File "/opt/hostedtoolcache/Python/3.7.6/x64/lib/python3.7/unittest/case.py", line 59, in testPartExecutor yield File "/opt/hostedtoolcache/Python/3.7.6/x64/lib/python3.7/unittest/case.py", line 628, in run testMethod() File "/tmp/tmp6bhgm0al/galaxy-dev/test/functional/test_toolbox.py", line 99, in test_tool self.do_it(tool_version=tool_version, test_index=test_index) File "/tmp/tmp6bhgm0al/galaxy-dev/test/functional/test_toolbox.py", line 36, in do_it verify_tool(tool_id, self.galaxy_interactor, resource_parameters=resource_parameters, test_index=test_index, tool_version=tool_version, register_job_data=register_job_data) File "/tmp/tmp6bhgm0al/galaxy-dev/lib/galaxy/tool_util/verify/interactor.py", line 789, in verify_tool raise e File "/tmp/tmp6bhgm0al/galaxy-dev/lib/galaxy/tool_util/verify/interactor.py", line 785, in verify_tool job_stdio = _verify_outputs(testdef, test_history, jobs, tool_id, data_list, data_collection_list, galaxy_interactor, quiet=quiet) File "/tmp/tmp6bhgm0al/galaxy-dev/lib/galaxy/tool_util/verify/interactor.py", line 1006, in _verify_outputs raise JobOutputsError(found_exceptions, job_stdio) Job in error state. Job in error state. Job in error state. -------------------- >> begin captured stdout << --------------------- Problem in history with id 4e27b888e0f89616 - summary of history's datasets and jobs below. -------------------------------------- | 1 - mm10_MT19.fa.gz (HID - NAME) | Dataset State: | ok | Dataset Blurb: | 2 sequences | Dataset Info: | uploaded fasta file | Peek: |

>19

NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

| Dataset Job Standard Output: | *Standard output was empty.* | Dataset Job Standard Error: | *Standard error was empty.* | -------------------------------------- | 2 - CB51_MT19_R1.gz (HID - NAME) | Dataset State: | ok | Dataset Blurb: | 3.8 MB | Dataset Info: | uploaded fastqsanger.gz file | Peek: | @NS500643:237:HTJH5BGX2:1:11101:12862:1126 2:N:0:0 | GCCTACTTTAATTACATTGCTTACAAGATTAAGGAATCTTTATCTTGAAGACCCCATGAAAGGGATCATT | + | AAAAAEEA1.Seqid2.Source3.Type4.Start5.End6.Score7.Strand8.Phase9.Attributes19Ensemblchromosome161431566...ID=chromosome:19;Alias=CM001012.2,NC_000085.6,chr1919NCBIbiological_region30001243000832.+.external_name=BMQ-420I16 (end);logic_name=mouse_bmq_clones19NCBIbiological_region30001243000860.+.external_name=BMQ-420B16 (end);logic_name=mouse_bmq_clones19NCBIbiological_region30040443004571.+.external_name=DN-246O22 (start);logic_name=mouse_dn_clones19NCBIbiological_region30121183012983.+.external_name=CH29-566C15 (end);logic_name=mouse_ch29_clones | Dataset Job Standard Output: | *Standard output was empty.* | Dataset Job Standard Error: | *Standard error was empty.* | -------------------------------------- | 5 - scPipe on data 4, data 3, and others: Count Matrix (HID - NAME) | Dataset State: | error | Dataset Blurb: | error | Dataset Info: | [1] "Trimming barcodes" | pass QC: 85430 | removed_have_N: 0 | removed_low_qual: 0 | [1] "Building genome index" | ========== _____ _ _ ____ _____ ______ _____ | ===== / ____| | | | _ \| __ \| ____| /\ | __ \ | Peek: | *Peek unavilable.* | Dataset Job Standard Output: | [1] "Trimming barcodes" | pass QC: 85430 | removed_have_N: 0 | removed_low_qual: 0 | [1] "Building genome index" | ========== _____ _ _ ____ _____ ______ _____ | ===== / ____| | | | _ \| __ \| ____| /\ | __ \ | ===== | (___ | | | | |_) | |__) | |__ / \ | | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ | Rsubread 1.28.1 | //=========================== indexBuilder setting ===========================\\ | || || | || Index name : ./mm10_MT19_fa_gz.fasta_index || | || Index space : base-space || | || Memory : 8000 Mbytes || | || Repeat threshold : 100 repeats || | || Distance to next subread : 3 || | || || | || Input files : 1 file in total || | || o mm10_MT19_fa_gz || | || || | \\===================== http://subread.sourceforge.net/ ======================// | //================================= Running ==================================\\ | || || | || Check the integrity of provided reference sequences ... || | || No format issues were found || | || Scan uninformative subreads in reference sequences ... || | || 8%, 0 mins elapsed, rate=1162.8k bps/s, total=7m || | || 16%, 0 mins elapsed, rate=2219.9k bps/s, total=7m || | || 24%, 0 mins elapsed, rate=3190.8k bps/s, total=7m || | || 33%, 0 mins elapsed, rate=4084.0k bps/s, total=7m || | || 41%, 0 mins elapsed, rate=4908.3k bps/s, total=7m || | || 49%, 0 mins elapsed, rate=5477.1k bps/s, total=7m || | || 58%, 0 mins elapsed, rate=5902.7k bps/s, total=7m || | || 66%, 0 mins elapsed, rate=6310.1k bps/s, total=7m || | || 74%, 0 mins elapsed, rate=6668.1k bps/s, total=7m || | || 83%, 0 mins elapsed, rate=6985.1k bps/s, total=7m || | || 91%, 0 mins elapsed, rate=7243.3k bps/s, total=7m || | || 14 uninformative subreads were found. || | || These subreads were excluded from index building. || | || Build the index... || | || 8%, 0 mins elapsed, rate=14293.9k bps/s, total=7m || | || 16%, 0 mins elapsed, rate=13953.6k bps/s, total=7m || | || 24%, 0 mins elapsed, rate=14178.7k bps/s, total=7m || | || 33%, 0 mins elapsed, rate=14207.3k bps/s, total=7m || | || 41%, 0 mins elapsed, rate=14155.8k bps/s, total=7m || | || 49%, 0 mins elapsed, rate=6697.7k bps/s, total=7m || | || 58%, 0 mins elapsed, rate=4014.1k bps/s, total=7m || | || 66%, 0 mins elapsed, rate=3414.7k bps/s, total=7m || | || 74%, 0 mins elapsed, rate=3239.8k bps/s, total=7m || | || 83%, 0 mins elapsed, rate=3167.8k bps/s, total=7m || | || 91%, 0 mins elapsed, rate=3199.3k bps/s, total=7m || | || Save current index block... || | || [ 0.0% finished ] || | || [ 10.0% finished ] || | || [ 20.0% finished ] || | || [ 30.0% finished ] || | || [ 40.0% finished ] || | || [ 50.0% finished ] || | || [ 60.0% finished ] || | || [ 70.0% finished ] || | || [ 80.0% finished ] || | || [ 90.0% finished ] || | || [ 100.0% finished ] || | || || | || Total running time: 0.1 minutes. || | || Index ./mm10_MT19_fa_gz.fasta_index was successfully built! || | || || | \\===================== http://subread.sourceforge.net/ ======================// | [1] "Aligning reads to genome" | ========== _____ _ _ ____ _____ ______ _____ | ===== / ____| | | | _ \| __ \| ____| /\ | __ \ | ===== | (___ | | | | |_) | |__) | |__ / \ | | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ | Rsubread 1.28.1 | //========================== subread-align setting ===========================\\ | || || | || Function : Read alignment (RNA-Seq) || | || Input file : ./combined.fastq || | || Output file : ./aligned.bam (BAM) || | || Index name : ./mm10_MT19_fa_gz.fasta_index || | || || | || ------------------------------------ || | || || | || Threads : 1 || | || Phred offset : 33 || | || Min votes : 3 / 10 || | || Maximum allowed mismatches : 3 || | || Maximum allowed indel bases : 5 || | || # of best alignments reported : 1 || | || Unique mapping : no || | || || | \\===================== http://subread.sourceforge.net/ ======================// | //================= Running (30-Jan-2020 09:28:29, pid=230) ==================\\ | || || | || The input file contains base space reads. || | || The range of Phred scores observed in the data is [14,36] || | || Load the 1-th index block... || | || 7% completed, 0.0 mins elapsed, rate=19.5k reads per second || | || 14% completed, 0.0 mins elapsed, rate=19.4k reads per second || | || 21% completed, 0.0 mins elapsed, rate=19.4k reads per second || | || 27% completed, 0.0 mins elapsed, rate=19.4k reads per second || | || 34% completed, 0.0 mins elapsed, rate=19.5k reads per second || | || 41% completed, 0.0 mins elapsed, rate=19.4k reads per second || | || 47% completed, 0.1 mins elapsed, rate=19.1k reads per second || | || 54% completed, 0.1 mins elapsed, rate=18.9k reads per second || | || 61% completed, 0.1 mins elapsed, rate=18.9k reads per second || | || 70% completed, 0.1 mins elapsed, rate=13.2k reads per second || | || 73% completed, 0.1 mins elapsed, rate=13.3k reads per second || | || 76% completed, 0.1 mins elapsed, rate=13.3k reads per second || | || 80% completed, 0.1 mins elapsed, rate=13.4k reads per second || | || 83% completed, 0.1 mins elapsed, rate=13.4k reads per second || | || 86% completed, 0.1 mins elapsed, rate=13.5k reads per second || | || 90% completed, 0.1 mins elapsed, rate=13.5k reads per second || | || 93% completed, 0.1 mins elapsed, rate=13.6k reads per second || | || 96% completed, 0.1 mins elapsed, rate=13.6k reads per second || | || || | || Completed successfully. || | || || | \\============================================================================// | //================================= Summary ==================================\\ | || || | || Processed : 85430 reads || | || Mapped : 84722 reads (99.2%), wherein || | || Uniquely mapped : 81914 || | || Multi-mapping : 2808 || | || || | || Not mapped : 708 || | || || | || Indels : 1366 || | || || | || Running time : 0.1 minutes || | || || | \\===================== http://subread.sourceforge.net/ ======================// | [1] "Detecting barcodes" | [1] "Assigning reads to exons" | add gff3 annotation: mm10_MT19_gff3_gz.gff3 | unique map to exon:51428 | ambiguous map to multiple exon:2090 | map to intron:14503 | not mapped:16701 | unaligned:708 | [1] "De-multiplexing data" | [1] "Counting genes" | [1] "Performing QC" | [1] "organism/gene_id_type not provided. make a guess: mmusculus_gene_ensembl / ensembl_gene_id" | [1] "spikeNames(sce)==NULL, no spike-in information." | [1] "the following QC metrics not find in colData from sce:" | [1] "non_ERCC_percent" | null device | 1 | [1] "Removing outliers" | [1] "Creating report" | | | | 0% | |.. | 2% | inline R code fragments | | |... | 5% | label: unnamed-chunk-1 (with options) | List of 3 | $ warning: logi FALSE | $ echo : logi FALSE | $ message: logi FALSE | | |..... | 7% | inline R code fragments | | |...... | 10% | label: unnamed-chunk-2 (with options) | List of 2 | $ warning: logi FALSE | $ message: logi FALSE | | |........ | 12% | ordinary text without R code | | |......... | 14% | label: unnamed-chunk-3 | | |........... | 17% | ordinary text without R code | | |............ | 19% | label: unnamed-chunk-4 | | |.............. | 21% | ordinary text without R code | | |............... | 24% | label: unnamed-chunk-5 | | |................. | 26% | ordinary text without R code | | |................... | 29% | label: unnamed-chunk-6 | | |.................... | 31% | inline R code fragments | | |...................... | 33% | label: unnamed-chunk-7 | Dataset Job Standard Error: | Warning message: | In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : | OS reports request to set locale to "en_US.UTF-8" cannot be honored | `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. | `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. | `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. | `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. | processing file: report.Rmd | Quitting from lines 147-152 (report.Rmd) | Error: Please install xml2 package | -------------------------------------- | 6 - scPipe on data 4, data 3, and others: Plots (HID - NAME) | Dataset State: | error | Dataset Blurb: | error | Dataset Info: | [1] "Trimming barcodes" | pass QC: 85430 | removed_have_N: 0 | removed_low_qual: 0 | [1] "Building genome index" | ========== _____ _ _ ____ _____ ______ _____ | ===== / ____| | | | _ \| __ \| ____| /\ | __ \ | Peek: | *Peek unavilable.