starting phase `set-SOURCE-DATE-EPOCH' phase `set-SOURCE-DATE-EPOCH' succeeded after 0.0 seconds starting phase `set-paths' environment variable `PATH' set to `/gnu/store/lp0g7mxkinaf4mhj79fdwzbdygnjcxc0-icedtea-3.7.0-jdk/bin:/gnu/store/f6py897yk352xrpf1vvc9laa7kvj40w9-ant-1.9.15/bin:/gnu/store/sm5b6s7zlhwbawxw1vyqxmhggahkb5s0-zip-3.0/bin:/gnu/store/1zx8knb7h79q6cr4kwhbz6z6v609309w-unzip-6.0/bin:/gnu/store/srq6803bhlz65l8pljxq0hwcjxgq681k-icedtea-3.7.0/bin:/gnu/store/v6f44zccwh9z5zk3pjlywjybbi8n2hjh-tar-1.32/bin:/gnu/store/ncydgq2znms5n1d2k5yqshhf58nsixwv-gzip-1.10/bin:/gnu/store/i8h2pcxqdq07ijm3ibkka8f4smn1w48v-bzip2-1.0.8/bin:/gnu/store/9860f1abqj8wjjnwl8a9v54pdcc3bhgf-xz-5.2.4/bin:/gnu/store/60g7r3l01fd7c58yjbm6krgcwj1jkpwg-file-5.38/bin:/gnu/store/n4n560pfvvw50a9369axw5vj5rrqfj1n-diffutils-3.7/bin:/gnu/store/cd5qf3kcnlq35p9k392pjdpdzpsnds70-patch-2.7.6/bin:/gnu/store/hic7snhayfl7m6cpfqqr73nmm19bpqkg-findutils-4.7.0/bin:/gnu/store/swqdvwri9dbv6zssg6v0by7l05hd6wxp-gawk-5.0.1/bin:/gnu/store/ishk7fswcs4gkwcp8mh788z4mvvl9bxh-sed-4.8/bin:/gnu/store/bhs4rj58v8j1narb2454raan2ps38xd8-grep-3.4/bin:/gnu/store/57xj5gcy1jbl9ai2lnrqnpr0dald9i65-coreutils-8.32/bin:/gnu/store/hm40bxnv8jxmbc1lpb7zfimii4xm9m81-make-4.3/bin:/gnu/store/pwcp239kjf7lnj5i4lkdzcfcxwcfyk72-bash-minimal-5.0.16/bin:/gnu/store/mpa04aq8lblbcviyxywxcsb1zbi0mf39-ld-wrapper-0/bin:/gnu/store/m1z7cdbqsqyp9xnjw5cvlb4a7gkcg3m4-binutils-2.34/bin:/gnu/store/rn75fm7adgx3pw5j8pg3bczfqq1y17lk-gcc-7.5.0/bin:/gnu/store/fa6wj5bxkj5ll1d7292a70knmyl7a0cr-glibc-2.31/bin:/gnu/store/fa6wj5bxkj5ll1d7292a70knmyl7a0cr-glibc-2.31/sbin' environment variable `BASH_LOADABLES_PATH' unset environment variable `C_INCLUDE_PATH' set to `/gnu/store/lp0g7mxkinaf4mhj79fdwzbdygnjcxc0-icedtea-3.7.0-jdk/include:/gnu/store/i8h2pcxqdq07ijm3ibkka8f4smn1w48v-bzip2-1.0.8/include:/gnu/store/9860f1abqj8wjjnwl8a9v54pdcc3bhgf-xz-5.2.4/include:/gnu/store/60g7r3l01fd7c58yjbm6krgcwj1jkpwg-file-5.38/include:/gnu/store/swqdvwri9dbv6zssg6v0by7l05hd6wxp-gawk-5.0.1/include:/gnu/store/hm40bxnv8jxmbc1lpb7zfimii4xm9m81-make-4.3/include:/gnu/store/m1z7cdbqsqyp9xnjw5cvlb4a7gkcg3m4-binutils-2.34/include:/gnu/store/rn75fm7adgx3pw5j8pg3bczfqq1y17lk-gcc-7.5.0/include:/gnu/store/fa6wj5bxkj5ll1d7292a70knmyl7a0cr-glibc-2.31/include:/gnu/store/sgci43gc5xrq051lk1qrd6nwpribiq1r-snappy-1.1.8/include:/gnu/store/lxhkf9gj2df9w8xxzvvnh70rqnyywzj4-bitshuffle-for-snappy-0.3.5/include:/gnu/store/gfapkk5c6hvl1d94m4sqnhn7f9l5gqyh-linux-libre-headers-5.4.20/include' environment variable `CPLUS_INCLUDE_PATH' set to `/gnu/store/lp0g7mxkinaf4mhj79fdwzbdygnjcxc0-icedtea-3.7.0-jdk/include:/gnu/store/i8h2pcxqdq07ijm3ibkka8f4smn1w48v-bzip2-1.0.8/include:/gnu/store/9860f1abqj8wjjnwl8a9v54pdcc3bhgf-xz-5.2.4/include:/gnu/store/60g7r3l01fd7c58yjbm6krgcwj1jkpwg-file-5.38/include:/gnu/store/swqdvwri9dbv6zssg6v0by7l05hd6wxp-gawk-5.0.1/include:/gnu/store/hm40bxnv8jxmbc1lpb7zfimii4xm9m81-make-4.3/include:/gnu/store/m1z7cdbqsqyp9xnjw5cvlb4a7gkcg3m4-binutils-2.34/include:/gnu/store/rn75fm7adgx3pw5j8pg3bczfqq1y17lk-gcc-7.5.0/include/c++:/gnu/store/rn75fm7adgx3pw5j8pg3bczfqq1y17lk-gcc-7.5.0/include:/gnu/store/fa6wj5bxkj5ll1d7292a70knmyl7a0cr-glibc-2.31/include:/gnu/store/sgci43gc5xrq051lk1qrd6nwpribiq1r-snappy-1.1.8/include:/gnu/store/lxhkf9gj2df9w8xxzvvnh70rqnyywzj4-bitshuffle-for-snappy-0.3.5/include:/gnu/store/gfapkk5c6hvl1d94m4sqnhn7f9l5gqyh-linux-libre-headers-5.4.20/include' environment variable `LIBRARY_PATH' set to `/gnu/store/lp0g7mxkinaf4mhj79fdwzbdygnjcxc0-icedtea-3.7.0-jdk/lib:/gnu/store/f6py897yk352xrpf1vvc9laa7kvj40w9-ant-1.9.15/lib:/gnu/store/srq6803bhlz65l8pljxq0hwcjxgq681k-icedtea-3.7.0/lib:/gnu/store/x4jdnj6d97ksf881c1c3zvsnnyf5bl5h-java-commons-io-2.5/lib:/gnu/store/vvs5fhlakll28h93ns4gvpwf2psjxhkz-java-guava-20.0/lib:/gnu/store/i8h2pcxqdq07ijm3ibkka8f4smn1w48v-bzip2-1.0.8/lib:/gnu/store/9860f1abqj8wjjnwl8a9v54pdcc3bhgf-xz-5.2.4/lib:/gnu/store/60g7r3l01fd7c58yjbm6krgcwj1jkpwg-file-5.38/lib:/gnu/store/swqdvwri9dbv6zssg6v0by7l05hd6wxp-gawk-5.0.1/lib:/gnu/store/m1z7cdbqsqyp9xnjw5cvlb4a7gkcg3m4-binutils-2.34/lib:/gnu/store/fa6wj5bxkj5ll1d7292a70knmyl7a0cr-glibc-2.31/lib:/gnu/store/s3dcqzwqaakv1yx37by9chksdbkgih17-glibc-2.31-static/lib:/gnu/store/hwcky7446s952w0mwchhmm211ll07zrq-glibc-utf8-locales-2.31/lib:/gnu/store/6lh89fr71qjs3h42v7mw9rzwdiz38wyr-java-guice-4.1/lib:/gnu/store/mjal5fmhazr0v822cwdsg3rrl0b4v1c5-java-bsh-2.0b6/lib:/gnu/store/msfsrvwf11cwm2dbh818vwmc0i7bcd0n-java-jsr305-3.0.1/lib:/gnu/store/vqwkkajyx46n1lcb553jqnxd4i7114i6-java-junit-4.12/lib:/gnu/store/59060arh2yp7223pqxnxw4ww7nz5iycv-apache-commons-parent-pom-39/lib:/gnu/store/sgci43gc5xrq051lk1qrd6nwpribiq1r-snappy-1.1.8/lib:/gnu/store/lxhkf9gj2df9w8xxzvvnh70rqnyywzj4-bitshuffle-for-snappy-0.3.5/lib:/gnu/store/m4694cpdb8zp9fpspx5d2x8qyjinc3ay-java-guava-parent-pom-20.0/lib:/gnu/store/q94flcxy5xpcpwaz5kxrxywzqcl82iab-java-slf4j-simple-1.7.25/lib:/gnu/store/za1jl59wn4h2dw725pbx3sqwsik95i17-java-slf4j-api-1.7.25/lib:/gnu/store/kd0p86hz0s9ssln397xx3g5k6z83jf2c-java-guice-parent-pom-4.1/lib:/gnu/store/5py7ji8gvmhpfzi1xi2h08zc1ywhmn17-java-javax-inject-1/lib:/gnu/store/q09fngygqy8yzb28c91zhygi2hgkc71l-java-asm-6.0/lib:/gnu/store/mg0ndw7xcjrznk09dqs9pbgqbmrkr7ys-java-aopalliance-1.0/lib:/gnu/store/z5i93bna7rq6p7wzzq575pbvsg8qhg4m-java-hamcrest-core-1.3/lib:/gnu/store/293ba0fqrkvm2faaaz3f5sc1b593hmp0-apache-parent-pom-16/lib:/gnu/store/1a03d96pl067z6zmnh63dqj43ks2vf1h-java-sonatype-oss-parent-pom-7/lib:/gnu/store/jq3a37bmyqqpv1g9jk7b6pnxi1yafiqz-java-slf4j-parent-1.7.25/lib:/gnu/store/gsn388fqw0wmnnh2xrkd1xhmmg3vgckc-java-commons-codec-1.14/lib:/gnu/store/h0sgskkx9r3fz136n5bbfz88jspl6d3r-java-google-parent-pom-5/lib:/gnu/store/kzda5k7456pz1cb78xsn6pqrv7xymkk7-java-org-ow2-parent-pom-1.3/lib:/gnu/store/yixsrzh73q60mvldnypk3ndv8jyxn46j-java-hamcrest-parent-pom-1.3/lib:/gnu/store/gzskbgsifmnfggjbimx747dkr351ahj9-apache-commons-parent-pom-50/lib:/gnu/store/fqlxirav9161gs1w2w22rqlffh51p8l4-apache-parent-pom-21/lib' environment variable `GUIX_LOCPATH' set to `/gnu/store/hwcky7446s952w0mwchhmm211ll07zrq-glibc-utf8-locales-2.31/lib/locale' phase `set-paths' succeeded after 0.2 seconds starting phase `install-locale' using 'en_US.utf8' locale for category "LC_ALL" phase `install-locale' succeeded after 0.0 seconds starting phase `unpack' Drop-seq_tools-1.13/ Drop-seq_tools-1.13/BAMTagHistogram Drop-seq_tools-1.13/BAMTagofTagCounts Drop-seq_tools-1.13/BaseDistributionAtReadPosition Drop-seq_tools-1.13/CollapseBarcodesInPlace Drop-seq_tools-1.13/CollapseTagWithContext Drop-seq_tools-1.13/ConvertToRefFlat Drop-seq_tools-1.13/CreateIntervalsFiles Drop-seq_tools-1.13/DetectBeadSynthesisErrors Drop-seq_tools-1.13/DigitalExpression Drop-seq_tools-1.13/Drop-seq_alignment.sh Drop-seq_tools-1.13/DropSeq.barnyard_1.13.tar.gz Drop-seq_tools-1.13/FilterBAM Drop-seq_tools-1.13/FilterBAMByTag Drop-seq_tools-1.13/GatherGeneGCLength Drop-seq_tools-1.13/GatherMolecularBarcodeDistributionByGene Drop-seq_tools-1.13/GatherReadQualityMetrics Drop-seq_tools-1.13/LICENSE.txt Drop-seq_tools-1.13/PolyATrimmer Drop-seq_tools-1.13/README Drop-seq_tools-1.13/ReduceGTF Drop-seq_tools-1.13/SelectCellsByNumTranscripts Drop-seq_tools-1.13/SingleCellRnaSeqMetricsCollector Drop-seq_tools-1.13/TagBamWithReadSequenceExtended Drop-seq_tools-1.13/TagReadWithGeneExon Drop-seq_tools-1.13/TagReadWithInterval Drop-seq_tools-1.13/TrimStartingSequence Drop-seq_tools-1.13/ValidateReference Drop-seq_tools-1.13/build.xml Drop-seq_tools-1.13/jar/ Drop-seq_tools-1.13/jar/dropseq.jar Drop-seq_tools-1.13/jar/lib/ Drop-seq_tools-1.13/jar/lib/libIntelDeflater.so Drop-seq_tools-1.13/jar/lib/test/ Drop-seq_tools-1.13/loadDotKits.sh Drop-seq_tools-1.13/public/ Drop-seq_tools-1.13/public/src/ Drop-seq_tools-1.13/public/src/java/ Drop-seq_tools-1.13/public/src/java/org/ Drop-seq_tools-1.13/public/src/java/org/broadinstitute/ Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/ Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/TranscriptomeException.