/dir_16894/pegasus.QLJWK6/20141106-042026-IRIS_313-10534_120227_I295_FCD0RG3ACXX_L1_RICwdsRSYHSD14-3-IPAAPEK-142_sorted_reads.bai' 'rynge@workflow.isi.edu:/local-scratch/http/rynge/irri/scratch/wf-20141106-042026/20141106-042026-IRIS_313-10534_120227_I295_FCD0RG3ACXX_L1_RICwdsRSYHSD14-3-IPAAPEK-142_sorted_reads.bai'
/var/lib/condor/execute/dir_16894/pegasus.QLJWK6/20141106-042026-IRIS_313-10534_120227_I295_FCD0RG3ACXX_L1_RICwdsRSYHSD14-3-IPAAPEK-142_sorted_reads.bai: No such file or directory
2014-11-05 22:42:27,484 ERROR: Command '/usr/bin/scp -q -B -o StrictHostKeyChecking=no -i /local-scratch/condor/execute/dir_16894/workflow '/var/lib/condor/execute/dir_16894/pegasus.QLJWK6/20141106-042026-IRIS_313-10534_120227_I295_FCD0RG3ACXX_L1_RICwdsRSYHSD14-3-IPAAPEK-142_sorted_reads.bai' 'rynge@workflow.isi.edu:/local-scratch/http/rynge/irri/scratch/wf-20141106-042026/20141106-042026-IRIS_313-10534_120227_I295_FCD0RG3ACXX_L1_RICwdsRSYHSD14-3-IPAAPEK-142_sorted_reads.bai'' failed with error code 1
2014-11-05 22:42:27,484 INFO: /usr/bin/scp -q -B -o StrictHostKeyChecking=no -i /local-scratch/condor/execute/dir_16894/workflow '/var/lib/condor/execute/dir_16894/pegasus.QLJWK6/20141106-042026-IRIS_313-10534_120227_I295_FCD0RG3ACXX_L1_RICwdsRSYHSD14-3-IPAAPEK-142_sorted_reads.bam' 'rynge@workflow.isi.edu:/local-scratch/http/rynge/irri/scratch/wf-20141106-042026/20141106-042026-IRIS_313-10534_120227_I295_FCD0RG3ACXX_L1_RICwdsRSYHSD14-3-IPAAPEK-142_sorted_reads.bam'
/var/lib/condor/execute/dir_16894/pegasus.QLJWK6/20141106-042026-IRIS_313-10534_120227_I295_FCD0RG3ACXX_L1_RICwdsRSYHSD14-3-IPAAPEK-142_sorted_reads.bam: No such file or directory
2014-11-05 22:42:27,578 ERROR: Command '/usr/bin/scp -q -B -o StrictHostKeyChecking=no -i /local-scratch/condor/execute/dir_16894/workflow '/var/lib/condor/execute/dir_16894/pegasus.QLJWK6/20141106-042026-IRIS_313-10534_120227_I295_FCD0RG3ACXX_L1_RICwdsRSYHSD14-3-IPAAPEK-142_sorted_reads.bam' 'rynge@workflow.isi.edu:/local-scratch/http/rynge/irri/scratch/wf-20141106-042026/20141106-042026-IRIS_313-10534_120227_I295_FCD0RG3ACXX_L1_RICwdsRSYHSD14-3-IPAAPEK-142_sorted_reads.bam'' failed with error code 1
2014-11-05 22:42:37,580 INFO: --------------------------------------------------------------------------------
2014-11-05 22:42:37,580 INFO: Starting transfers - attempt 3
2014-11-05 22:42:37,581 INFO: Using 1 threads for this round of transfers