* | Dataset Job Standard Output: | [1] "Trimming barcodes" | pass QC: 85430 | removed_have_N: 0 | removed_low_qual: 0 | [1] "Building genome index" | ========== _____ _ _ ____ _____ ______ _____ | ===== / ____| | | | _ \| __ \| ____| /\ | __ \ | ===== | (___ | | | | |_) | |__) | |__ / \ | | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ | Rsubread 1.28.1 | //=========================== indexBuilder setting ===========================\\ | || || | || Index name : ./mm10_MT19_fa_gz.fasta_index || | || Index space : base-space || | || Memory : 8000 Mbytes || | || Repeat threshold : 100 repeats || | || Distance to next subread : 3 || | || || | || Input files : 1 file in total || | || o mm10_MT19_fa_gz || | || || | \\===================== http://subread.sourceforge.net/ ======================// | //================================= Running ==================================\\ | || || | || Check the integrity of provided reference sequences ... || | || No format issues were found || | || Scan uninformative subreads in reference sequences ... || | || 8%, 0 mins elapsed, rate=1162.8k bps/s, total=7m || | || 16%, 0 mins elapsed, rate=2219.9k bps/s, total=7m || | || 24%, 0 mins elapsed, rate=3190.8k bps/s, total=7m || | || 33%, 0 mins elapsed, rate=4084.0k bps/s, total=7m || | || 41%, 0 mins elapsed, rate=4908.3k bps/s, total=7m || | || 49%, 0 mins elapsed, rate=5477.1k bps/s, total=7m || | || 58%, 0 mins elapsed, rate=5902.7k bps/s, total=7m || | || 66%, 0 mins elapsed, rate=6310.1k bps/s, total=7m || | || 74%, 0 mins elapsed, rate=6668.1k bps/s, total=7m || | || 83%, 0 mins elapsed, rate=6985.1k bps/s, total=7m || | || 91%, 0 mins elapsed, rate=7243.3k bps/s, total=7m || | || 14 uninformative subreads were found. || | || These subreads were excluded from index building. || | || Build the index... || | || 8%, 0 mins elapsed, rate=14293.9k bps/s, total=7m || | || 16%, 0 mins elapsed, rate=13953.6k bps/s, total=7m || | || 24%, 0 mins elapsed, rate=14178.7k bps/s, total=7m || | || 33%, 0 mins elapsed, rate=14207.3k bps/s, total=7m || | || 41%, 0 mins elapsed, rate=14155.8k bps/s, total=7m || | || 49%, 0 mins elapsed, rate=6697.7k bps/s, total=7m || | || 58%, 0 mins elapsed, rate=4014.1k bps/s, total=7m || | || 66%, 0 mins elapsed, rate=3414.7k bps/s, total=7m || | || 74%, 0 mins elapsed, rate=3239.8k bps/s, total=7m || | || 83%, 0 mins elapsed, rate=3167.8k bps/s, total=7m || | || 91%, 0 mins elapsed, rate=3199.3k bps/s, total=7m || | || Save current index block... || | || [ 0.0% finished ] || | || [ 10.0% finished ] || | || [ 20.0% finished ] || | || [ 30.0% finished ] || | || [ 40.0% finished ] || | || [ 50.0% finished ] || | || [ 60.0% finished ] || | || [ 70.0% finished ] || | || [ 80.0% finished ] || | || [ 90.0% finished ] || | || [ 100.0% finished ] || | || || | || Total running time: 0.1 minutes. || | || Index ./mm10_MT19_fa_gz.fasta_index was successfully built! || | || || | \\===================== http://subread.sourceforge.net/ ======================// | [1] "Aligning reads to genome" | ========== _____ _ _ ____ _____ ______ _____ | ===== / ____| | | | _ \| __ \| ____| /\ | __ \ | ===== | (___ | | | | |_) | |__) | |__ / \ | | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ | Rsubread 1.28.1 | //========================== subread-align setting ===========================\\ | || || | || Function : Read alignment (RNA-Seq) || | || Input file : ./combined.fastq || | || Output file : ./aligned.bam (BAM) || | || Index name : ./mm10_MT19_fa_gz.fasta_index || | || || | || ------------------------------------ || | || || | || Threads : 1 || | || Phred offset : 33 || | || Min votes : 3 / 10 || | || Maximum allowed mismatches : 3 || | || Maximum allowed indel bases : 5 || | || # of best alignments reported : 1 || | || Unique mapping : no || | || || | \\===================== http://subread.sourceforge.net/ ======================// | //================= Running (30-Jan-2020 09:28:29, pid=230) ==================\\ | || || | || The input file contains base space reads. || | || The range of Phred scores observed in the data is [14,36] || | || Load the 1-th index block... || | || 7% completed, 0.0 mins elapsed, rate=19.5k reads per second || | || 14% completed, 0.0 mins elapsed, rate=19.4k reads per second || | || 21% completed, 0.0 mins elapsed, rate=19.4k reads per second || | || 27% completed, 0.0 mins elapsed, rate=19.4k reads per second || | || 34% completed, 0.0 mins elapsed, rate=19.5k reads per second || | || 41% completed, 0.0 mins elapsed, rate=19.4k reads per second || | || 47% completed, 0.1 mins elapsed, rate=19.1k reads per second || | || 54% completed, 0.1 mins elapsed, rate=18.9k reads per second || | || 61% completed, 0.1 mins elapsed, rate=18.9k reads per second || | || 70% completed, 0.1 mins elapsed, rate=13.2k reads per second || | || 73% completed, 0.1 mins elapsed, rate=13.3k reads per second || | || 76% completed, 0.1 mins elapsed, rate=13.3k reads per second || | || 80% completed, 0.1 mins elapsed, rate=13.4k reads per second || | || 83% completed, 0.1 mins elapsed, rate=13.4k reads per second || | || 86% completed, 0.1 mins elapsed, rate=13.5k reads per second || | || 90% completed, 0.1 mins elapsed, rate=13.5k reads per second || | || 93% completed, 0.1 mins elapsed, rate=13.6k reads per second || | || 96% completed, 0.1 mins elapsed, rate=13.6k reads per second || | || || | || Completed successfully. || | || || | \\============================================================================// | //================================= Summary ==================================\\ | || || | || Processed : 85430 reads || | || Mapped : 84722 reads (99.2%), wherein || | || Uniquely mapped : 81914 || | || Multi-mapping : 2808 || | || || | || Not mapped : 708 || | || || | || Indels : 1366 || | || || | || Running time : 0.1 minutes || | || || | \\===================== http://subread.sourceforge.net/ ======================// | [1] "Detecting barcodes" | [1] "Assigning reads to exons" | add gff3 annotation: mm10_MT19_gff3_gz.gff3 | unique map to exon:51428 | ambiguous map to multiple exon:2090 | map to intron:14503 | not mapped:16701 | unaligned:708 | [1] "De-multiplexing data" | [1] "Counting genes" | [1] "Performing QC" | [1] "organism/gene_id_type not provided. make a guess: mmusculus_gene_ensembl / ensembl_gene_id" | [1] "spikeNames(sce)==NULL, no spike-in information." | [1] "the following QC metrics not find in colData from sce:" | [1] "non_ERCC_percent" | null device | 1 | [1] "Removing outliers" | [1] "Creating report" | | | | 0% | |.. | 2% | inline R code fragments | | |... | 5% | label: unnamed-chunk-1 (with options) | List of 3 | $ warning: logi FALSE | $ echo : logi FALSE | $ message: logi FALSE | | |..... | 7% | inline R code fragments | | |...... | 10% | label: unnamed-chunk-2 (with options) | List of 2 | $ warning: logi FALSE | $ message: logi FALSE | | |........ | 12% | ordinary text without R code | | |......... | 14% | label: unnamed-chunk-3 | | |........... | 17% | ordinary text without R code | | |............ | 19% | label: unnamed-chunk-4 | | |.............. | 21% | ordinary text without R code | | |............... | 24% | label: unnamed-chunk-5 | | |................. | 26% | ordinary text without R code | | |................... | 29% | label: unnamed-chunk-6 | | |.................... | 31% | inline R code fragments | | |...................... | 33% | label: unnamed-chunk-7 | Dataset Job Standard Error: | Warning message: | In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : | OS reports request to set locale to "en_US.UTF-8" cannot be honored | `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. | `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. | `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. | `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. | processing file: report.Rmd | Quitting from lines 147-152 (report.Rmd) | Error: Please install xml2 package | -------------------------------------- | 7 - scPipe on data 4, data 3, and others: QC metrics matrix (HID - NAME) | Dataset State: | error | Dataset Blurb: | error | Dataset Info: | [1] "Trimming barcodes" | pass QC: 85430 | removed_have_N: 0 | removed_low_qual: 0 | [1] "Building genome index" | ========== _____ _ _ ____ _____ ______ _____ | ===== / ____| | | | _ \| __ \| ____| /\ | __ \ | Peek: | *Peek unavilable.* | Dataset Job Standard Output: | [1] "Trimming barcodes" | pass QC: 85430 | removed_have_N: 0 | removed_low_qual: 0 | [1] "Building genome index" | ========== _____ _ _ ____ _____ ______ _____ | ===== / ____| | | | _ \| __ \| ____| /\ | __ \ | ===== | (___ | | | | |_) | |__) | |__ / \ | | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ | Rsubread 1.28.1 | //=========================== indexBuilder setting ===========================\\ | || || | || Index name : ./mm10_MT19_fa_gz.fasta_index || | || Index space : base-space || | || Memory : 8000 Mbytes || | || Repeat threshold : 100 repeats || | || Distance to next subread : 3 || | || || | || Input files : 1 file in total || | || o mm10_MT19_fa_gz || | || || | \\===================== http://subread.sourceforge.net/ ======================// | //================================= Running ==================================\\ | || || | || Check the integrity of provided reference sequences ... || | || No format issues were found || | || Scan uninformative subreads in reference sequences ... || | || 8%, 0 mins elapsed, rate=1162.8k bps/s, total=7m || | || 16%, 0 mins elapsed, rate=2219.9k bps/s, total=7m || | || 24%, 0 mins elapsed, rate=3190.8k bps/s, total=7m || | || 33%, 0 mins elapsed, rate=4084.0k bps/s, total=7m || | || 41%, 0 mins elapsed, rate=4908.3k bps/s, total=7m || | || 49%, 0 mins elapsed, rate=5477.1k bps/s, total=7m || | || 58%, 0 mins elapsed, rate=5902.7k bps/s, total=7m || | || 66%, 0 mins elapsed, rate=6310.1k bps/s, total=7m || | || 74%, 0 mins elapsed, rate=6668.1k bps/s, total=7m || | || 83%, 0 mins elapsed, rate=6985.1k bps/s, total=7m || | || 91%, 0 mins elapsed, rate=7243.3k bps/s, total=7m || | || 14 uninformative subreads were found. || | || These subreads were excluded from index building. || | || Build the index... || | || 8%, 0 mins elapsed, rate=14293.9k bps/s, total=7m || | || 16%, 0 mins elapsed, rate=13953.6k bps/s, total=7m || | || 24%, 0 mins elapsed, rate=14178.7k bps/s, total=7m || | || 33%, 0 mins elapsed, rate=14207.3k bps/s, total=7m || | || 41%, 0 mins elapsed, rate=14155.8k bps/s, total=7m || | || 49%, 0 mins elapsed, rate=6697.7k bps/s, total=7m || | || 58%, 0 mins elapsed, rate=4014.1k bps/s, total=7m || | || 66%, 0 mins elapsed, rate=3414.7k bps/s, total=7m || | || 74%, 0 mins elapsed, rate=3239.8k bps/s, total=7m || | || 83%, 0 mins elapsed, rate=3167.8k bps/s, total=7m || | || 91%, 0 mins elapsed, rate=3199.3k bps/s, total=7m || | || Save current index block... || | || [ 0.0% finished ] || | || [ 10.0% finished ] || | || [ 20.0% finished ] || | || [ 30.0% finished ] || | || [ 40.0% finished ] || | || [ 50.0% finished ] || | || [ 60.0% finished ] || | || [ 70.0% finished ] || | || [ 80.0% finished ] || | || [ 90.0% finished ] || | || [ 100.0% finished ] || | || || | || Total running time: 0.1 minutes. || | || Index ./mm10_MT19_fa_gz.fasta_index was successfully built! || | || || | \\===================== http://subread.sourceforge.net/ ======================// | [1] "Aligning reads to genome" | ========== _____ _ _ ____ _____ ______ _____ | ===== / ____| | | | _ \| __ \| ____| /\ | __ \ | ===== | (___ | | | | |_) | |__) | |__ / \ | | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ | Rsubread 1.28.1 | //========================== subread-align setting ===========================\\ | || || | || Function : Read alignment (RNA-Seq) || | || Input file : ./combined.fastq || | || Output file : ./aligned.bam (BAM) || | || Index name : ./mm10_MT19_fa_gz.fasta_index || | || || | || ------------------------------------ || | || || | || Threads : 1 || | || Phred offset : 33 || | || Min votes : 3 / 10 || | || Maximum allowed mismatches : 3 || | || Maximum allowed indel bases : 5 || | || # of best alignments reported : 1 || | || Unique mapping : no || | || || | \\===================== http://subread.sourceforge.net/ ======================// | //================= Running (30-Jan-2020 09:28:29, pid=230) ==================\\ | || || | || The input file contains base space reads. || | || The range of Phred scores observed in the data is [14,36] || | || Load the 1-th index block... || | || 7% completed, 0.0 mins elapsed, rate=19.5k reads per second || | || 14% completed, 0.0 mins elapsed, rate=19.4k reads per second || | || 21% completed, 0.0 mins elapsed, rate=19.4k reads per second || | || 27% completed, 0.0 mins elapsed, rate=19.4k reads per second || | || 34% completed, 0.0 mins elapsed, rate=19.5k reads per second || | || 41% completed, 0.0 mins elapsed, rate=19.4k reads per second || | || 47% completed, 0.1 mins elapsed, rate=19.1k reads per second || | || 54% completed, 0.1 mins elapsed, rate=18.9k reads per second || | || 61% completed, 0.1 mins elapsed, rate=18.9k reads per second || | || 70% completed, 0.1 mins elapsed, rate=13.2k reads per second || | || 73% completed, 0.1 mins elapsed, rate=13.3k reads per second || | || 76% completed, 0.1 mins elapsed, rate=13.3k reads per second || | || 80% completed, 0.1 mins elapsed, rate=13.4k reads per second || | || 83% completed, 0.1 mins elapsed, rate=13.4k reads per second || | || 86% completed, 0.1 mins elapsed, rate=13.5k reads per second || | || 90% completed, 0.1 mins elapsed, rate=13.5k reads per second || | || 93% completed, 0.1 mins elapsed, rate=13.6k reads per second || | || 96% completed, 0.1 mins elapsed, rate=13.6k reads per second || | || || | || Completed successfully. || | || || | \\============================================================================// | //================================= Summary ==================================\\ | || || | || Processed : 85430 reads || | || Mapped : 84722 reads (99.2%), wherein || | || Uniquely mapped : 81914 || | || Multi-mapping : 2808 || | || || | || Not mapped : 708 || | || || | || Indels : 1366 || | || || | || Running time : 0.1 minutes || | || || | \\===================== http://subread.sourceforge.net/ ======================// | [1] "Detecting barcodes" | [1] "Assigning reads to exons" | add gff3 annotation: mm10_MT19_gff3_gz.gff3 | unique map to exon:51428 | ambiguous map to multiple exon:2090 | map to intron:14503 | not mapped:16701 | unaligned:708 | [1] "De-multiplexing data" | [1] "Counting genes" | [1] "Performing QC" | [1] "organism/gene_id_type not provided. make a guess: mmusculus_gene_ensembl / ensembl_gene_id" | [1] "spikeNames(sce)==NULL, no spike-in information." | [1] "the following QC metrics not find in colData from sce:" | [1] "non_ERCC_percent" | null device | 1 | [1] "Removing outliers" | [1] "Creating report" | | | | 0% | |.. | 2% | inline R code fragments | | |... | 5% | label: unnamed-chunk-1 (with options) | List of 3 | $ warning: logi FALSE | $ echo : logi FALSE | $ message: logi FALSE | | |..... | 7% | inline R code fragments | | |...... | 10% | label: unnamed-chunk-2 (with options) | List of 2 | $ warning: logi FALSE | $ message: logi FALSE | | |........ | 12% | ordinary text without R code | | |......... | 14% | label: unnamed-chunk-3 | | |........... | 17% | ordinary text without R code | | |............ | 19% | label: unnamed-chunk-4 | | |.............. | 21% | ordinary text without R code | | |............... | 24% | label: unnamed-chunk-5 | | |................. | 26% | ordinary text without R code | | |................... | 29% | label: unnamed-chunk-6 | | |.................... | 31% | inline R code fragments | | |...................... | 33% | label: unnamed-chunk-7 | Dataset Job Standard Error: | Warning message: | In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : | OS reports request to set locale to "en_US.UTF-8" cannot be honored | `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. | `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. | `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. | `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. | processing file: report.Rmd | Quitting from lines 147-152 (report.Rmd) | Error: Please install xml2 package | -------------------------------------- | 8 - scPipe on data 4, data 3, and others: HTML Report (HID - NAME) | Dataset State: | error | Dataset Blurb: | error | Dataset Info: | [1] "Trimming barcodes" | pass QC: 85430 | removed_have_N: 0 | removed_low_qual: 0 | [1] "Building genome index" | ========== _____ _ _ ____ _____ ______ _____ | ===== / ____| | | | _ \| __ \| ____| /\ | __ \ | Peek: | *Peek unavilable.* | Dataset Job Standard Output: | [1] "Trimming barcodes" | pass QC: 85430 | removed_have_N: 0 | removed_low_qual: 0 | [1] "Building genome index" | ========== _____ _ _ ____ _____ ______ _____ | ===== / ____| | | | _ \| __ \| ____| /\ | __ \ | ===== | (___ | | | | |_) | |__) | |__ / \ | | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ | Rsubread 1.28.1 | //=========================== indexBuilder setting ===========================\\ | || || | || Index name : ./mm10_MT19_fa_gz.fasta_index || | || Index space : base-space || | || Memory : 8000 Mbytes || | || Repeat threshold : 100 repeats || | || Distance to next subread : 3 || | || || | || Input files : 1 file in total || | || o mm10_MT19_fa_gz || | || || | \\===================== http://subread.sourceforge.net/ ======================// | //================================= Running ==================================\\ | || || | || Check the integrity of provided reference sequences ... || | || No format issues were found || | || Scan uninformative subreads in reference sequences ... || | || 8%, 0 mins elapsed, rate=1162.8k bps/s, total=7m || | || 16%, 0 mins elapsed, rate=2219.9k bps/s, total=7m || | || 24%, 0 mins elapsed, rate=3190.8k bps/s, total=7m || | || 33%, 0 mins elapsed, rate=4084.0k bps/s, total=7m || | || 41%, 0 mins elapsed, rate=4908.3k bps/s, total=7m || | || 49%, 0 mins elapsed, rate=5477.1k bps/s, total=7m || | || 58%, 0 mins elapsed, rate=5902.7k bps/s, total=7m || | || 66%, 0 mins elapsed, rate=6310.1k bps/s, total=7m || | || 74%, 0 mins elapsed, rate=6668.1k bps/s, total=7m || | || 83%, 0 mins elapsed, rate=6985.1k bps/s, total=7m || | || 91%, 0 mins elapsed, rate=7243.3k bps/s, total=7m || | || 14 uninformative subreads were found. || | || These subreads were excluded from index building. || | || Build the index... || | || 8%, 0 mins elapsed, rate=14293.9k bps/s, total=7m || | || 16%, 0 mins elapsed, rate=13953.6k bps/s, total=7m || | || 24%, 0 mins elapsed, rate=14178.7k bps/s, total=7m || | || 33%, 0 mins elapsed, rate=14207.3k bps/s, total=7m || | || 41%, 0 mins elapsed, rate=14155.8k bps/s, total=7m || | || 49%, 0 mins elapsed, rate=6697.7k bps/s, total=7m || | || 58%, 0 mins elapsed, rate=4014.1k bps/s, total=7m || | || 66%, 0 mins elapsed, rate=3414.7k bps/s, total=7m || | || 74%, 0 mins elapsed, rate=3239.8k bps/s, total=7m || | || 83%, 0 mins elapsed, rate=3167.8k bps/s, total=7m || | || 91%, 0 mins elapsed, rate=3199.3k bps/s, total=7m || | || Save current index block... || | || [ 0.0% finished ] || | || [ 10.0% finished ] || | || [ 20.0% finished ] || | || [ 30.0% finished ] || | || [ 40.0% finished ] || | || [ 50.0% finished ] || | || [ 60.0% finished ] || | || [ 70.0% finished ] || | || [ 80.0% finished ] || | || [ 90.0% finished ] || | || [ 100.0% finished ] || | || || | || Total running time: 0.1 minutes. || | || Index ./mm10_MT19_fa_gz.fasta_index was successfully built! || | || || | \\===================== http://subread.sourceforge.net/ ======================// | [1] "Aligning reads to genome" | ========== _____ _ _ ____ _____ ______ _____ | ===== / ____| | | | _ \| __ \| ____| /\ | __ \ | ===== | (___ | | | | |_) | |__) | |__ / \ | | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ | Rsubread 1.28.1 | //========================== subread-align setting ===========================\\ | || || | || Function : Read alignment (RNA-Seq) || | || Input file : ./combined.fastq || | || Output file : ./aligned.bam (BAM) || | || Index name : ./mm10_MT19_fa_gz.fasta_index || | || || | || ------------------------------------ || | || || | || Threads : 1 || | || Phred offset : 33 || | || Min votes : 3 / 10 || | || Maximum allowed mismatches : 3 || | || Maximum allowed indel bases : 5 || | || # of best alignments reported : 1 || | || Unique mapping : no || | || || | \\===================== http://subread.sourceforge.net/ ======================// | //================= Running (30-Jan-2020 09:28:29, pid=230) ==================\\ | || || | || The input file contains base space reads. || | || The range of Phred scores observed in the data is [14,36] || | || Load the 1-th index block... || | || 7% completed, 0.0 mins elapsed, rate=19.5k reads per second || | || 14% completed, 0.0 mins elapsed, rate=19.4k reads per second || | || 21% completed, 0.0 mins elapsed, rate=19.4k reads per second || | || 27% completed, 0.0 mins elapsed, rate=19.4k reads per second || | || 34% completed, 0.0 mins elapsed, rate=19.5k reads per second || | || 41% completed, 0.0 mins elapsed, rate=19.4k reads per second || | || 47% completed, 0.1 mins elapsed, rate=19.1k reads per second || | || 54% completed, 0.1 mins elapsed, rate=18.9k reads per second || | || 61% completed, 0.1 mins elapsed, rate=18.9k reads per second || | || 70% completed, 0.1 mins elapsed, rate=13.2k reads per second || | || 73% completed, 0.1 mins elapsed, rate=13.3k reads per second || | || 76% completed, 0.1 mins elapsed, rate=13.3k reads per second || | || 80% completed, 0.1 mins elapsed, rate=13.4k reads per second || | || 83% completed, 0.1 mins elapsed, rate=13.4k reads per second || | || 86% completed, 0.1 mins elapsed, rate=13.5k reads per second || | || 90% completed, 0.1 mins elapsed, rate=13.5k reads per second || | || 93% completed, 0.1 mins elapsed, rate=13.6k reads per second || | || 96% completed, 0.1 mins elapsed, rate=13.6k reads per second || | || || | || Completed successfully. || | || || | \\============================================================================// | //================================= Summary ==================================\\ | || || | || Processed : 85430 reads || | || Mapped : 84722 reads (99.2%), wherein || | || Uniquely mapped : 81914 || | || Multi-mapping : 2808 || | || || | || Not mapped : 708 || | || || | || Indels : 1366 || | || || | || Running time : 0.1 minutes || | || || | \\===================== http://subread.sourceforge.net/ ======================// | [1] "Detecting barcodes" | [1] "Assigning reads to exons" | add gff3 annotation: mm10_MT19_gff3_gz.gff3 | unique map to exon:51428 | ambiguous map to multiple exon:2090 | map to intron:14503 | not mapped:16701 | unaligned:708 | [1] "De-multiplexing data" | [1] "Counting genes" | [1] "Performing QC" | [1] "organism/gene_id_type not provided. make a guess: mmusculus_gene_ensembl / ensembl_gene_id" | [1] "spikeNames(sce)==NULL, no spike-in information." | [1] "the following QC metrics not find in colData from sce:" | [1] "non_ERCC_percent" | null device | 1 | [1] "Removing outliers" | [1] "Creating report" | | | | 0% | |.. | 2% | inline R code fragments | | |... | 5% | label: unnamed-chunk-1 (with options) | List of 3 | $ warning: logi FALSE | $ echo : logi FALSE | $ message: logi FALSE | | |..... | 7% | inline R code fragments | | |...... | 10% | label: unnamed-chunk-2 (with options) | List of 2 | $ warning: logi FALSE | $ message: logi FALSE | | |........ | 12% | ordinary text without R code | | |......... | 14% | label: unnamed-chunk-3 | | |........... | 17% | ordinary text without R code | | |............ | 19% | label: unnamed-chunk-4 | | |.............. | 21% | ordinary text without R code | | |............... | 24% | label: unnamed-chunk-5 | | |................. | 26% | ordinary text without R code | | |................... | 29% | label: unnamed-chunk-6 | | |.................... | 31% | inline R code fragments | | |...................... | 33% | label: unnamed-chunk-7 | Dataset Job Standard Error: | Warning message: | In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : | OS reports request to set locale to "en_US.UTF-8" cannot be honored | `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. | `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. | `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. | `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. | processing file: report.Rmd | Quitting from lines 147-152 (report.Rmd) | Error: Please install xml2 package | -------------------------------------- | 9 - scPipe on data 4, data 3, and others: Rscript (HID - NAME) | Dataset State: | error | Dataset Blurb: | error | Dataset Info: | [1] "Trimming barcodes" | pass QC: 85430 | removed_have_N: 0 | removed_low_qual: 0 | [1] "Building genome index" | ========== _____ _ _ ____ _____ ______ _____ | ===== / ____| | | | _ \| __ \| ____| /\ | __ \ | Peek: | *Peek unavilable.* | Dataset Job Standard Output: | [1] "Trimming barcodes" | pass QC: 85430 | removed_have_N: 0 | removed_low_qual: 0 | [1] "Building genome index" | ========== _____ _ _ ____ _____ ______ _____ | ===== / ____| | | | _ \| __ \| ____| /\ | __ \ | ===== | (___ | | | | |_) | |__) | |__ / \ | | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ | Rsubread 1.28.1 | //=========================== indexBuilder setting ===========================\\ | || || | || Index name : ./mm10_MT19_fa_gz.fasta_index || | || Index space : base-space || | || Memory : 8000 Mbytes || | || Repeat threshold : 100 repeats || | || Distance to next subread : 3 || | || || | || Input files : 1 file in total || | || o mm10_MT19_fa_gz || | || || | \\===================== http://subread.sourceforge.net/ ======================// | //================================= Running ==================================\\ | || || | || Check the integrity of provided reference sequences ... || | || No format issues were found || | || Scan uninformative subreads in reference sequences ... || | || 8%, 0 mins elapsed, rate=1162.8k bps/s, total=7m || | || 16%, 0 mins elapsed, rate=2219.9k bps/s, total=7m || | || 24%, 0 mins elapsed, rate=3190.8k bps/s, total=7m || | || 33%, 0 mins elapsed, rate=4084.0k bps/s, total=7m || | || 41%, 0 mins elapsed, rate=4908.3k bps/s, total=7m || | || 49%, 0 mins elapsed, rate=5477.1k bps/s, total=7m || | || 58%, 0 mins elapsed, rate=5902.7k bps/s, total=7m || | || 66%, 0 mins elapsed, rate=6310.1k bps/s, total=7m || | || 74%, 0 mins elapsed, rate=6668.1k bps/s, total=7m || | || 83%, 0 mins elapsed, rate=6985.1k bps/s, total=7m || | || 91%, 0 mins elapsed, rate=7243.3k bps/s, total=7m || | || 14 uninformative subreads were found. || | || These subreads were excluded from index building. || | || Build the index... || | || 8%, 0 mins elapsed, rate=14293.9k bps/s, total=7m || | || 16%, 0 mins elapsed, rate=13953.6k bps/s, total=7m || | || 24%, 0 mins elapsed, rate=14178.7k bps/s, total=7m || | || 33%, 0 mins elapsed, rate=14207.3k bps/s, total=7m || | || 41%, 0 mins elapsed, rate=14155.8k bps/s, total=7m || | || 49%, 0 mins elapsed, rate=6697.7k bps/s, total=7m || | || 58%, 0 mins elapsed, rate=4014.1k bps/s, total=7m || | || 66%, 0 mins elapsed, rate=3414.7k bps/s, total=7m || | || 74%, 0 mins elapsed, rate=3239.8k bps/s, total=7m || | || 83%, 0 mins elapsed, rate=3167.8k bps/s, total=7m || | || 91%, 0 mins elapsed, rate=3199.3k bps/s, total=7m || | || Save current index block... || | || [ 0.0% finished ] || | || [ 10.0% finished ] || | || [ 20.0% finished ] || | || [ 30.0% finished ] || | || [ 40.0% finished ] || | || [ 50.0% finished ] || | || [ 60.0% finished ] || | || [ 70.0% finished ] || | || [ 80.0% finished ] || | || [ 90.0% finished ] || | || [ 100.0% finished ] || | || || | || Total running time: 0.1 minutes. || | || Index ./mm10_MT19_fa_gz.fasta_index was successfully built! || | || || | \\===================== http://subread.sourceforge.net/ ======================// | [1] "Aligning reads to genome" | ========== _____ _ _ ____ _____ ______ _____ | ===== / ____| | | | _ \| __ \| ____| /\ | __ \ | ===== | (___ | | | | |_) | |__) | |__ / \ | | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ | Rsubread 1.28.1 | //========================== subread-align setting ===========================\\ | || || | || Function : Read alignment (RNA-Seq) || | || Input file : ./combined.fastq || | || Output file : ./aligned.bam (BAM) || | || Index name : ./mm10_MT19_fa_gz.fasta_index || | || || | || ------------------------------------ || | || || | || Threads : 1 || | || Phred offset : 33 || | || Min votes : 3 / 10 || | || Maximum allowed mismatches : 3 || | || Maximum allowed indel bases : 5 || | || # of best alignments reported : 1 || | || Unique mapping : no || | || || | \\===================== http://subread.sourceforge.net/ ======================// | //================= Running (30-Jan-2020 09:28:29, pid=230) ==================\\ | || || | || The input file contains base space reads. || | || The range of Phred scores observed in the data is [14,36] || | || Load the 1-th index block... || | || 7% completed, 0.0 mins elapsed, rate=19.5k reads per second || | || 14% completed, 0.0 mins elapsed, rate=19.4k reads per second || | || 21% completed, 0.0 mins elapsed, rate=19.4k reads per second || | || 27% completed, 0.0 mins elapsed, rate=19.4k reads per second || | || 34% completed, 0.0 mins elapsed, rate=19.5k reads per second || | || 41% completed, 0.0 mins elapsed, rate=19.4k reads per second || | || 47% completed, 0.1 mins elapsed, rate=19.1k reads per second || | || 54% completed, 0.1 mins elapsed, rate=18.9k reads per second || | || 61% completed, 0.1 mins elapsed, rate=18.9k reads per second || | || 70% completed, 0.1 mins elapsed, rate=13.2k reads per second || | || 73% completed, 0.1 mins elapsed, rate=13.3k reads per second || | || 76% completed, 0.1 mins elapsed, rate=13.3k reads per second || | || 80% completed, 0.1 mins elapsed, rate=13.4k reads per second || | || 83% completed, 0.1 mins elapsed, rate=13.4k reads per second || | || 86% completed, 0.1 mins elapsed, rate=13.5k reads per second || | || 90% completed, 0.1 mins elapsed, rate=13.5k reads per second || | || 93% completed, 0.1 mins elapsed, rate=13.6k reads per second || | || 96% completed, 0.1 mins elapsed, rate=13.6k reads per second || | || || | || Completed successfully. || | || || | \\============================================================================// | //================================= Summary ==================================\\ | || || | || Processed : 85430 reads || | || Mapped : 84722 reads (99.2%), wherein || | || Uniquely mapped : 81914 || | || Multi-mapping : 2808 || | || || | || Not mapped : 708 || | || || | || Indels : 1366 || | || || | || Running time : 0.1 minutes || | || || | \\===================== http://subread.sourceforge.net/ ======================// | [1] "Detecting barcodes" | [1] "Assigning reads to exons" | add gff3 annotation: mm10_MT19_gff3_gz.gff3 | unique map to exon:51428 | ambiguous map to multiple exon:2090 | map to intron:14503 | not mapped:16701 | unaligned:708 | [1] "De-multiplexing data" | [1] "Counting genes" | [1] "Performing QC" | [1] "organism/gene_id_type not provided. make a guess: mmusculus_gene_ensembl / ensembl_gene_id" | [1] "spikeNames(sce)==NULL, no spike-in information." | [1] "the following QC metrics not find in colData from sce:" | [1] "non_ERCC_percent" | null device | 1 | [1] "Removing outliers" | [1] "Creating report" | | | | 0% | |.. | 2% | inline R code fragments | | |... | 5% | label: unnamed-chunk-1 (with options) | List of 3 | $ warning: logi FALSE | $ echo : logi FALSE | $ message: logi FALSE | | |..... | 7% | inline R code fragments | | |...... | 10% | label: unnamed-chunk-2 (with options) | List of 2 | $ warning: logi FALSE | $ message: logi FALSE | | |........ | 12% | ordinary text without R code | | |......... | 14% | label: unnamed-chunk-3 | | |........... | 17% | ordinary text without R code | | |............ | 19% | label: unnamed-chunk-4 | | |.............. | 21% | ordinary text without R code | | |............... | 24% | label: unnamed-chunk-5 | | |................. | 26% | ordinary text without R code | | |................... | 29% | label: unnamed-chunk-6 | | |.................... | 31% | inline R code fragments | | |...................... | 33% | label: unnamed-chunk-7 | Dataset Job Standard Error: | Warning message: | In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : | OS reports request to set locale to "en_US.UTF-8" cannot be honored | `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. | `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. | `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. | `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. | processing file: report.Rmd | Quitting from lines 147-152 (report.Rmd) | Error: Please install xml2 package | -------------------------------------- | 10 - scPipe on data 4, data 3, and others: RData file (HID - NAME) | Dataset State: | error | Dataset Blurb: | error | Dataset Info: | [1] "Trimming barcodes" | pass QC: 85430 | removed_have_N: 0 | removed_low_qual: 0 | [1] "Building genome index" | ========== _____ _ _ ____ _____ ______ _____ | ===== / ____| | | | _ \| __ \| ____| /\ | __ \ | Peek: | *Peek unavilable.* | Dataset Job Standard Output: | [1] "Trimming barcodes" | pass QC: 85430 | removed_have_N: 0 | removed_low_qual: 0 | [1] "Building genome index" | ========== _____ _ _ ____ _____ ______ _____ | ===== / ____| | | | _ \| __ \| ____| /\ | __ \ | ===== | (___ | | | | |_) | |__) | |__ / \ | | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ | Rsubread 1.28.1 | //=========================== indexBuilder setting ===========================\\ | || || | || Index name : ./mm10_MT19_fa_gz.fasta_index || | || Index space : base-space || | || Memory : 8000 Mbytes || | || Repeat threshold : 100 repeats || | || Distance to next subread : 3 || | || || | || Input files : 1 file in total || | || o mm10_MT19_fa_gz || | || || | \\===================== http://subread.sourceforge.net/ ======================// | //================================= Running ==================================\\ | || || | || Check the integrity of provided reference sequences ... || | || No format issues were found || | || Scan uninformative subreads in reference sequences ... || | || 8%, 0 mins elapsed, rate=1162.8k bps/s, total=7m || | || 16%, 0 mins elapsed, rate=2219.9k bps/s, total=7m || | || 24%, 0 mins elapsed, rate=3190.8k bps/s, total=7m || | || 33%, 0 mins elapsed, rate=4084.0k bps/s, total=7m || | || 41%, 0 mins elapsed, rate=4908.3k bps/s, total=7m || | || 49%, 0 mins elapsed, rate=5477.1k bps/s, total=7m || | || 58%, 0 mins elapsed, rate=5902.7k bps/s, total=7m || | || 66%, 0 mins elapsed, rate=6310.1k bps/s, total=7m || | || 74%, 0 mins elapsed, rate=6668.1k bps/s, total=7m || | || 83%, 0 mins elapsed, rate=6985.1k bps/s, total=7m || | || 91%, 0 mins elapsed, rate=7243.3k bps/s, total=7m || | || 14 uninformative subreads were found. || | || These subreads were excluded from index building. || | || Build the index... || | || 8%, 0 mins elapsed, rate=14293.9k