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/annotation/ Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/annotation/AnnotationUtils.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/annotation/ConvertToRefFlat.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/annotation/CreateIntervalsFiles.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/annotation/EnhanceGTFRecords.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/annotation/GQuadruplex.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/annotation/GTFParser.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/annotation/GTFReader.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/annotation/GTFRecord.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/annotation/GatherGeneGCLength.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/annotation/GeneAnnotationReader.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/annotation/GeneFromGTF.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/annotation/GeneFromGTFBuilder.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/annotation/GenomicOrderComparator.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/annotation/ReduceGTF.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/annotation/RefFlatRecord.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/annotation/ValidateReference.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/barnyard/ Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/barnyard/BarcodeListRetrieval.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/barnyard/DGECommandLineBase.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/barnyard/DigitalExpression.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/barnyard/GatherMolecularBarcodeDistributionByGene.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/barnyard/ParseBarcodeFile.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/barnyard/SelectCellsByNumTranscripts.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/barnyard/SingleCellRnaSeqMetricsCollector.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/barnyard/Utils.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/barnyard/digitalexpression/ Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/barnyard/digitalexpression/DgeHeader.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/barnyard/digitalexpression/DgeHeaderCodec.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/barnyard/digitalexpression/DgeHeaderCommand.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/barnyard/digitalexpression/DgeHeaderLibrary.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/barnyard/digitalexpression/UMICollection.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/beadsynthesis/ Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/beadsynthesis/AbstractDetectBeadSynthesisErrors.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/beadsynthesis/BarcodeNeighborGroup.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/beadsynthesis/BeadSynthesisErrorData.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/beadsynthesis/BeadSynthesisErrorTypes.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/beadsynthesis/BiasedBarcodeCollection.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/beadsynthesis/BiasedBarcodeCollectionFactory.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/beadsynthesis/DetectBeadSynthesisErrors.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/beadsynthesis/DetectIncompleteBeadSynthesisErrors.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/beadsynthesis/DetectPrimerInUMI.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/cmdline/ Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/cmdline/CustomCommandLineValidationHelper.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/cmdline/DropNet.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/cmdline/DropSeq.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/cmdline/DropSeqMain.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/cmdline/MetaData.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/junctionlibrary/ Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/junctionlibrary/JunctionSamUtils.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/metrics/ Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/metrics/BAMTagHistogram.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/metrics/BAMTagofTagCounts.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/metrics/GatherReadQualityMetrics.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/metrics/ReadQualityMetrics.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/metrics/TagOfTagResults.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/metrics/TagReadWithGeneExon.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/metrics/TagReadWithInterval.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/readtrimming/ Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/readtrimming/AdapterDescriptor.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/readtrimming/PolyAFinder.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/readtrimming/PolyATrimmer.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/readtrimming/PolyAWithAdapterFinder.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/readtrimming/SimplePolyAFinder.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/readtrimming/TrimSequenceTemplate.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/readtrimming/TrimStartingSequence.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/ Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/BaseDistributionAtReadPosition.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/BaseDistributionMetric.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/BaseDistributionMetricCollection.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/BaseRange.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/Bases.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/CountChangingIteratorWrapper.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/CustomBAMIterators.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/DropSeqSamUtil.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/FastaSequenceFileWriter.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/FilterBAM.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/FilterBAMByTag.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/FilteredIterator.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/GroupingIterator.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/IntervalTagComparator.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/MultiComparator.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/ObjectCounter.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/OutputWriterUtil.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/PeekableGroupingIterator.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/ProgressLoggingIterator.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/ReadNameComparator.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/SamHeaderUtil.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/SortingIteratorFactory.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/StringInterner.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/StringTagComparator.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/TagBamWithReadSequenceExtended.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/TransformingIterator.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/VariantContextProgressLoggerIterator.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/VariantContextSingletonFilter.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/editdistance/ Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/editdistance/BarcodeCollapseMetric.