remove out

smoke_test/output_dir/mpfr/3.1.5

-find: ‘/usr/local/mpfr/3.1.5/bin’: No such file or directory

smoke_test/output_dir/picard/2.9.2

-USAGE: PicardCommandLine <program name> [-h]
-
-Available Programs:
---------------------------------------------------------------------------------------
-Alpha Tools:                                     Tools that are currently UNSUPPORTED until further testing and maturation.
-    CollectIndependentReplicateMetrics           Estimates the rate of independent replication of reads within a bam.
-    CollectWgsMetricsWithNonZeroCoverage         Collect metrics about coverage and performance of whole genome sequencing (WGS) experiments.  
-    UmiAwareMarkDuplicatesWithMateCigar          Identifies duplicate reads using information from read positions and UMIs. 
-
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-Fasta:                                           Tools for manipulating FASTA, or related data.
-    CreateSequenceDictionary                     Creates a sequence dictionary for a reference sequence.  
-    ExtractSequences                             Subsets intervals from a reference sequence to a new FASTA file.
-    NonNFastaSize                                Counts the number of non-N bases in a fasta file.
-    NormalizeFasta                               Normalizes lines of sequence in a FASTA file to be of the same length.
-
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-Fingerprinting Tools:                            Tools for manipulating fingerprints, or related data.
-    CheckFingerprint                             Computes a fingerprint from the supplied input (SAM/BAM or VCF) file and compares it to the provided genotypes
-    CrosscheckReadGroupFingerprints              Checks if all read groups appear to come from the same individual
-
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-Illumina Tools:                                  Tools for manipulating data specific to Illumina sequencers.
-    CheckIlluminaDirectory                       Asserts the validity for specified Illumina basecalling data.  
-    CollectIlluminaBasecallingMetrics            Collects Illumina Basecalling metrics for a sequencing run.  
-    CollectIlluminaLaneMetrics                   Collects Illumina lane metrics for the given BaseCalling analysis directory.  
-    ExtractIlluminaBarcodes                      Tool determines the barcode for each read in an Illumina lane.  
-    IlluminaBasecallsToFastq                     Generate FASTQ file(s) from Illumina basecall read data.  
-    IlluminaBasecallsToSam                       Transforms raw Illumina sequencing data into an unmapped SAM or BAM file.
-    MarkIlluminaAdapters                         Reads a SAM or BAM file and rewrites it with new adapter-trimming tags.  
-
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-Interval Tools:                                  Tools for manipulating Picard interval lists.
-    BedToIntervalList                            Converts a BED file to a Picard Interval List.  
-    IntervalListToBed                            Converts an Picard IntervalList file to a BED file.
-    IntervalListTools                            Manipulates interval lists.  
-    LiftOverIntervalList                         Lifts over an interval list from one reference build to another.  
-    ScatterIntervalsByNs                         Writes an interval list based on splitting a reference by Ns.  
-
---------------------------------------------------------------------------------------
-Metrics:                                         Tools for reporting metrics on various data types.
-    CollectAlignmentSummaryMetrics               <b>Produces a summary of alignment metrics from a SAM or BAM file.</b>  
-    CollectBaseDistributionByCycle               Chart the nucleotide distribution per cycle in a SAM or BAM file
-    CollectGcBiasMetrics                         Collect metrics regarding GC bias. 
-    CollectHiSeqXPfFailMetrics                   Classify PF-Failing reads in a HiSeqX Illumina Basecalling directory into various categories.
-    CollectHsMetrics                             Collects hybrid-selection (HS) metrics for a SAM or BAM file.  
-    CollectInsertSizeMetrics                     Collect metrics about the insert size distribution of a paired-end library.
-    CollectJumpingLibraryMetrics                 Collect jumping library metrics. 
-    CollectMultipleMetrics                       Collect multiple classes of metrics.  
-    CollectOxoGMetrics                           Collect metrics to assess oxidative artifacts.
-    CollectQualityYieldMetrics                   Collect metrics about reads that pass quality thresholds and Illumina-specific filters.  
-    CollectRawWgsMetrics                         Collect whole genome sequencing-related metrics.  
-    CollectRnaSeqMetrics                         Produces RNA alignment metrics for a SAM or BAM file.  
-    CollectRrbsMetrics                           <b>Collects metrics from reduced representation bisulfite sequencing (Rrbs) data.</b>  
-    CollectSequencingArtifactMetrics             Collect metrics to quantify single-base sequencing artifacts.  
-    CollectTargetedPcrMetrics                    Calculate PCR-related metrics from targeted sequencing data. 
-    CollectVariantCallingMetrics                 Collects per-sample and aggregate (spanning all samples) metrics from the provided VCF file
-    CollectWgsMetrics                            Collect metrics about coverage and performance of whole genome sequencing (WGS) experiments.
-    CompareMetrics                               Compare two metrics files.
-    ConvertSequencingArtifactToOxoG              Extract OxoG metrics from generalized artifacts metrics.  
-    EstimateLibraryComplexity                    Estimates the numbers of unique molecules in a sequencing library.  
-    MeanQualityByCycle                           Collect mean quality by cycle.
-    QualityScoreDistribution                     Chart the distribution of quality scores.  
-
---------------------------------------------------------------------------------------
-Miscellaneous Tools:                             A set of miscellaneous tools.                
-    BaitDesigner                                 <b>Designs oligonucleotide baits for hybrid selection reactions.</b>  
-    FifoBuffer                                   FIFO buffer used to buffer input and output streams with a customizable buffer size 
-
---------------------------------------------------------------------------------------
-SAM/BAM:                                         Tools for manipulating SAM, BAM, or related data.
-    AddCommentsToBam                             Adds comments to the header of a BAM file.
-    AddOrReplaceReadGroups                       Replace read groups in a BAM file.
-    BamIndexStats                                Generate index statistics from a BAM file
-    BamToBfq                                     Create BFQ files from a BAM file for use by the maq aligner.  
-    BuildBamIndex                                Generates a BAM index ".bai" file.  
-    CalculateReadGroupChecksum                   Creates a hash code based on the read groups (RG).  
-    CheckTerminatorBlock                         Asserts the provided gzip file's (e.g., BAM) last block is well-formed; RC 100 otherwise
-    CleanSam                                     Cleans the provided SAM/BAM, soft-clipping beyond-end-of-reference alignments and setting MAPQ to 0 for unmapped reads
-    CompareSAMs                                  Compare two input ".sam" or ".bam" files.  
-    DownsampleSam                                Downsample a SAM or BAM file.  
-    FastqToSam                                   Converts a FASTQ file to an unaligned BAM or SAM file.  
-    FilterSamReads                               Subset read data from a SAM or BAM file
-    FixMateInformation                           Verify mate-pair information between mates and fix if needed.
-    GatherBamFiles                               Concatenate one or more BAM files as efficiently as possible
-    MarkDuplicates                               Identifies duplicate reads.  
-    MarkDuplicatesWithMateCigar                  Identifies duplicate reads, accounting for mate CIGAR.  
-    MergeBamAlignment                            Merge alignment data from a SAM or BAM with data in an unmapped BAM file.  
-    MergeSamFiles                                Merges multiple SAM and/or BAM files into a single file.  
-    PositionBasedDownsampleSam                   Downsample a SAM or BAM file to retain a subset of the reads based on the reads location in each tile in the flowcell.
-    ReorderSam                                   Reorders reads in a SAM or BAM file to match ordering in reference
-    ReplaceSamHeader                             Replaces the SAMFileHeader in a SAM or BAM file.  
-    RevertOriginalBaseQualitiesAndAddMateCigar   Reverts the original base qualities and adds the mate cigar tag to read-group BAMs
-    RevertSam                                    Reverts SAM or BAM files to a previous state.  
-    SamFormatConverter                           Convert a BAM file to a SAM file, or a SAM to a BAM
-    SamToFastq                                   Converts a SAM or BAM file to FASTQ.  
-    SetNmAndUqTags                               DEPRECATED: Use SetNmMdAndUqTags instead.
-    SetNmMdAndUqTags                             Fixes the NM, MD, and UQ tags in a SAM file.  
-    SortSam                                      Sorts a SAM or BAM file.  
-    SplitSamByLibrary                            Splits a SAM or BAM file into individual files by library
-    ValidateSamFile                              Validates a SAM or BAM file.  
-    ViewSam                                      Prints a SAM or BAM file to the screen
-
---------------------------------------------------------------------------------------
-Unit Testing:                                    Unit testing                                 
-    SimpleMarkDuplicatesWithMateCigar            Examines aligned records in the supplied SAM or BAM file to locate duplicate molecules.
-
---------------------------------------------------------------------------------------
-VCF/BCF:                                         Tools for manipulating VCF, BCF, or related data.
-    FilterVcf                                    Hard filters a VCF.
-    FindMendelianViolations                      Finds mendelian violations of all types within a VCF
-    FixVcfHeader                                 Replaces or fixes a VCF header.
-    GatherVcfs                                   Gathers multiple VCF files from a scatter operation into a single VCF file
-    GenotypeConcordance                          Evaluate genotype concordance between callsets.
-    LiftoverVcf                                  Lifts over a VCF file from one reference build to another.  
-    MakeSitesOnlyVcf                             Creates a VCF bereft of genotype information from an input VCF or BCF
-    MergeVcfs                                    Merges multiple VCF or BCF files into one VCF file or BCF
-    RenameSampleInVcf                            Renames a sample within a VCF or BCF.  
-    SortVcf                                      Sorts one or more VCF files.  
-    SplitVcfs                                    Splits SNPs and INDELs into separate files.  
-    UpdateVcfSequenceDictionary                  Takes a VCF and a second file that contains a sequence dictionary and updates the VCF with the new sequence dictionary.
-    VcfFormatConverter                           Converts VCF to BCF or BCF to VCF.  
-    VcfToIntervalList                            Converts a VCF or BCF file to a Picard Interval List.
-
---------------------------------------------------------------------------------------
-
-'--version' is not a valid command. See PicardCommandLine -h for more information.