2014-11-05 22:42:39,583 INFO: /usr/bin/scp -q -B -o StrictHostKeyChecking=no -i /local-scratch/condor/execute/dir_16894/workflow '/var/lib/condor/execute/dir_16894/pegasus.QLJWK6/20141106-042026-IRIS_313-10534_120227_I295_FCD0RG3ACXX_L1_RICwdsRSYHSD14-3-IPAAPEK-142_sorted_reads.bai' 'rynge@workflow.isi.edu:/local-scratch/http/rynge/irri/scratch/wf-20141106-042026/20141106-042026-IRIS_313-10534_120227_I295_FCD0RG3ACXX_L1_RICwdsRSYHSD14-3-IPAAPEK-142_sorted_reads.bai'
/var/lib/condor/execute/dir_16894/pegasus.QLJWK6/20141106-042026-IRIS_313-10534_120227_I295_FCD0RG3ACXX_L1_RICwdsRSYHSD14-3-IPAAPEK-142_sorted_reads.bai: No such file or directory
2014-11-05 22:42:39,678 ERROR: Command '/usr/bin/scp -q -B -o StrictHostKeyChecking=no -i /local-scratch/condor/execute/dir_16894/workflow '/var/lib/condor/execute/dir_16894/pegasus.QLJWK6/20141106-042026-IRIS_313-10534_120227_I295_FCD0RG3ACXX_L1_RICwdsRSYHSD14-3-IPAAPEK-142_sorted_reads.bai' 'rynge@workflow.isi.edu:/local-scratch/http/rynge/irri/scratch/wf-20141106-042026/20141106-042026-IRIS_313-10534_120227_I295_FCD0RG3ACXX_L1_RICwdsRSYHSD14-3-IPAAPEK-142_sorted_reads.bai'' failed with error code 1
2014-11-05 22:42:39,678 INFO: /usr/bin/scp -q -B -o StrictHostKeyChecking=no -i /local-scratch/condor/execute/dir_16894/workflow '/var/lib/condor/execute/dir_16894/pegasus.QLJWK6/20141106-042026-IRIS_313-10534_120227_I295_FCD0RG3ACXX_L1_RICwdsRSYHSD14-3-IPAAPEK-142_sorted_reads.bam' 'rynge@workflow.isi.edu:/local-scratch/http/rynge/irri/scratch/wf-20141106-042026/20141106-042026-IRIS_313-10534_120227_I295_FCD0RG3ACXX_L1_RICwdsRSYHSD14-3-IPAAPEK-142_sorted_reads.bam'
/var/lib/condor/execute/dir_16894/pegasus.QLJWK6/20141106-042026-IRIS_313-10534_120227_I295_FCD0RG3ACXX_L1_RICwdsRSYHSD14-3-IPAAPEK-142_sorted_reads.bam: No such file or directory
2014-11-05 22:42:39,770 ERROR: Command '/usr/bin/scp -q -B -o StrictHostKeyChecking=no -i /local-scratch/condor/execute/dir_16894/workflow '/var/lib/condor/execute/dir_16894/pegasus.QLJWK6/20141106-042026-IRIS_313-10534_120227_I295_FCD0RG3ACXX_L1_RICwdsRSYHSD14-3-IPAAPEK-142_sorted_reads.bam' 'rynge@workflow.isi.edu:/local-scratch/http/rynge/irri/scratch/wf-20141106-042026/20141106-042026-IRIS_313-10534_120227_I295_FCD0RG3ACXX_L1_RICwdsRSYHSD14-3-IPAAPEK-142_sorted_reads.bam'' failed with error code 1
2014-11-05 22:42:39,770 INFO: --------------------------------------------------------------------------------
2014-11-05 22:42:39,770 INFO: Stats: no local files in the transfer set
2014-11-05 22:42:39,771 CRITICAL: Some transfers failed! See above, and possibly stderr.
2014-11-05 22:42:39: Job failed with exitcode 1
2014-11-05 22:42:39: FAILURE: Last command exited with 1
2014-11-05 22:42:40: /var/lib/condor/execute/dir_16894/pegasus.QLJWK6 cleaned up
PegasusLite: exitcode 1