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/editdistance/BarcodeWithCount.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/editdistance/CollapseBarcodeThreaded.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/editdistance/CollapseBarcodesInPlace.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/editdistance/CollapseBarcodesTask.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/editdistance/CollapseTagWithContext.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/editdistance/EDUtils.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/editdistance/HammingDistance.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/editdistance/LevenshteinDistance.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/editdistance/LevenshteinDistanceResult.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/editdistance/MapBarcodesByEditDistance.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/io/ Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/io/ErrorCheckingPrintStream.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/io/ErrorCheckingPrintWriter.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/modularfileparser/ Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/modularfileparser/BEDFileParser.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/modularfileparser/DelimiterParser.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/modularfileparser/ModularFileParser.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/modularfileparser/ModularFileParserException.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/modularfileparser/Parser.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/modularfileparser/ParserFactory.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/modularfileparser/ReducedGTFLine.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/modularfileparser/ReducedGTFParser.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/readiterators/ Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/readiterators/BamTagCountingIterator.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/readiterators/CellBarcodeFilteringIterator.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/readiterators/ChromosomeFilteringIterator.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/readiterators/DEIteratorUtils.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/readiterators/EditDistanceFilteringIterator.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/readiterators/GeneStrandFilteringIterator.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/readiterators/MapQualityFilteredIterator.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/readiterators/MissingTagFilteringIterator.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/readiterators/PCRDuplicateFilteringIterator.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/readiterators/SamFileMergeUtil.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/readiterators/SamHeaderAndIterator.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/readiterators/SamRecordSortingIteratorFactory.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/readiterators/UMIIterator.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/readiterators/UMIReadIterator.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/readiterators/UmiIteratorWrapper.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/readpairs/ Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/readpairs/ReadPair.java Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/referencetools/ Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/utils/referencetools/ReferenceUtils.java Drop-seq_tools-1.13/public/src/tests/ Drop-seq_tools-1.13/public/src/tests/java/ Drop-seq_tools-1.13/public/src/tests/java/org/ Drop-seq_tools-1.13/public/src/tests/java/org/broadinstitute/ Drop-seq_tools-1.13/public/src/tests/java/org/broadinstitute/dropseqrna/ Drop-seq_tools-1.13/public/src/tests/java/org/broadinstitute/dropseqrna/annotation/ Drop-seq_tools-1.13/public/src/tests/java/org/broadinstitute/dropseqrna/annotation/ConvertToRefFlatTest.java Drop-seq_tools-1.13/public/src/tests/java/org/broadinstitute/dropseqrna/annotation/EnhanceGTFRecordsTest.java Drop-seq_tools-1.13/public/src/tests/java/org/broadinstitute/dropseqrna/annotation/FindGQuadruplexTest.java Drop-seq_tools-1.13/public/src/tests/java/org/broadinstitute/dropseqrna/annotation/GTFReaderTest.java Drop-seq_tools-1.13/public/src/tests/java/org/broadinstitute/dropseqrna/annotation/GatherGeneGCLengthTest.java Drop-seq_tools-1.13/public/src/tests/java/org/broadinstitute/dropseqrna/annotation/ReduceGTFTest.java Drop-seq_tools-1.13/public/src/tests/java/org/broadinstitute/dropseqrna/barnyard/ Drop-seq_tools-1.13/public/src/tests/java/org/broadinstitute/dropseqrna/barnyard/DigitalExpressionTest.java Drop-seq_tools-1.13/public/src/tests/java/org/broadinstitute/dropseqrna/barnyard/SingleCellRnaSeqMetricsCollectorTest.java Drop-seq_tools-1.13/public/src/tests/java/org/broadinstitute/dropseqrna/barnyard/digitalexpression/ Drop-seq_tools-1.13/public/src/tests/java/org/broadinstitute/dropseqrna/barnyard/digitalexpression/DgeHeaderCodecTest.java Drop-seq_tools-1.13/public/src/tests/java/org/broadinstitute/dropseqrna/beadsynthesis/ Drop-seq_tools-1.13/public/src/tests/java/org/broadinstitute/dropseqrna/beadsynthesis/BeadSynthesisErrorDataTest.java Drop-seq_tools-1.13/public/src/tests/java/org/broadinstitute/dropseqrna/beadsynthesis/DetectBeadSynthesisErrorsTest.java Drop-seq_tools-1.13/public/src/tests/java/org/broadinstitute/dropseqrna/beadsynthesis/DetectPrimerTest.java Drop-seq_tools-1.13/public/src/tests/java/org/broadinstitute/dropseqrna/utils/ Drop-seq_tools-1.13/public/src/tests/java/org/broadinstitute/dropseqrna/utils/BaseRangeTest.java Drop-seq_tools-1.13/public/src/tests/java/org/broadinstitute/dropseqrna/utils/FilterBAMByTagTest.java Drop-seq_tools-1.13/public/src/tests/java/org/broadinstitute/dropseqrna/utils/FilterBAMTest.java Drop-seq_tools-1.13/public/src/tests/java/org/broadinstitute/dropseqrna/utils/IntervalTagComparatorTest.java Drop-seq_tools-1.13/public/src/tests/java/org/broadinstitute/dropseqrna/utils/PeekableGroupingIteratorTest.java Drop-seq_tools-1.13/public/src/tests/java/org/broadinstitute/dropseqrna/utils/TagBamWithReadSequenceExtendedTest.java Drop-seq_tools-1.13/public/src/tests/java/org/broadinstitute/dropseqrna/utils/editdistance/ Drop-seq_tools-1.13/public/src/tests/java/org/broadinstitute/dropseqrna/utils/editdistance/CollapseBarcodeThreadedTest.java Drop-seq_tools-1.13/public/src/tests/java/org/broadinstitute/dropseqrna/utils/editdistance/MapBarcodesByEditDistanceTest.java Drop-seq_tools-1.13/public/src/tests/java/org/broadinstitute/dropseqrna/utils/editdistance/ModifiedLevenshteinDistanceTest.java Drop-seq_tools-1.13/public/src/tests/java/org/broadinstitute/dropseqrna/utils/readiterators/ Drop-seq_tools-1.13/public/src/tests/java/org/broadinstitute/dropseqrna/utils/readiterators/AggregatedTagOrderIteratorTest.java Drop-seq_tools-1.13/public/src/tests/java/org/broadinstitute/dropseqrna/utils/readiterators/MapQualityProcessorTest.java Drop-seq_tools-1.13/public/src/tests/java/org/broadinstitute/dropseqrna/utils/readiterators/TagOrderIteratorTest.java Drop-seq_tools-1.13/public/src/tests/java/org/broadinstitute/dropseqrna/utils/readiterators/TagValueProcessorTest.java phase `unpack' succeeded after 0.1 seconds starting phase `record-references' phase `record-references' succeeded after 0.3 seconds starting phase `patch-usr-bin-file' phase `patch-usr-bin-file' succeeded after 0.0 seconds starting phase `patch-source-shebangs' patch-shebang: ./BAMTagHistogram: changing `/bin/bash' to `/gnu/store/pwcp239kjf7lnj5i4lkdzcfcxwcfyk72-bash-minimal-5.0.16/bin/bash' patch-shebang: ./BAMTagofTagCounts: changing `/bin/bash' to `/gnu/store/pwcp239kjf7lnj5i4lkdzcfcxwcfyk72-bash-minimal-5.0.16/bin/bash' patch-shebang: ./BaseDistributionAtReadPosition: changing `/bin/bash' to `/gnu/store/pwcp239kjf7lnj5i4lkdzcfcxwcfyk72-bash-minimal-5.0.16/bin/bash' patch-shebang: ./CollapseBarcodesInPlace: changing `/bin/bash' to `/gnu/store/pwcp239kjf7lnj5i4lkdzcfcxwcfyk72-bash-minimal-5.0.16/bin/bash' patch-shebang: ./CollapseTagWithContext: changing `/bin/bash' to `/gnu/store/pwcp239kjf7lnj5i4lkdzcfcxwcfyk72-bash-minimal-5.0.16/bin/bash' patch-shebang: ./ConvertToRefFlat: changing `/bin/bash' to `/gnu/store/pwcp239kjf7lnj5i4lkdzcfcxwcfyk72-bash-minimal-5.0.16/bin/bash' patch-shebang: ./CreateIntervalsFiles: changing `/bin/bash' to `/gnu/store/pwcp239kjf7lnj5i4lkdzcfcxwcfyk72-bash-minimal-5.0.16/bin/bash' patch-shebang: ./DetectBeadSynthesisErrors: changing `/bin/bash' to `/gnu/store/pwcp239kjf7lnj5i4lkdzcfcxwcfyk72-bash-minimal-5.0.16/bin/bash' patch-shebang: ./DigitalExpression: changing `/bin/bash' to `/gnu/store/pwcp239kjf7lnj5i4lkdzcfcxwcfyk72-bash-minimal-5.0.16/bin/bash' patch-shebang: ./Drop-seq_alignment.sh: changing `/usr/bin/env bash' to `/gnu/store/pwcp239kjf7lnj5i4lkdzcfcxwcfyk72-bash-minimal-5.0.16/bin/bash' patch-shebang: ./FilterBAM: changing `/bin/bash' to `/gnu/store/pwcp239kjf7lnj5i4lkdzcfcxwcfyk72-bash-minimal-5.0.16/bin/bash' patch-shebang: ./FilterBAMByTag: changing `/bin/bash' to `/gnu/store/pwcp239kjf7lnj5i4lkdzcfcxwcfyk72-bash-minimal-5.0.16/bin/bash' patch-shebang: ./GatherGeneGCLength: changing `/bin/bash' to `/gnu/store/pwcp239kjf7lnj5i4lkdzcfcxwcfyk72-bash-minimal-5.0.16/bin/bash' patch-shebang: ./GatherMolecularBarcodeDistributionByGene: changing `/bin/bash' to `/gnu/store/pwcp239kjf7lnj5i4lkdzcfcxwcfyk72-bash-minimal-5.0.16/bin/bash' patch-shebang: ./GatherReadQualityMetrics: changing `/bin/bash' to `/gnu/store/pwcp239kjf7lnj5i4lkdzcfcxwcfyk72-bash-minimal-5.0.16/bin/bash' patch-shebang: ./PolyATrimmer: changing `/bin/bash' to `/gnu/store/pwcp239kjf7lnj5i4lkdzcfcxwcfyk72-bash-minimal-5.0.16/bin/bash' patch-shebang: ./ReduceGTF: changing `/bin/bash' to `/gnu/store/pwcp239kjf7lnj5i4lkdzcfcxwcfyk72-bash-minimal-5.0.16/bin/bash' patch-shebang: ./SelectCellsByNumTranscripts: changing `/bin/bash' to `/gnu/store/pwcp239kjf7lnj5i4lkdzcfcxwcfyk72-bash-minimal-5.0.16/bin/bash' patch-shebang: ./SingleCellRnaSeqMetricsCollector: changing `/bin/bash' to `/gnu/store/pwcp239kjf7lnj5i4lkdzcfcxwcfyk72-bash-minimal-5.0.16/bin/bash' patch-shebang: ./TagBamWithReadSequenceExtended: changing `/bin/bash' to `/gnu/store/pwcp239kjf7lnj5i4lkdzcfcxwcfyk72-bash-minimal-5.0.16/bin/bash' patch-shebang: ./TagReadWithGeneExon: changing `/bin/bash' to `/gnu/store/pwcp239kjf7lnj5i4lkdzcfcxwcfyk72-bash-minimal-5.0.16/bin/bash' patch-shebang: ./TagReadWithInterval: changing `/bin/bash' to `/gnu/store/pwcp239kjf7lnj5i4lkdzcfcxwcfyk72-bash-minimal-5.0.16/bin/bash' patch-shebang: ./TrimStartingSequence: changing `/bin/bash' to `/gnu/store/pwcp239kjf7lnj5i4lkdzcfcxwcfyk72-bash-minimal-5.0.16/bin/bash' patch-shebang: ./ValidateReference: changing `/bin/bash' to `/gnu/store/pwcp239kjf7lnj5i4lkdzcfcxwcfyk72-bash-minimal-5.0.16/bin/bash' phase `patch-source-shebangs' succeeded after 0.1 seconds starting phase `configure' phase `configure' succeeded after 0.2 seconds starting phase `patch-generated-file-shebangs' phase `patch-generated-file-shebangs' succeeded after 0.0 seconds starting phase `build' Buildfile: /tmp/guix-build-dropseq-tools-1.13.drv-0/Drop-seq_tools-1.13/build.xml compile-public-src: [mkdir] Created dir: /tmp/guix-build-dropseq-tools-1.13.drv-0/Drop-seq_tools-1.13/public_classes [javac] /tmp/guix-build-dropseq-tools-1.13.drv-0/Drop-seq_tools-1.13/build.xml:78: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 125 source files to /tmp/guix-build-dropseq-tools-1.13.drv-0/Drop-seq_tools-1.13/public_classes [javac] Note: /tmp/guix-build-dropseq-tools-1.13.drv-0/Drop-seq_tools-1.13/public/src/java/org/broadinstitute/dropseqrna/annotation/GeneFromGTFBuilder.java uses or overrides a deprecated API. [javac] Note: Recompile with -Xlint:deprecation for details. [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. compile-public-tests: [mkdir] Created dir: /tmp/guix-build-dropseq-tools-1.13.drv-0/Drop-seq_tools-1.13/public_testclasses [javac] /tmp/guix-build-dropseq-tools-1.13.drv-0/Drop-seq_tools-1.13/build.xml:78: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 25 source files to /tmp/guix-build-dropseq-tools-1.13.drv-0/Drop-seq_tools-1.13/public_testclasses [javac] Note: Some input files use or override a deprecated API. [javac] Note: Recompile with -Xlint:deprecation for details. [javac] Note: /tmp/guix-build-dropseq-tools-1.13.drv-0/Drop-seq_tools-1.13/public/src/tests/java/org/broadinstitute/dropseqrna/utils/FilterBAMTest.java uses unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. compile-tests: compile: jar-public-executable: [mkdir] Created dir: /tmp/guix-build-dropseq-tools-1.13.drv-0/Drop-seq_tools-1.13/dist [jar] Building jar: /tmp/guix-build-dropseq-tools-1.13.drv-0/Drop-seq_tools-1.13/dist/dropseq.jar all: BUILD SUCCESSFUL Total time: 5 seconds phase `build' succeeded after 5.8 seconds starting phase `check' test suite not run phase `check' succeeded after 0.0 seconds starting phase `install' phase `install' succeeded after 0.0 seconds starting phase `reorder-jar-content' repacking /gnu/store/kijz2x2r2v2z0qnarzn4v7dnf7k8pszb-dropseq-tools-1.13/share/java/dropseq.jar adding: META-INF/ (stored 0%) adding: META-INF/MANIFEST.MF (stored 0%) adding: org/ (stored 0%) adding: org/broadinstitute/ (stored 0%) adding: org/broadinstitute/dropseqrna/ (stored 0%) adding: org/broadinstitute/dropseqrna/TranscriptomeException.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/ (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/AnnotationUtils.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/ConvertToRefFlat.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/CreateIntervalsFiles$AnnotationType.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/CreateIntervalsFiles$ReducedGtfColumn.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/CreateIntervalsFiles$TranscriptType.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/CreateIntervalsFiles.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/EnhanceGTFRecords.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/GQuadruplex.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/GTFParser$GTFFeature.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/GTFParser$GTFFlatColumns.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/GTFParser.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/GTFReader$1.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/GTFReader$FilteringGTFParser.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/GTFReader.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/GTFRecord.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/GatherGeneGCLength$GCIsoformSummary.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/GatherGeneGCLength$GCResult.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/GatherGeneGCLength.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/GeneAnnotationReader.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/GeneFromGTF$TranscriptFromGTF.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/GeneFromGTF.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/GeneFromGTFBuilder$1.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/GeneFromGTFBuilder$2.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/GeneFromGTFBuilder$3.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/GeneFromGTFBuilder$Exon.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/GeneFromGTFBuilder$GeneAnnotationFilter.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/GeneFromGTFBuilder.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/GenomicOrderComparator.