smoke_test/output_dir/report.txt

-
-virtualgl 2.5.0 return non-zero exitcode 1 for testcase /home/luhanc/HPCasCode/smoke_test/tests/virtualgl/bashcmd
-tigervnc 1.8.0 return non-zero exitcode 1 for testcase /home/luhanc/HPCasCode/smoke_test/tests/tigervnc/bashcmd
-java 1.8.0_77 return non-zero exitcode 1 for testcase /home/luhanc/HPCasCode/smoke_test/tests/java/bintest
-cuda 7.5 return non-zero exitcode 1 for testcase /home/luhanc/HPCasCode/smoke_test/tests/cuda/bashcmd
-mpfr 3.1.5 return non-zero exitcode 1 for testcase /home/luhanc/HPCasCode/smoke_test/tests/mpfr/bashcmd
-picard 2.9.2 return non-zero exitcode 1 for testcase /home/luhanc/HPCasCode/smoke_test/tests/picard/bintest
-Summary
-Failed: 0
-Success: 40
-minor error: 6, this is often due to executable not having --version option
-Num applications that has no test case: 0

smoke_test/output_dir/samtools/1.9-gcc5

-samtools 1.9-24-gff68e70
-Using htslib 1.9-20-ge1650a9
-Copyright (C) 2018 Genome Research Ltd.

smoke_test/output_dir/singularity/3.2.1

-singularity version 3.2.1