bps/s, total=7m || | || 16%, 0 mins elapsed, rate=13953.6k bps/s, total=7m || | || 24%, 0 mins elapsed, rate=14178.7k bps/s, total=7m || | || 33%, 0 mins elapsed, rate=14207.3k bps/s, total=7m || | || 41%, 0 mins elapsed, rate=14155.8k bps/s, total=7m || | || 49%, 0 mins elapsed, rate=6697.7k bps/s, total=7m || | || 58%, 0 mins elapsed, rate=4014.1k bps/s, total=7m || | || 66%, 0 mins elapsed, rate=3414.7k bps/s, total=7m || | || 74%, 0 mins elapsed, rate=3239.8k bps/s, total=7m || | || 83%, 0 mins elapsed, rate=3167.8k bps/s, total=7m || | || 91%, 0 mins elapsed, rate=3199.3k bps/s, total=7m || | || Save current index block... || | || [ 0.0% finished ] || | || [ 10.0% finished ] || | || [ 20.0% finished ] || | || [ 30.0% finished ] || | || [ 40.0% finished ] || | || [ 50.0% finished ] || | || [ 60.0% finished ] || | || [ 70.0% finished ] || | || [ 80.0% finished ] || | || [ 90.0% finished ] || | || [ 100.0% finished ] || | || || | || Total running time: 0.1 minutes. || | || Index ./mm10_MT19_fa_gz.fasta_index was successfully built! || | || || | \\===================== http://subread.sourceforge.net/ ======================// | [1] "Aligning reads to genome" | ========== _____ _ _ ____ _____ ______ _____ | ===== / ____| | | | _ \| __ \| ____| /\ | __ \ | ===== | (___ | | | | |_) | |__) | |__ / \ | | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ | Rsubread 1.28.1 | //========================== subread-align setting ===========================\\ | || || | || Function : Read alignment (RNA-Seq) || | || Input file : ./combined.fastq || | || Output file : ./aligned.bam (BAM) || | || Index name : ./mm10_MT19_fa_gz.fasta_index || | || || | || ------------------------------------ || | || || | || Threads : 1 || | || Phred offset : 33 || | || Min votes : 3 / 10 || | || Maximum allowed mismatches : 3 || | || Maximum allowed indel bases : 5 || | || # of best alignments reported : 1 || | || Unique mapping : no || | || || | \\===================== http://subread.sourceforge.net/ ======================// | //================= Running (30-Jan-2020 09:28:29, pid=230) ==================\\ | || || | || The input file contains base space reads. || | || The range of Phred scores observed in the data is [14,36] || | || Load the 1-th index block... || | || 7% completed, 0.0 mins elapsed, rate=19.5k reads per second || | || 14% completed, 0.0 mins elapsed, rate=19.4k reads per second || | || 21% completed, 0.0 mins elapsed, rate=19.4k reads per second || | || 27% completed, 0.0 mins elapsed, rate=19.4k reads per second || | || 34% completed, 0.0 mins elapsed, rate=19.5k reads per second || | || 41% completed, 0.0 mins elapsed, rate=19.4k reads per second || | || 47% completed, 0.1 mins elapsed, rate=19.1k reads per second || | || 54% completed, 0.1 mins elapsed, rate=18.9k reads per second || | || 61% completed, 0.1 mins elapsed, rate=18.9k reads per second || | || 70% completed, 0.1 mins elapsed, rate=13.2k reads per second || | || 73% completed, 0.1 mins elapsed, rate=13.3k reads per second || | || 76% completed, 0.1 mins elapsed, rate=13.3k reads per second || | || 80% completed, 0.1 mins elapsed, rate=13.4k reads per second || | || 83% completed, 0.1 mins elapsed, rate=13.4k reads per second || | || 86% completed, 0.1 mins elapsed, rate=13.5k reads per second || | || 90% completed, 0.1 mins elapsed, rate=13.5k reads per second || | || 93% completed, 0.1 mins elapsed, rate=13.6k reads per second || | || 96% completed, 0.1 mins elapsed, rate=13.6k reads per second || | || || | || Completed successfully. || | || || | \\============================================================================// | //================================= Summary ==================================\\ | || || | || Processed : 85430 reads || | || Mapped : 84722 reads (99.2%), wherein || | || Uniquely mapped : 81914 || | || Multi-mapping : 2808 || | || || | || Not mapped : 708 || | || || | || Indels : 1366 || | || || | || Running time : 0.1 minutes || | || || | \\===================== http://subread.sourceforge.net/ ======================// | [1] "Detecting barcodes" | [1] "Assigning reads to exons" | add gff3 annotation: mm10_MT19_gff3_gz.gff3 | unique map to exon:51428 | ambiguous map to multiple exon:2090 | map to intron:14503 | not mapped:16701 | unaligned:708 | [1] "De-multiplexing data" | [1] "Counting genes" | [1] "Performing QC" | [1] "organism/gene_id_type not provided. make a guess: mmusculus_gene_ensembl / ensembl_gene_id" | [1] "spikeNames(sce)==NULL, no spike-in information." | [1] "the following QC metrics not find in colData from sce:" | [1] "non_ERCC_percent" | null device | 1 | [1] "Removing outliers" | [1] "Creating report" | | | | 0% | |.. | 2% | inline R code fragments | | |... | 5% | label: unnamed-chunk-1 (with options) | List of 3 | $ warning: logi FALSE | $ echo : logi FALSE | $ message: logi FALSE | | |..... | 7% | inline R code fragments | | |...... | 10% | label: unnamed-chunk-2 (with options) | List of 2 | $ warning: logi FALSE | $ message: logi FALSE | | |........ | 12% | ordinary text without R code | | |......... | 14% | label: unnamed-chunk-3 | | |........... | 17% | ordinary text without R code | | |............ | 19% | label: unnamed-chunk-4 | | |.............. | 21% | ordinary text without R code | | |............... | 24% | label: unnamed-chunk-5 | | |................. | 26% | ordinary text without R code | | |................... | 29% | label: unnamed-chunk-6 | | |.................... | 31% | inline R code fragments | | |...................... | 33% | label: unnamed-chunk-7 | Dataset Job Standard Error: | Warning message: | In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : | OS reports request to set locale to "en_US.UTF-8" cannot be honored | `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. | `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. | `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. | `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. | processing file: report.Rmd | Quitting from lines 147-152 (report.Rmd) | Error: Please install xml2 package | -------------------------------------- | Job 82ea1c58d22fbeef | State: | error | Update Time: | 2020-01-30T09:31:45.123969 | Create Time: | 2020-01-30T09:27:17.766642 | -------------------------------------- | Job 4c469a959b869c08 | State: | ok | Update Time: | 2020-01-30T09:27:11.455972 | Create Time: | 2020-01-30T09:27:04.680425 | -------------------------------------- | Job 8c559fb88d75a36b | State: | ok | Update Time: | 2020-01-30T09:27:02.716234 | Create Time: | 2020-01-30T09:26:58.092806 | -------------------------------------- | Job aa6cc630da5109fb | State: | ok | Update Time: | 2020-01-30T09:26:55.692257 | Create Time: | 2020-01-30T09:26:51.506336 | -------------------------------------- | Job 37f9ab3378d23774 | State: | ok | Update Time: | 2020-01-30T09:26:49.432773 | Create Time: | 2020-01-30T09:26:44.843867 | -------------------------------------- Problem in history with id 4e27b888e0f89616 - summary of history's datasets and jobs below. -------------------------------------- | 1 - mm10_MT19.fa.gz (HID - NAME) | Dataset State: | ok | Dataset Blurb: | 2 sequences | Dataset Info: | uploaded fasta file | Peek: |

>19

NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

>19

NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

| Dataset Job Standard Output: | *Standard output was empty.* | Dataset Job Standard Error: | *Standard error was empty.* | -------------------------------------- | 2 - CB51_MT19_R1.gz (HID - NAME) | Dataset State: | ok | Dataset Blurb: | 3.8 MB | Dataset Info: | uploaded fastqsanger.gz file | Peek: | @NS500643:237:HTJH5BGX2:1:11101:12862:1126 2:N:0:0 | GCCTACTTTAATTACATTGCTTACAAGATTAAGGAATCTTTATCTTGAAGACCCCATGAAAGGGATCATT | + | AAAAAEEA1.Seqid2.Source3.Type4.Start5.End6.Score7.Strand8.Phase9.Attributes19Ensemblchromosome161431566...ID=chromosome:19;Alias=CM001012.2,NC_000085.6,chr1919NCBIbiological_region30001243000832.+.external_name=BMQ-420I16 (end);logic_name=mouse_bmq_clones19NCBIbiological_region30001243000860.+.external_name=BMQ-420B16 (end);logic_name=mouse_bmq_clones19NCBIbiological_region30040443004571.+.external_name=DN-246O22 (start);logic_name=mouse_dn_clones19NCBIbiological_region30121183012983.+.external_name=CH29-566C15 (end);logic_name=mouse_ch29_clones | Dataset Job Standard Output: | *Standard output was empty.* | Dataset Job Standard Error: | *Standard error was empty.* | -------------------------------------- | 5 - scPipe on data 4, data 3, and others: Count Matrix (HID - NAME) | Dataset State: | error | Dataset Blurb: | error | Dataset Info: | [1] "Trimming barcodes" | pass QC: 85430 | removed_have_N: 0 | removed_low_qual: 0 | [1] "Building genome index" | ========== _____ _ _ ____ _____ ______ _____ | ===== / ____| | | | _ \| __ \| ____| /\ | __ \ | Peek: | *Peek unavilable.* | Dataset Job Standard Output: | [1] "Trimming barcodes" | pass QC: 85430 | removed_have_N: 0 | removed_low_qual: 0 | [1] "Building genome index" | ========== _____ _ _ ____ _____ ______ _____ | ===== / ____| | | | _ \| __ \| ____| /\ | __ \ | ===== | (___ | | | | |_) | |__) | |__ / \ | | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ | Rsubread 1.28.1 | //=========================== indexBuilder setting ===========================\\ | || || | || Index name : ./mm10_MT19_fa_gz.fasta_index || | || Index space : base-space || | || Memory : 8000 Mbytes || | || Repeat threshold : 100 repeats || | || Distance to next subread : 3 || | || || | || Input files : 1 file in total || | || o mm10_MT19_fa_gz || | || || | \\===================== http://subread.sourceforge.net/ ======================// | //================================= Running ==================================\\ | || || | || Check the integrity of provided reference sequences ... || | || No format issues were found || | || Scan uninformative subreads in reference sequences ... || | || 8%, 0 mins elapsed, rate=1162.8k bps/s, total=7m || | || 16%, 0 mins elapsed, rate=2219.9k bps/s, total=7m || | || 24%, 0 mins elapsed, rate=3190.8k bps/s, total=7m || | || 33%, 0 mins elapsed, rate=4084.0k bps/s, total=7m || | || 41%, 0 mins elapsed, rate=4908.3k bps/s, total=7m || | || 49%, 0 mins elapsed, rate=5477.1k bps/s, total=7m || | || 58%, 0 mins elapsed, rate=5902.7k bps/s, total=7m || | || 66%, 0 mins elapsed, rate=6310.1k bps/s, total=7m || | || 74%, 0 mins elapsed, rate=6668.1k bps/s, total=7m || | || 83%, 0 mins elapsed, rate=6985.1k bps/s, total=7m || | || 91%, 0 mins elapsed, rate=7243.3k bps/s, total=7m || | || 14 uninformative subreads were found. || | || These subreads were excluded from index building. || | || Build the index... || | || 8%, 0 mins elapsed, rate=14293.9k bps/s, total=7m || | || 16%, 0 mins elapsed, rate=13953.6k bps/s, total=7m || | || 24%, 0 mins elapsed, rate=14178.7k bps/s, total=7m || | || 33%, 0 mins elapsed, rate=14207.3k bps/s, total=7m || | || 41%, 0 mins elapsed, rate=14155.8k bps/s, total=7m || | || 49%, 0 mins elapsed, rate=6697.7k bps/s, total=7m || | || 58%, 0 mins elapsed, rate=4014.1k bps/s, total=7m || | || 66%, 0 mins elapsed, rate=3414.7k bps/s, total=7m || | || 74%, 0 mins elapsed, rate=3239.8k bps/s, total=7m || | || 83%, 0 mins elapsed, rate=3167.8k bps/s, total=7m || | || 91%, 0 mins elapsed, rate=3199.3k bps/s, total=7m || | || Save current index block... || | || [ 0.0% finished ] || | || [ 10.0% finished ] || | || [ 20.0% finished ] || | || [ 30.0% finished ] || | || [ 40.0% finished ] || | || [ 50.0% finished ] || | || [ 60.0% finished ] || | || [ 70.0% finished ] || | || [ 80.0% finished ] || | || [ 90.0% finished ] || | || [ 100.0% finished ] || | || || | || Total