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/ReduceGTF$1.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/ReduceGTF$FilteringGTFParser.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/ReduceGTF.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/RefFlatRecord.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/ValidateReference.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/ (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/BarcodeListRetrieval.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/DGECommandLineBase.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/DigitalExpression$1.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/DigitalExpression$DESummary.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/DigitalExpression.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/GatherMolecularBarcodeDistributionByGene.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/ParseBarcodeFile.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/SelectCellsByNumTranscripts$1.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/SelectCellsByNumTranscripts$EntryComparator.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/SelectCellsByNumTranscripts$MapContainer.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/SelectCellsByNumTranscripts$MultiOrganismMapContainer.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/SelectCellsByNumTranscripts$PrefixGeneWithOrganismIterator.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/SelectCellsByNumTranscripts$SingleOrganismMapContainer.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/SelectCellsByNumTranscripts.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/SingleCellRnaSeqMetricsCollector$1.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/SingleCellRnaSeqMetricsCollector$CollectorFactory.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/SingleCellRnaSeqMetricsCollector$RnaSeqMtMetrics.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/SingleCellRnaSeqMetricsCollector$RnaSeqMtMetricsCollector$PerUnitRnaSeqMtMetricsCollector.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/SingleCellRnaSeqMetricsCollector$RnaSeqMtMetricsCollector.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/SingleCellRnaSeqMetricsCollector.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/Utils.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/digitalexpression/ (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/digitalexpression/DgeHeader$ExpressionFormat.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/digitalexpression/DgeHeader.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/digitalexpression/DgeHeaderCodec$1.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/digitalexpression/DgeHeaderCodec$CommandRecordTag.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/digitalexpression/DgeHeaderCodec$DgeBufferedInputStream.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/digitalexpression/DgeHeaderCodec$DgeBufferedReader.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/digitalexpression/DgeHeaderCodec$DgeHeaderLineReader.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/digitalexpression/DgeHeaderCodec$DgeRecordTag.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/digitalexpression/DgeHeaderCodec$LibraryRecordTag.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/digitalexpression/DgeHeaderCodec$OutputRecordBuilder.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/digitalexpression/DgeHeaderCodec.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/digitalexpression/DgeHeaderCommand.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/digitalexpression/DgeHeaderLibrary.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/digitalexpression/UMICollection.class (stored 0%) adding: 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org/broadinstitute/dropseqrna/beadsynthesis/DetectBeadSynthesisErrors$BeadSynthesisErrorsSummaryMetric.class (stored 0%) adding: org/broadinstitute/dropseqrna/beadsynthesis/DetectBeadSynthesisErrors.class (stored 0%) adding: org/broadinstitute/dropseqrna/beadsynthesis/DetectIncompleteBeadSynthesisErrors.class (stored 0%) adding: org/broadinstitute/dropseqrna/beadsynthesis/DetectPrimerInUMI.class (stored 0%) adding: org/broadinstitute/dropseqrna/cmdline/ (stored 0%) adding: org/broadinstitute/dropseqrna/cmdline/CustomCommandLineValidationHelper.class (stored 0%) adding: org/broadinstitute/dropseqrna/cmdline/DropNet.class (stored 0%) adding: org/broadinstitute/dropseqrna/cmdline/DropSeq.class (stored 0%) adding: org/broadinstitute/dropseqrna/cmdline/DropSeqMain.class (stored 0%) adding: org/broadinstitute/dropseqrna/cmdline/MetaData.class (stored 0%) adding: org/broadinstitute/dropseqrna/junctionlibrary/ (stored 0%) adding: org/broadinstitute/dropseqrna/junctionlibrary/JunctionSamUtils.class (stored 0%) adding: org/broadinstitute/dropseqrna/metrics/ (stored 0%) adding: org/broadinstitute/dropseqrna/metrics/BAMTagHistogram.class (stored 0%) adding: org/broadinstitute/dropseqrna/metrics/BAMTagofTagCounts.class (stored 0%) adding: org/broadinstitute/dropseqrna/metrics/GatherReadQualityMetrics.class (stored 0%) adding: org/broadinstitute/dropseqrna/metrics/ReadQualityMetrics.class (stored 0%) adding: org/broadinstitute/dropseqrna/metrics/TagOfTagResults.class (stored 0%) adding: org/broadinstitute/dropseqrna/metrics/TagReadWithGeneExon$ReadTaggingMetric.class (stored 0%) adding: org/broadinstitute/dropseqrna/metrics/TagReadWithGeneExon.class (stored 0%) adding: org/broadinstitute/dropseqrna/metrics/TagReadWithInterval.class (stored 0%) adding: org/broadinstitute/dropseqrna/readtrimming/ (stored 0%) adding: org/broadinstitute/dropseqrna/readtrimming/AdapterDescriptor$AdapterElement.class (stored 0%) adding: org/broadinstitute/dropseqrna/readtrimming/AdapterDescriptor$FixedAdapterElement.class (stored 0%) adding: org/broadinstitute/dropseqrna/readtrimming/AdapterDescriptor$TagAdapterElement.class (stored 0%) adding: org/broadinstitute/dropseqrna/readtrimming/AdapterDescriptor.class (stored 0%) adding: org/broadinstitute/dropseqrna/readtrimming/PolyAFinder$PolyARun.class (stored 0%) adding: org/broadinstitute/dropseqrna/readtrimming/PolyAFinder.class (stored 0%) adding: org/broadinstitute/dropseqrna/readtrimming/PolyATrimmer$TrimMetric.class (stored 0%) adding: org/broadinstitute/dropseqrna/readtrimming/PolyATrimmer.class (stored 0%) adding: org/broadinstitute/dropseqrna/readtrimming/PolyAWithAdapterFinder.class (stored 0%) adding: org/broadinstitute/dropseqrna/readtrimming/SimplePolyAFinder.class (stored 0%) adding: org/broadinstitute/dropseqrna/readtrimming/TrimSequenceTemplate.class (stored 0%) adding: org/broadinstitute/dropseqrna/readtrimming/TrimStartingSequence$TrimMetric.class 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org/broadinstitute/dropseqrna/utils/FilterBAM.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/FilterBAMByTag.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/FilteredIterator.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/GroupingIterator.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/IntervalTagComparator.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/MultiComparator.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/ObjectCounter.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/OutputWriterUtil.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/PeekableGroupingIterator.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/ProgressLoggingIterator.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/ReadNameComparator.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/SamHeaderUtil.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/SortingIteratorFactory$ProgressCallback.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/SortingIteratorFactory.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/StringInterner.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/StringTagComparator.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/TagBamWithReadSequenceExtended$FailedBaseMetric.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/TagBamWithReadSequenceExtended.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/TransformingIterator.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/VariantContextProgressLoggerIterator.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/VariantContextSingletonFilter.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/editdistance/ (stored 0%) adding: org/broadinstitute/dropseqrna/utils/editdistance/BarcodeCollapseMetric.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/editdistance/BarcodeWithCount$CountComparator.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/editdistance/BarcodeWithCount.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/editdistance/CollapseBarcodeThreaded.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/editdistance/CollapseBarcodesInPlace.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/editdistance/CollapseBarcodesTask.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/editdistance/CollapseTagWithContext.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/editdistance/EDUtils.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/editdistance/HammingDistance.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/editdistance/LevenshteinDistance.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/editdistance/LevenshteinDistanceResult$AdjacentScores$Operation.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/editdistance/LevenshteinDistanceResult$AdjacentScores.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/editdistance/LevenshteinDistanceResult$Operations.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/editdistance/LevenshteinDistanceResult.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/editdistance/MapBarcodesByEditDistance.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/io/ (stored 0%) adding: org/broadinstitute/dropseqrna/utils/io/ErrorCheckingPrintStream$1.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/io/ErrorCheckingPrintStream.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/io/ErrorCheckingPrintWriter$1.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/io/ErrorCheckingPrintWriter.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/modularfileparser/ (stored 0%) adding: org/broadinstitute/dropseqrna/utils/modularfileparser/BEDFileParser.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/modularfileparser/DelimiterParser.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/modularfileparser/ModularFileParser.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/modularfileparser/ModularFileParserException.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/modularfileparser/Parser.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/modularfileparser/ReducedGTFLine.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/modularfileparser/ReducedGTFParser.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/readiterators/ (stored 0%) adding: org/broadinstitute/dropseqrna/utils/readiterators/BamTagCountingIterator.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/readiterators/CellBarcodeFilteringIterator.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/readiterators/ChromosomeFilteringIterator.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/readiterators/DEIteratorUtils.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/readiterators/EditDistanceFilteringIterator.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/readiterators/GeneStrandFilteringIterator.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/readiterators/MapQualityFilteredIterator.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/readiterators/MissingTagFilteringIterator.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/readiterators/PCRDuplicateFilteringIterator.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/readiterators/SamFileMergeUtil.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/readiterators/SamHeaderAndIterator.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/readiterators/SamRecordSortingIteratorFactory$1.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/readiterators/SamRecordSortingIteratorFactory.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/readiterators/UMIIterator.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/readiterators/UMIReadIterator.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/readiterators/UmiIteratorWrapper.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/readpairs/ (stored 0%) adding: org/broadinstitute/dropseqrna/utils/readpairs/ReadPair.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/referencetools/ (stored 0%) adding: org/broadinstitute/dropseqrna/utils/referencetools/ReferenceUtils.class (stored 0%) phase `reorder-jar-content' succeeded after 0.2 seconds starting phase `strip-jar-timestamps' repacking /gnu/store/kijz2x2r2v2z0qnarzn4v7dnf7k8pszb-dropseq-tools-1.13/share/java/dropseq.jar adding: META-INF/ (stored 0%) adding: META-INF/MANIFEST.MF (stored 0%) adding: org/ (stored 0%) adding: org/broadinstitute/ (stored 0%) adding: org/broadinstitute/dropseqrna/ (stored 0%) adding: org/broadinstitute/dropseqrna/TranscriptomeException.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/ (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/AnnotationUtils.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/ConvertToRefFlat.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/CreateIntervalsFiles$AnnotationType.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/CreateIntervalsFiles$ReducedGtfColumn.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/CreateIntervalsFiles$TranscriptType.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/CreateIntervalsFiles.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/EnhanceGTFRecords.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/GQuadruplex.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/GTFParser$GTFFeature.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/GTFParser$GTFFlatColumns.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/GTFParser.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/GTFReader$1.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/GTFReader$FilteringGTFParser.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/GTFReader.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/GTFRecord.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/GatherGeneGCLength$GCIsoformSummary.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/GatherGeneGCLength$GCResult.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/GatherGeneGCLength.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/GeneAnnotationReader.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/GeneFromGTF$TranscriptFromGTF.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/GeneFromGTF.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/GeneFromGTFBuilder$1.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/GeneFromGTFBuilder$2.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/GeneFromGTFBuilder$3.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/GeneFromGTFBuilder$Exon.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/GeneFromGTFBuilder$GeneAnnotationFilter.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/GeneFromGTFBuilder.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/GenomicOrderComparator.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/ReduceGTF$1.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/ReduceGTF$FilteringGTFParser.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/ReduceGTF.