running time: 0.1 minutes. || | || Index ./mm10_MT19_fa_gz.fasta_index was successfully built! || | || || | \\===================== http://subread.sourceforge.net/ ======================// | [1] "Aligning reads to genome" | ========== _____ _ _ ____ _____ ______ _____ | ===== / ____| | | | _ \| __ \| ____| /\ | __ \ | ===== | (___ | | | | |_) | |__) | |__ / \ | | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ | Rsubread 1.28.1 | //========================== subread-align setting ===========================\\ | || || | || Function : Read alignment (RNA-Seq) || | || Input file : ./combined.fastq || | || Output file : ./aligned.bam (BAM) || | || Index name : ./mm10_MT19_fa_gz.fasta_index || | || || | || ------------------------------------ || | || || | || Threads : 1 || | || Phred offset : 33 || | || Min votes : 3 / 10 || | || Maximum allowed mismatches : 3 || | || Maximum allowed indel bases : 5 || | || # of best alignments reported : 1 || | || Unique mapping : no || | || || | \\===================== http://subread.sourceforge.net/ ======================// | //================= Running (30-Jan-2020 09:28:29, pid=230) ==================\\ | || || | || The input file contains base space reads. || | || The range of Phred scores observed in the data is [14,36] || | || Load the 1-th index block... || | || 7% completed, 0.0 mins elapsed, rate=19.5k reads per second || | || 14% completed, 0.0 mins elapsed, rate=19.4k reads per second || | || 21% completed, 0.0 mins elapsed, rate=19.4k reads per second || | || 27% completed, 0.0 mins elapsed, rate=19.4k reads per second || | || 34% completed, 0.0 mins elapsed, rate=19.5k reads per second || | || 41% completed, 0.0 mins elapsed, rate=19.4k reads per second || | || 47% completed, 0.1 mins elapsed, rate=19.1k reads per second || | || 54% completed, 0.1 mins elapsed, rate=18.9k reads per second || | || 61% completed, 0.1 mins elapsed, rate=18.9k reads per second || | || 70% completed, 0.1 mins elapsed, rate=13.2k reads per second || | || 73% completed, 0.1 mins elapsed, rate=13.3k reads per second || | || 76% completed, 0.1 mins elapsed, rate=13.3k reads per second || | || 80% completed, 0.1 mins elapsed, rate=13.4k reads per second || | || 83% completed, 0.1 mins elapsed, rate=13.4k reads per second || | || 86% completed, 0.1 mins elapsed, rate=13.5k reads per second || | || 90% completed, 0.1 mins elapsed, rate=13.5k reads per second || | || 93% completed, 0.1 mins elapsed, rate=13.6k reads per second || | || 96% completed, 0.1 mins elapsed, rate=13.6k reads per second || | || || | || Completed successfully. || | || || | \\============================================================================// | //================================= Summary ==================================\\ | || || | || Processed : 85430 reads || | || Mapped : 84722 reads (99.2%), wherein || | || Uniquely mapped : 81914 || | || Multi-mapping : 2808 || | || || | || Not mapped : 708 || | || || | || Indels : 1366 || | || || | || Running time : 0.1 minutes || | || || | \\===================== http://subread.sourceforge.net/ ======================// | [1] "Detecting barcodes" | [1] "Assigning reads to exons" | add gff3 annotation: mm10_MT19_gff3_gz.gff3 | unique map to exon:51428 | ambiguous map to multiple exon:2090 | map to intron:14503 | not mapped:16701 | unaligned:708 | [1] "De-multiplexing data" | [1] "Counting genes" | [1] "Performing QC" | [1] "organism/gene_id_type not provided. make a guess: mmusculus_gene_ensembl / ensembl_gene_id" | [1] "spikeNames(sce)==NULL, no spike-in information." | [1] "the following QC metrics not find in colData from sce:" | [1] "non_ERCC_percent" | null device | 1 | [1] "Removing outliers" | [1] "Creating report" | | | | 0% | |.. | 2% | inline R code fragments | | |... | 5% | label: unnamed-chunk-1 (with options) | List of 3 | $ warning: logi FALSE | $ echo : logi FALSE | $ message: logi FALSE | | |..... | 7% | inline R code fragments | | |...... | 10% | label: unnamed-chunk-2 (with options) | List of 2 | $ warning: logi FALSE | $ message: logi FALSE | | |........ | 12% | ordinary text without R code | | |......... | 14% | label: unnamed-chunk-3 | | |........... | 17% | ordinary text without R code | | |............ | 19% | label: unnamed-chunk-4 | | |.............. | 21% | ordinary text without R code | | |............... | 24% | label: unnamed-chunk-5 | | |................. | 26% | ordinary text without R code | | |................... | 29% | label: unnamed-chunk-6 | | |.................... | 31% | inline R code fragments | | |...................... | 33% | label: unnamed-chunk-7 | Dataset Job Standard Error: | Warning message: | In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : | OS reports request to set locale to "en_US.UTF-8" cannot be honored | `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. | `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. | `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. | `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. | processing file: report.Rmd | Quitting from lines 147-152 (report.Rmd) | Error: Please install xml2 package | -------------------------------------- | 6 - scPipe on data 4, data 3, and others: Plots (HID - NAME) | Dataset State: | error | Dataset Blurb: | error | Dataset Info: | [1] "Trimming barcodes" | pass QC: 85430 | removed_have_N: 0 | removed_low_qual: 0 | [1] "Building genome index" | ========== _____ _ _ ____ _____ ______ _____ | ===== / ____| | | | _ \| __ \| ____| /\ | __ \ | Peek: | *Peek unavilable.* | Dataset Job Standard Output: | [1] "Trimming barcodes" | pass QC: 85430 | removed_have_N: 0 | removed_low_qual: 0 | [1] "Building genome index" | ========== _____ _ _ ____ _____ ______ _____ | ===== / ____| | | | _ \| __ \| ____| /\ | __ \ | ===== | (___ | | | | |_) | |__) | |__ / \ | | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ | Rsubread 1.28.1 | //=========================== indexBuilder setting ===========================\\ | || || | || Index name : ./mm10_MT19_fa_gz.fasta_index || | || Index space : base-space || | || Memory : 8000 Mbytes || | || Repeat threshold : 100 repeats || | || Distance to next subread : 3 || | || || | || Input files : 1 file in total || | || o mm10_MT19_fa_gz || | || || | \\===================== http://subread.sourceforge.net/ ======================// | //================================= Running ==================================\\ | || || | || Check the integrity of provided reference sequences ... || | || No format issues were found || | || Scan uninformative subreads in reference sequences ... || | || 8%, 0 mins elapsed, rate=1162.8k bps/s, total=7m || | || 16%, 0 mins elapsed, rate=2219.9k bps/s, total=7m || | || 24%, 0 mins elapsed, rate=3190.8k bps/s, total=7m || | || 33%, 0 mins elapsed, rate=4084.0k bps/s, total=7m || | || 41%, 0 mins elapsed, rate=4908.3k bps/s, total=7m || | || 49%, 0 mins elapsed, rate=5477.1k bps/s, total=7m || | || 58%, 0 mins elapsed, rate=5902.7k bps/s, total=7m || | || 66%, 0 mins elapsed, rate=6310.1k bps/s, total=7m || | || 74%, 0 mins elapsed, rate=6668.1k bps/s, total=7m || | || 83%, 0 mins elapsed, rate=6985.1k bps/s, total=7m || | || 91%, 0 mins elapsed, rate=7243.3k bps/s, total=7m || | || 14 uninformative subreads were found. || | || These subreads were excluded from index building. || | || Build the index... || | || 8%, 0 mins elapsed, rate=14293.9k bps/s, total=7m || | || 16%, 0 mins elapsed, rate=13953.6k bps/s, total=7m || | || 24%, 0 mins elapsed, rate=14178.7k bps/s, total=7m || | || 33%, 0 mins elapsed, rate=14207.3k bps/s, total=7m || | || 41%, 0 mins elapsed, rate=14155.8k bps/s, total=7m || | || 49%, 0 mins elapsed, rate=6697.7k bps/s, total=7m || | || 58%, 0 mins elapsed, rate=4014.1k bps/s, total=7m || | || 66%, 0 mins elapsed, rate=3414.7k bps/s, total=7m || | || 74%, 0 mins elapsed, rate=3239.8k bps/s, total=7m || | || 83%, 0 mins elapsed, rate=3167.8k bps/s, total=7m || | || 91%, 0 mins elapsed, rate=3199.3k bps/s, total=7m || | || Save current index block... || | || [ 0.0% finished ] || | || [ 10.0% finished ] || | || [ 20.0% finished ] || | || [ 30.0% finished ] || | || [ 40.0% finished ] || | || [ 50.0% finished ] || | || [ 60.0% finished ] || | || [ 70.0% finished ] || | || [ 80.0% finished ] || | || [ 90.0% finished ] || | || [ 100.0% finished ] || | || || | || Total running time: 0.1 minutes. || | || Index ./mm10_MT19_fa_gz.fasta_index was successfully built! || | || || | \\===================== http://subread.sourceforge.net/ ======================// | [1] "Aligning reads to genome" | ========== _____ _ _ ____ _____ ______ _____ | ===== / ____| | | | _ \| __ \| ____| /\ | __ \ | ===== | (___ | | | | |_) | |__) | |__ / \ | | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ | Rsubread 1.28.1 | //========================== subread-align setting ===========================\\ | || || | || Function : Read alignment (RNA-Seq) || | || Input file : ./combined.fastq || | || Output file : ./aligned.bam (BAM) || | || Index name : ./mm10_MT19_fa_gz.fasta_index || | || || | || ------------------------------------ || | || || | || Threads : 1 || | || Phred offset : 33 || | || Min votes : 3 / 10 || | || Maximum allowed mismatches : 3 || | || Maximum allowed indel bases : 5 || | || # of best alignments reported : 1 || | || Unique mapping : no || | || || | \\===================== http://subread.sourceforge.net/ ======================// | //================= Running (30-Jan-2020 09:28:29, pid=230) ==================\\ | || || | || The input file contains base space reads. || | || The range of Phred scores observed in the data is [14,36] || | || Load the 1-th index block... || | || 7% completed, 0.0 mins elapsed, rate=19.5k reads per second || | || 14% completed, 0.0 mins elapsed, rate=19.4k reads per second || | || 21% completed, 0.0 mins elapsed, rate=19.4k reads per second || | || 27% completed, 0.0 mins elapsed, rate=19.4k reads per second || | || 34% completed, 0.0 mins elapsed, rate=19.5k reads per second || | || 41% completed, 0.0 mins elapsed, rate=19.4k reads per second || | || 47% completed, 0.1 mins elapsed, rate=19.1k reads per second || | || 54% completed, 0.1 mins elapsed, rate=18.9k reads per second || | || 61% completed, 0.1 mins elapsed, rate=18.9k reads per second || | || 70% completed, 0.1 mins elapsed, rate=13.2k reads per second || | || 73% completed, 0.1 mins elapsed, rate=13.3k reads per second || | || 76% completed, 0.1 mins elapsed, rate=13.3k reads per second || | || 80% completed, 0.1 mins elapsed, rate=13.4k reads per second || | || 83% completed, 0.1 mins elapsed, rate=13.4k reads per second || | || 86% completed, 0.1 mins elapsed, rate=13.5k reads per second || | || 90% completed, 0.1 mins elapsed, rate=13.5k reads per second || | || 93% completed, 0.1 mins elapsed, rate=13.6k reads per second || | || 96% completed, 0.1 mins elapsed, rate=13.6k reads per second || | || || | || Completed successfully. || | || || | \\============================================================================// | //================================= Summary ==================================\\ | || || | || Processed : 85430 reads || | || Mapped : 84722 reads (99.2%), wherein || | || Uniquely mapped : 81914 || | || Multi-mapping : 2808 || | || || | || Not mapped : 708 || | || || | || Indels : 1366 || | || || | || Running time : 0.1 minutes || | || || | \\===================== http://subread.sourceforge.net/ ======================// | [1] "Detecting barcodes" | [1] "Assigning reads to exons" | add gff3 annotation: mm10_MT19_gff3_gz.gff3 | unique map to exon:51428 | ambiguous map to multiple exon:2090 | map to intron:14503 | not mapped:16701 | unaligned:708 | [1] "De-multiplexing data" | [1] "Counting genes" | [1] "Performing QC" | [1] "organism/gene_id_type not provided. make a guess: mmusculus_gene_ensembl / ensembl_gene_id" | [1] "spikeNames(sce)==NULL, no spike-in information." | [1] "the following QC metrics not find in colData from sce:" | [1] "non_ERCC_percent" | null device | 1 | [1] "Removing outliers" | [1] "Creating report" | | | | 0% | |.. | 2% | inline R code fragments | | |... | 5% | label: unnamed-chunk-1 (with options) | List of 3 | $ warning: logi FALSE | $ echo : logi FALSE | $ message: logi FALSE | | |..... | 7% | inline R code fragments | | |...... | 10% | label: unnamed-chunk-2 (with options) | List of 2 | $ warning: logi FALSE | $ message: logi FALSE | | |........ | 12% | ordinary text without R code | | |......... | 14% | label: unnamed-chunk-3 | | |........... | 17% | ordinary text without R code | | |............ | 19% | label: unnamed-chunk-4 | | |.............. | 21% | ordinary text without R code | | |............... | 24% | label: unnamed-chunk-5 | | |................. | 26% | ordinary text without R code | | |................... | 29% | label: unnamed-chunk-6 | | |.................... | 31% | inline R code fragments | | |...................... | 33% | label: unnamed-chunk-7 | Dataset Job Standard Error: | Warning message: | In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : | OS reports request to set locale to "en_US.UTF-8" cannot be honored | `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. | `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. | `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. | `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. | processing file: report.Rmd | Quitting from lines 147-152 (report.Rmd) | Error: Please install xml2 package | -------------------------------------- | 7 - scPipe on data 4, data 3, and others: QC metrics matrix (HID - NAME) | Dataset State: | error | Dataset Blurb: | error | Dataset Info: | [1] "Trimming barcodes" | pass QC: 85430 | removed_have_N: 0 | removed_low_qual: 0 | [1] "Building genome index" | ========== _____ _ _ ____ _____ ______ _____ | ===== / ____| | | | _ \| __ \| ____| /\ | __ \ | Peek: | *Peek unavilable.* | Dataset Job Standard Output: | [1] "Trimming barcodes" | pass QC: 85430 | removed_have_N: 0 | removed_low_qual: 0 | [1] "Building genome index" | ========== _____ _ _ ____ _____ ______ _____ | ===== / ____| | | | _ \| __ \| ____| /\ | __ \ | ===== | (___ | | | | |_) | |__) | |__ / \ | | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ | Rsubread 1.28.1 | //=========================== indexBuilder setting ===========================\\ | || || | || Index name : ./mm10_MT19_fa_gz.fasta_index || | || Index space : base-space || | || Memory : 8000 Mbytes || | || Repeat threshold : 100 repeats || | || Distance to next subread : 3 || | || || | || Input files : 1 file in total || | || o mm10_MT19_fa_gz || | || || | \\===================== http://subread.sourceforge.net/ ======================// | //================================= Running ==================================\\ | || || | || Check the integrity of provided reference sequences ... || | || No format issues were found || | || Scan uninformative subreads in reference sequences ... || | || 8%, 0 mins elapsed, rate=1162.8k bps/s, total=7m || | || 16%, 0 mins elapsed, rate=2219.9k bps/s, total=7m || | || 24%, 0 mins elapsed, rate=3190.8k bps/s, total=7m || | || 33%, 0 mins elapsed, rate=4084.0k bps/s, total=7m || | || 41%, 0 mins elapsed, rate=4908.3k bps/s, total=7m || | || 49%, 0 mins elapsed, rate=5477.1k bps/s, total=7m || | || 58%, 0 mins elapsed, rate=5902.7k bps/s, total=7m || | || 66%, 0 mins elapsed, rate=6310.1k bps/s, total=7m || | || 74%, 0 mins elapsed, rate=6668.1k bps/s, total=7m || | || 83%, 0 mins elapsed, rate=6985.1k bps/s, total=7m || | || 91%, 0 mins elapsed, rate=7243.3k bps/s, total=7m || | || 14 uninformative subreads were found. || | || These subreads were excluded from index building. || | || Build the index... || | || 8%, 0 mins elapsed, rate=14293.9k bps/s, total=7m || | || 16%, 0 mins elapsed, rate=13953.6k bps/s, total=7m || | || 24%, 0 mins elapsed, rate=14178.7k bps/s, total=7m || | || 33%, 0 mins elapsed, rate=14207.3k bps/s, total=7m || | || 41%, 0 mins elapsed, rate=14155.8k bps/s, total=7m || | || 49%, 0 mins elapsed, rate=6697.7k bps/s, total=7m || | || 58%, 0 mins elapsed, rate=4014.1k bps/s, total=7m || | || 66%, 0 mins elapsed, rate=3414.7k bps/s, total=7m || | || 74%, 0 mins elapsed, rate=3239.8k bps/s, total=7m || | || 83%, 0 mins elapsed, rate=3167.8k bps/s, total=7m || | || 91%, 0 mins elapsed, rate=3199.3k bps/s, total=7m || | || Save current index block... || | || [ 0.0% finished ] || | || [ 10.0% finished ] || | || [ 20.0% finished ] || | || [ 30.0% finished ] || | || [ 40.0% finished ] || | || [ 50.0% finished ] || | || [ 60.0% finished ] || | || [ 70.0% finished ] || | || [ 80.0% finished ] || | || [ 90.0% finished ] || | || [ 100.0% finished ] || | || || | || Total running time: 0.1 minutes. || | || Index ./mm10_MT19_fa_gz.fasta_index was successfully built! || | || || | \\===================== http://subread.sourceforge.net/ ======================// | [1] "Aligning reads to genome" | ========== _____ _ _ ____ _____ ______ _____ | ===== / ____| | | | _ \| __ \| ____| /\ | __ \ | ===== | (___ | | | | |_) | |__) | |__ / \ | | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ | Rsubread 1.28.1 | //========================== subread-align setting ===========================\\ | || || | || Function : Read alignment (RNA-Seq) || | || Input file : ./combined.fastq || | || Output file : ./aligned.bam (BAM) || | || Index name : ./mm10_MT19_fa_gz.fasta_index || | || || | || ------------------------------------ || | || || | || Threads : 1 || | || Phred offset : 33 || | || Min votes : 3 / 10 || | || Maximum allowed mismatches : 3 || | || Maximum allowed indel bases : 5 || | || # of best alignments reported : 1 || | || Unique mapping : no || | || || | \\===================== http://subread.sourceforge.net/ ======================// | //================= Running (30-Jan-2020 09:28:29, pid=230) ==================\\ | || || | || The input file contains base space reads. || | || The range of Phred scores observed in the data is [14,36] || | || Load the 1-th index block... || | || 7% completed, 0.0 mins elapsed, rate=19.5k reads per second || | || 14% completed, 0.0 mins elapsed, rate=19.4k reads per second || | || 21% completed, 0.0 mins elapsed, rate=19.4k reads per second || | || 27% completed, 0.0 mins elapsed, rate=19.4k reads per second || | || 34% completed, 0.0 mins elapsed, rate=19.5k reads per second || | || 41% completed, 0.0 mins elapsed, rate=19.4k reads per second || | || 47% completed, 0.1 mins elapsed, rate=19.1k reads per second || | || 54% completed, 0.1 mins elapsed, rate=18.9k reads per second || | || 61% completed, 0.1 mins elapsed, rate=18.9k reads per second || | || 70% completed, 0.1 mins elapsed, rate=13.2k reads per second || | || 73% completed, 0.1 mins elapsed, rate=13.3k reads per second || | || 76% completed, 0.1 mins elapsed, rate=13.3k reads per second || | || 80% completed, 0.1 mins elapsed, rate=13.4k reads per second || | || 83% completed, 0.1 mins elapsed, rate=13.4k reads per second || | || 86% completed, 0.1 mins elapsed, rate=13.5k reads per second || | || 90% completed, 0.1 mins elapsed, rate=13.5k reads per second || | || 93% completed, 0.1 mins elapsed, rate=13.6k reads per second || | || 96% completed, 0.1 mins elapsed, rate=13.6k reads per second || | || || | || Completed successfully. || | || || | \\============================================================================// | //================================= Summary ==================================\\ | || || | || Processed : 85430 reads || | || Mapped : 84722 reads (99.2%), wherein || | || Uniquely mapped : 81914 || | || Multi-mapping : 2808 || | || || | || Not mapped : 708 || | || || | || Indels : 1366 || | || || | || Running time : 0.1 minutes || | || || | \\===================== http://subread.sourceforge.net/ ======================// | [1] "Detecting barcodes" | [1] "Assigning reads to exons" | add gff3 annotation: mm10_MT19_gff3_gz.gff3 | unique map to exon:51428 | ambiguous map to multiple exon:2090 | map to intron:14503 | not mapped:16701 | unaligned:708 | [1] "De-multiplexing data" | [1] "Counting genes" | [1] "Performing QC" | [1] "organism/gene_id_type not provided. make a guess: mmusculus_gene_ensembl / ensembl_gene_id" | [1] "spikeNames(sce)==NULL, no spike-in information." | [1] "the following QC metrics not find in colData from sce:" | [1] "non_ERCC_percent" | null device | 1 | [1] "Removing outliers" | [1] "Creating report" | | | | 0% | |.. | 2% | inline R code fragments | | |... | 5% | label: unnamed-chunk-1 (with options) | List of 3 | $ warning: logi FALSE | $ echo : logi FALSE | $ message: logi FALSE | | |..... | 7% | inline R code fragments | | |...... | 10% | label: unnamed-chunk-2 (with options) | List of 2 | $ warning: logi FALSE | $ message: logi FALSE | | |........ | 12% | ordinary text without R code | | |......... | 14% | label: unnamed-chunk-3 | | |........... | 17% | ordinary text without R code | | |............ | 19% | label: unnamed-chunk-4 | | |.............. | 21% | ordinary text without R code | | |............... | 24% | label: unnamed-chunk-5 | | |................. | 26% | ordinary text without R code | | |................... | 29% | label: unnamed-chunk-6 | | |.................... | 31% | inline R code fragments | | |...................... | 33% | label: unnamed-chunk-7 | Dataset Job Standard Error: | Warning message: | In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : | OS reports request to set locale to "en_US.UTF-8" cannot be honored | `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. | `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. | `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. | `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. | processing file: report.Rmd | Quitting from lines 147-152 (report.Rmd) | Error: Please install xml2 package | -------------------------------------- | 8 - scPipe on data 4, data 3, and others: HTML Report (HID - NAME) | Dataset State: | error | Dataset Blurb: | error | Dataset Info: | [1] "Trimming barcodes" | pass QC: 85430 | removed_have_N: 0 | removed_low_qual: 0 | [1] "Building genome index" | ========== _____ _ _ ____ _____ ______ _____ | ===== / ____| | | | _ \| __ \| ____| /\ | __ \ | Peek: | *Peek unavilable.