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/RefFlatRecord.class (stored 0%) adding: org/broadinstitute/dropseqrna/annotation/ValidateReference.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/ (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/BarcodeListRetrieval.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/DGECommandLineBase.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/DigitalExpression$1.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/DigitalExpression$DESummary.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/DigitalExpression.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/GatherMolecularBarcodeDistributionByGene.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/ParseBarcodeFile.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/SelectCellsByNumTranscripts$1.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/SelectCellsByNumTranscripts$EntryComparator.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/SelectCellsByNumTranscripts$MapContainer.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/SelectCellsByNumTranscripts$MultiOrganismMapContainer.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/SelectCellsByNumTranscripts$PrefixGeneWithOrganismIterator.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/SelectCellsByNumTranscripts$SingleOrganismMapContainer.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/SelectCellsByNumTranscripts.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/SingleCellRnaSeqMetricsCollector$1.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/SingleCellRnaSeqMetricsCollector$CollectorFactory.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/SingleCellRnaSeqMetricsCollector$RnaSeqMtMetrics.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/SingleCellRnaSeqMetricsCollector$RnaSeqMtMetricsCollector$PerUnitRnaSeqMtMetricsCollector.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/SingleCellRnaSeqMetricsCollector$RnaSeqMtMetricsCollector.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/SingleCellRnaSeqMetricsCollector.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/Utils.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/digitalexpression/ (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/digitalexpression/DgeHeader$ExpressionFormat.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/digitalexpression/DgeHeader.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/digitalexpression/DgeHeaderCodec$1.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/digitalexpression/DgeHeaderCodec$CommandRecordTag.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/digitalexpression/DgeHeaderCodec$DgeBufferedInputStream.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/digitalexpression/DgeHeaderCodec$DgeBufferedReader.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/digitalexpression/DgeHeaderCodec$DgeHeaderLineReader.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/digitalexpression/DgeHeaderCodec$DgeRecordTag.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/digitalexpression/DgeHeaderCodec$LibraryRecordTag.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/digitalexpression/DgeHeaderCodec$OutputRecordBuilder.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/digitalexpression/DgeHeaderCodec.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/digitalexpression/DgeHeaderCommand.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/digitalexpression/DgeHeaderLibrary.class (stored 0%) adding: org/broadinstitute/dropseqrna/barnyard/digitalexpression/UMICollection.class (stored 0%) adding: org/broadinstitute/dropseqrna/beadsynthesis/ (stored 0%) adding: org/broadinstitute/dropseqrna/beadsynthesis/AbstractDetectBeadSynthesisErrors$1.class (stored 0%) adding: org/broadinstitute/dropseqrna/beadsynthesis/AbstractDetectBeadSynthesisErrors.class (stored 0%) adding: org/broadinstitute/dropseqrna/beadsynthesis/BarcodeNeighborGroup.class (stored 0%) adding: org/broadinstitute/dropseqrna/beadsynthesis/BeadSynthesisErrorData.class (stored 0%) adding: org/broadinstitute/dropseqrna/beadsynthesis/BeadSynthesisErrorTypes.class (stored 0%) adding: org/broadinstitute/dropseqrna/beadsynthesis/BiasedBarcodeCollection.class (stored 0%) adding: org/broadinstitute/dropseqrna/beadsynthesis/BiasedBarcodeCollectionFactory.class (stored 0%) adding: org/broadinstitute/dropseqrna/beadsynthesis/DetectBeadSynthesisErrors$1.class (stored 0%) adding: org/broadinstitute/dropseqrna/beadsynthesis/DetectBeadSynthesisErrors$2.class (stored 0%) adding: org/broadinstitute/dropseqrna/beadsynthesis/DetectBeadSynthesisErrors$BeadSynthesisErrorsSummaryMetric.class (stored 0%) adding: org/broadinstitute/dropseqrna/beadsynthesis/DetectBeadSynthesisErrors.class (stored 0%) adding: org/broadinstitute/dropseqrna/beadsynthesis/DetectIncompleteBeadSynthesisErrors.class (stored 0%) adding: org/broadinstitute/dropseqrna/beadsynthesis/DetectPrimerInUMI.class (stored 0%) adding: org/broadinstitute/dropseqrna/cmdline/ (stored 0%) adding: org/broadinstitute/dropseqrna/cmdline/CustomCommandLineValidationHelper.class (stored 0%) adding: org/broadinstitute/dropseqrna/cmdline/DropNet.class (stored 0%) adding: org/broadinstitute/dropseqrna/cmdline/DropSeq.class (stored 0%) adding: org/broadinstitute/dropseqrna/cmdline/DropSeqMain.class (stored 0%) adding: org/broadinstitute/dropseqrna/cmdline/MetaData.class (stored 0%) adding: org/broadinstitute/dropseqrna/junctionlibrary/ (stored 0%) adding: org/broadinstitute/dropseqrna/junctionlibrary/JunctionSamUtils.class (stored 0%) adding: org/broadinstitute/dropseqrna/metrics/ (stored 0%) adding: org/broadinstitute/dropseqrna/metrics/BAMTagHistogram.class (stored 0%) adding: org/broadinstitute/dropseqrna/metrics/BAMTagofTagCounts.class (stored 0%) adding: org/broadinstitute/dropseqrna/metrics/GatherReadQualityMetrics.class (stored 0%) adding: org/broadinstitute/dropseqrna/metrics/ReadQualityMetrics.class (stored 0%) adding: org/broadinstitute/dropseqrna/metrics/TagOfTagResults.class (stored 0%) adding: org/broadinstitute/dropseqrna/metrics/TagReadWithGeneExon$ReadTaggingMetric.class (stored 0%) adding: org/broadinstitute/dropseqrna/metrics/TagReadWithGeneExon.class (stored 0%) adding: org/broadinstitute/dropseqrna/metrics/TagReadWithInterval.class (stored 0%) adding: org/broadinstitute/dropseqrna/readtrimming/ (stored 0%) adding: org/broadinstitute/dropseqrna/readtrimming/AdapterDescriptor$AdapterElement.class (stored 0%) adding: org/broadinstitute/dropseqrna/readtrimming/AdapterDescriptor$FixedAdapterElement.class (stored 0%) adding: org/broadinstitute/dropseqrna/readtrimming/AdapterDescriptor$TagAdapterElement.class (stored 0%) adding: org/broadinstitute/dropseqrna/readtrimming/AdapterDescriptor.class (stored 0%) adding: org/broadinstitute/dropseqrna/readtrimming/PolyAFinder$PolyARun.class (stored 0%) adding: org/broadinstitute/dropseqrna/readtrimming/PolyAFinder.class (stored 0%) adding: org/broadinstitute/dropseqrna/readtrimming/PolyATrimmer$TrimMetric.class (stored 0%) adding: org/broadinstitute/dropseqrna/readtrimming/PolyATrimmer.class (stored 0%) adding: org/broadinstitute/dropseqrna/readtrimming/PolyAWithAdapterFinder.class (stored 0%) adding: org/broadinstitute/dropseqrna/readtrimming/SimplePolyAFinder.class (stored 0%) adding: org/broadinstitute/dropseqrna/readtrimming/TrimSequenceTemplate.class (stored 0%) adding: org/broadinstitute/dropseqrna/readtrimming/TrimStartingSequence$TrimMetric.class (stored 0%) adding: org/broadinstitute/dropseqrna/readtrimming/TrimStartingSequence.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/ (stored 0%) adding: org/broadinstitute/dropseqrna/utils/BaseDistributionAtReadPosition.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/BaseDistributionMetric.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/BaseDistributionMetricCollection.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/BaseRange.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/Bases.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/CountChangingIteratorWrapper.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/CustomBAMIterators.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/DropSeqSamUtil.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/FastaSequenceFileWriter.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/FilterBAM$MatchTypes.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/FilterBAM.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/FilterBAMByTag.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/FilteredIterator.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/GroupingIterator.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/IntervalTagComparator.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/MultiComparator.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/ObjectCounter.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/OutputWriterUtil.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/PeekableGroupingIterator.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/ProgressLoggingIterator.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/ReadNameComparator.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/SamHeaderUtil.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/SortingIteratorFactory$ProgressCallback.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/SortingIteratorFactory.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/StringInterner.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/StringTagComparator.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/TagBamWithReadSequenceExtended$FailedBaseMetric.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/TagBamWithReadSequenceExtended.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/TransformingIterator.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/VariantContextProgressLoggerIterator.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/VariantContextSingletonFilter.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/editdistance/ (stored 0%) adding: org/broadinstitute/dropseqrna/utils/editdistance/BarcodeCollapseMetric.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/editdistance/BarcodeWithCount$CountComparator.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/editdistance/BarcodeWithCount.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/editdistance/CollapseBarcodeThreaded.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/editdistance/CollapseBarcodesInPlace.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/editdistance/CollapseBarcodesTask.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/editdistance/CollapseTagWithContext.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/editdistance/EDUtils.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/editdistance/HammingDistance.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/editdistance/LevenshteinDistance.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/editdistance/LevenshteinDistanceResult$AdjacentScores$Operation.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/editdistance/LevenshteinDistanceResult$AdjacentScores.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/editdistance/LevenshteinDistanceResult$Operations.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/editdistance/LevenshteinDistanceResult.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/editdistance/MapBarcodesByEditDistance.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/io/ (stored 0%) adding: org/broadinstitute/dropseqrna/utils/io/ErrorCheckingPrintStream$1.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/io/ErrorCheckingPrintStream.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/io/ErrorCheckingPrintWriter$1.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/io/ErrorCheckingPrintWriter.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/modularfileparser/ (stored 0%) adding: org/broadinstitute/dropseqrna/utils/modularfileparser/BEDFileParser.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/modularfileparser/DelimiterParser.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/modularfileparser/ModularFileParser.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/modularfileparser/ModularFileParserException.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/modularfileparser/Parser.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/modularfileparser/ReducedGTFLine.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/modularfileparser/ReducedGTFParser.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/readiterators/ (stored 0%) adding: org/broadinstitute/dropseqrna/utils/readiterators/BamTagCountingIterator.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/readiterators/CellBarcodeFilteringIterator.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/readiterators/ChromosomeFilteringIterator.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/readiterators/DEIteratorUtils.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/readiterators/EditDistanceFilteringIterator.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/readiterators/GeneStrandFilteringIterator.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/readiterators/MapQualityFilteredIterator.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/readiterators/MissingTagFilteringIterator.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/readiterators/PCRDuplicateFilteringIterator.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/readiterators/SamFileMergeUtil.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/readiterators/SamHeaderAndIterator.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/readiterators/SamRecordSortingIteratorFactory$1.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/readiterators/SamRecordSortingIteratorFactory.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/readiterators/UMIIterator.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/readiterators/UMIReadIterator.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/readiterators/UmiIteratorWrapper.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/readpairs/ (stored 0%) adding: org/broadinstitute/dropseqrna/utils/readpairs/ReadPair.class (stored 0%) adding: org/broadinstitute/dropseqrna/utils/referencetools/ (stored 0%) adding: org/broadinstitute/dropseqrna/utils/referencetools/ReferenceUtils.class (stored 0%) phase `strip-jar-timestamps' succeeded after 0.3 seconds starting phase `install-links' phase `install-links' succeeded after 0.0 seconds starting phase `patch-shebangs' phase `patch-shebangs' succeeded after 0.0 seconds starting phase `strip' stripping binaries in "/gnu/store/kijz2x2r2v2z0qnarzn4v7dnf7k8pszb-dropseq-tools-1.13/bin" with "strip" and flags ("--strip-debug" "--enable-deterministic-archives") phase `strip' succeeded after 0.0 seconds starting phase `validate-runpath' validating RUNPATH of 0 binaries in "/gnu/store/kijz2x2r2v2z0qnarzn4v7dnf7k8pszb-dropseq-tools-1.13/bin"... phase `validate-runpath' succeeded after 0.0 seconds starting phase `validate-documentation-location' phase `validate-documentation-location' succeeded after 0.0 seconds starting phase `delete-info-dir-file' phase `delete-info-dir-file' succeeded after 0.0 seconds starting phase `patch-dot-desktop-files' phase `patch-dot-desktop-files' succeeded after 0.0 seconds starting phase `install-license-files' installing 1 license files from '.' phase `install-license-files' succeeded after 0.0 seconds starting phase `reset-gzip-timestamps' phase `reset-gzip-timestamps' succeeded after 0.0 seconds starting phase `compress-documentation' phase `compress-documentation' succeeded after 0.0 seconds