* | Dataset Job Standard Output: | [1] "Trimming barcodes" | pass QC: 85430 | removed_have_N: 0 | removed_low_qual: 0 | [1] "Building genome index" | ========== _____ _ _ ____ _____ ______ _____ | ===== / ____| | | | _ \| __ \| ____| /\ | __ \ | ===== | (___ | | | | |_) | |__) | |__ / \ | | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ | Rsubread 1.28.1 | //=========================== indexBuilder setting ===========================\\ | || || | || Index name : ./mm10_MT19_fa_gz.fasta_index || | || Index space : base-space || | || Memory : 8000 Mbytes || | || Repeat threshold : 100 repeats || | || Distance to next subread : 3 || | || || | || Input files : 1 file in total || | || o mm10_MT19_fa_gz || | || || | \\===================== http://subread.sourceforge.net/ ======================// | //================================= Running ==================================\\ | || || | || Check the integrity of provided reference sequences ... || | || No format issues were found || | || Scan uninformative subreads in reference sequences ... || | || 8%, 0 mins elapsed, rate=1162.8k bps/s, total=7m || | || 16%, 0 mins elapsed, rate=2219.9k bps/s, total=7m || | || 24%, 0 mins elapsed, rate=3190.8k bps/s, total=7m || | || 33%, 0 mins elapsed, rate=4084.0k bps/s, total=7m || | || 41%, 0 mins elapsed, rate=4908.3k bps/s, total=7m || | || 49%, 0 mins elapsed, rate=5477.1k bps/s, total=7m || | || 58%, 0 mins elapsed, rate=5902.7k bps/s, total=7m || | || 66%, 0 mins elapsed, rate=6310.1k bps/s, total=7m || | || 74%, 0 mins elapsed, rate=6668.1k bps/s, total=7m || | || 83%, 0 mins elapsed, rate=6985.1k bps/s, total=7m || | || 91%, 0 mins elapsed, rate=7243.3k bps/s, total=7m || | || 14 uninformative subreads were found. || | || These subreads were excluded from index building. || | || Build the index... || | || 8%, 0 mins elapsed, rate=14293.9k bps/s, total=7m || | || 16%, 0 mins elapsed, rate=13953.6k bps/s, total=7m || | || 24%, 0 mins elapsed, rate=14178.7k bps/s, total=7m || | || 33%, 0 mins elapsed, rate=14207.3k bps/s, total=7m || | || 41%, 0 mins elapsed, rate=14155.8k bps/s, total=7m || | || 49%, 0 mins elapsed, rate=6697.7k bps/s, total=7m || | || 58%, 0 mins elapsed, rate=4014.1k bps/s, total=7m || | || 66%, 0 mins elapsed, rate=3414.7k bps/s, total=7m || | || 74%, 0 mins elapsed, rate=3239.8k bps/s, total=7m || | || 83%, 0 mins elapsed, rate=3167.8k bps/s, total=7m || | || 91%, 0 mins elapsed, rate=3199.3k bps/s, total=7m || | || Save current index block... || | || [ 0.0% finished ] || | || [ 10.0% finished ] || | || [ 20.0% finished ] || | || [ 30.0% finished ] || | || [ 40.0% finished ] || | || [ 50.0% finished ] || | || [ 60.0% finished ] || | || [ 70.0% finished ] || | || [ 80.0% finished ] || | || [ 90.0% finished ] || | || [ 100.0% finished ] || | || || | || Total running time: 0.1 minutes. || | || Index ./mm10_MT19_fa_gz.fasta_index was successfully built! || | || || | \\===================== http://subread.sourceforge.net/ ======================// | [1] "Aligning reads to genome" | ========== _____ _ _ ____ _____ ______ _____ | ===== / ____| | | | _ \| __ \| ____| /\ | __ \ | ===== | (___ | | | | |_) | |__) | |__ / \ | | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ | Rsubread 1.28.1 | //========================== subread-align setting ===========================\\ | || || | || Function : Read alignment (RNA-Seq) || | || Input file : ./combined.fastq || | || Output file : ./aligned.bam (BAM) || | || Index name : ./mm10_MT19_fa_gz.fasta_index || | || || | || ------------------------------------ || | || || | || Threads : 1 || | || Phred offset : 33 || | || Min votes : 3 / 10 || | || Maximum allowed mismatches : 3 || | || Maximum allowed indel bases : 5 || | || # of best alignments reported : 1 || | || Unique mapping : no || | || || | \\===================== http://subread.sourceforge.net/ ======================// | //================= Running (30-Jan-2020 09:28:29, pid=230) ==================\\ | || || | || The input file contains base space reads. || | || The range of Phred scores observed in the data is [14,36] || | || Load the 1-th index block... || | || 7% completed, 0.0 mins elapsed, rate=19.5k reads per second || | || 14% completed, 0.0 mins elapsed, rate=19.4k reads per second || | || 21% completed, 0.0 mins elapsed, rate=19.4k reads per second || | || 27% completed, 0.0 mins elapsed, rate=19.4k reads per second || | || 34% completed, 0.0 mins elapsed, rate=19.5k reads per second || | || 41% completed, 0.0 mins elapsed, rate=19.4k reads per second || | || 47% completed, 0.1 mins elapsed, rate=19.1k reads per second || | || 54% completed, 0.1 mins elapsed, rate=18.9k reads per second || | || 61% completed, 0.1 mins elapsed, rate=18.9k reads per second || | || 70% completed, 0.1 mins elapsed, rate=13.2k reads per second || | || 73% completed, 0.1 mins elapsed, rate=13.3k reads per second || | || 76% completed, 0.1 mins elapsed, rate=13.3k reads per second || | || 80% completed, 0.1 mins elapsed, rate=13.4k reads per second || | || 83% completed, 0.1 mins elapsed, rate=13.4k reads per second || | || 86% completed, 0.1 mins elapsed, rate=13.5k reads per second || | || 90% completed, 0.1 mins elapsed, rate=13.5k reads per second || | || 93% completed, 0.1 mins elapsed, rate=13.6k reads per second || | || 96% completed, 0.1 mins elapsed, rate=13.6k reads per second || | || || | || Completed successfully. || | || || | \\============================================================================// | //================================= Summary ==================================\\ | || || | || Processed : 85430 reads || | || Mapped : 84722 reads (99.2%), wherein || | || Uniquely mapped : 81914 || | || Multi-mapping : 2808 || | || || | || Not mapped : 708 || | || || | || Indels : 1366 || | || || | || Running time : 0.1 minutes || | || || | \\===================== http://subread.sourceforge.net/ ======================// | [1] "Detecting barcodes" | [1] "Assigning reads to exons" | add gff3 annotation: mm10_MT19_gff3_gz.gff3 | unique map to exon:51428 | ambiguous map to multiple exon:2090 | map to intron:14503 | not mapped:16701 | unaligned:708 | [1] "De-multiplexing data" | [1] "Counting genes" | [1] "Performing QC" | [1] "organism/gene_id_type not provided. make a guess: mmusculus_gene_ensembl / ensembl_gene_id" | [1] "spikeNames(sce)==NULL, no spike-in information." | [1] "the following QC metrics not find in colData from sce:" | [1] "non_ERCC_percent" | null device | 1 | [1] "Removing outliers" | [1] "Creating report" | | | | 0% | |.. | 2% | inline R code fragments | | |... | 5% | label: unnamed-chunk-1 (with options) | List of 3 | $ warning: logi FALSE | $ echo : logi FALSE | $ message: logi FALSE | | |..... | 7% | inline R code fragments | | |...... | 10% | label: unnamed-chunk-2 (with options) | List of 2 | $ warning: logi FALSE | $ message: logi FALSE | | |........ | 12% | ordinary text without R code | | |......... | 14% | label: unnamed-chunk-3 | | |........... | 17% | ordinary text without R code | | |............ | 19% | label: unnamed-chunk-4 | | |.............. | 21% | ordinary text without R code | | |............... | 24% | label: unnamed-chunk-5 | | |................. | 26% | ordinary text without R code | | |................... | 29% | label: unnamed-chunk-6 | | |.................... | 31% | inline R code fragments | | |...................... | 33% | label: unnamed-chunk-7 | Dataset Job Standard Error: | Warning message: | In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : | OS reports request to set locale to "en_US.UTF-8" cannot be honored | `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. | `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. | `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. | `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. | processing file: report.Rmd | Quitting from lines 147-152 (report.Rmd) | Error: Please install xml2 package | -------------------------------------- | 9 - scPipe on data 4, data 3, and others: Rscript (HID - NAME) | Dataset State: | error | Dataset Blurb: | error | Dataset Info: | [1] "Trimming barcodes" | pass QC: 85430 | removed_have_N: 0 | removed_low_qual: 0 | [1] "Building genome index" | ========== _____ _ _ ____ _____ ______ _____ | ===== / ____| | | | _ \| __ \| ____| /\ | __ \ | Peek: | *Peek unavilable.* | Dataset Job Standard Output: | [1] "Trimming barcodes" | pass QC: 85430 | removed_have_N: 0 | removed_low_qual: 0 | [1] "Building genome index" | ========== _____ _ _ ____ _____ ______ _____ | ===== / ____| | | | _ \| __ \| ____| /\ | __ \ | ===== | (___ | | | | |_) | |__) | |__ / \ | | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ | Rsubread 1.28.1 | //=========================== indexBuilder setting ===========================\\ | || || | || Index name : ./mm10_MT19_fa_gz.fasta_index || | || Index space : base-space || | || Memory : 8000 Mbytes || | || Repeat threshold : 100 repeats || | || Distance to next subread : 3 || | || || | || Input files : 1 file in total || | || o mm10_MT19_fa_gz || | || || | \\===================== http://subread.sourceforge.net/ ======================// | //================================= Running ==================================\\ | || || | || Check the integrity of provided reference sequences ... || | || No format issues were found || | || Scan uninformative subreads in reference sequences ... || | || 8%, 0 mins elapsed, rate=1162.8k bps/s, total=7m || | || 16%, 0 mins elapsed, rate=2219.9k bps/s, total=7m || | || 24%, 0 mins elapsed, rate=3190.8k bps/s, total=7m || | || 33%, 0 mins elapsed, rate=4084.0k bps/s, total=7m || | || 41%, 0 mins elapsed, rate=4908.3k bps/s, total=7m || | || 49%, 0 mins elapsed, rate=5477.1k bps/s, total=7m || | || 58%, 0 mins elapsed, rate=5902.7k bps/s, total=7m || | || 66%, 0 mins elapsed, rate=6310.1k bps/s, total=7m || | || 74%, 0 mins elapsed, rate=6668.1k bps/s, total=7m || | || 83%, 0 mins elapsed, rate=6985.1k bps/s, total=7m || | || 91%, 0 mins elapsed, rate=7243.3k bps/s, total=7m || | || 14 uninformative subreads were found. || | || These subreads were excluded from index building. || | || Build the index... || | || 8%, 0 mins elapsed, rate=14293.9k bps/s, total=7m || | || 16%, 0 mins elapsed, rate=13953.6k bps/s, total=7m || | || 24%, 0 mins elapsed, rate=14178.7k bps/s, total=7m || | || 33%, 0 mins elapsed, rate=14207.3k bps/s, total=7m || | || 41%, 0 mins elapsed, rate=14155.8k bps/s, total=7m || | || 49%, 0 mins elapsed, rate=6697.7k bps/s, total=7m || | || 58%, 0 mins elapsed, rate=4014.1k bps/s, total=7m || | || 66%, 0 mins elapsed, rate=3414.7k bps/s, total=7m || | || 74%, 0 mins elapsed, rate=3239.8k bps/s, total=7m || | || 83%, 0 mins elapsed, rate=3167.8k bps/s, total=7m || | || 91%, 0 mins elapsed, rate=3199.3k bps/s, total=7m || | || Save current index block... || | || [ 0.0% finished ] || | || [ 10.0% finished ] || | || [ 20.0% finished ] || | || [ 30.0% finished ] || | || [ 40.0% finished ] || | || [ 50.0% finished ] || | || [ 60.0% finished ] || | || [ 70.0% finished ] || | || [ 80.0% finished ] || | || [ 90.0% finished ] || | || [ 100.0% finished ] || | || || | || Total running time: 0.1 minutes. || | || Index ./mm10_MT19_fa_gz.fasta_index was successfully built! || | || || | \\===================== http://subread.sourceforge.net/ ======================// | [1] "Aligning reads to genome" | ========== _____ _ _ ____ _____ ______ _____ | ===== / ____| | | | _ \| __ \| ____| /\ | __ \ | ===== | (___ | | | | |_) | |__) | |__ / \ | | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ | Rsubread 1.28.1 | //========================== subread-align setting ===========================\\ | || || | || Function : Read alignment (RNA-Seq) || | || Input file : ./combined.fastq || | || Output file : ./aligned.bam (BAM) || | || Index name : ./mm10_MT19_fa_gz.fasta_index || | || || | || ------------------------------------ || | || || | || Threads : 1 || | || Phred offset : 33 || | || Min votes : 3 / 10 || | || Maximum allowed mismatches : 3 || | || Maximum allowed indel bases : 5 || | || # of best alignments reported : 1 || | || Unique mapping : no || | || || | \\===================== http://subread.sourceforge.net/ ======================// | //================= Running (30-Jan-2020 09:28:29, pid=230) ==================\\ | || || | || The input file contains base space reads. || | || The range of Phred scores observed in the data is [14,36] || | || Load the 1-th index block... || | || 7% completed, 0.0 mins elapsed, rate=19.5k reads per second || | || 14% completed, 0.0 mins elapsed, rate=19.4k reads per second || | || 21% completed, 0.0 mins elapsed, rate=19.4k reads per second || | || 27% completed, 0.0 mins elapsed, rate=19.4k reads per second || | || 34% completed, 0.0 mins elapsed, rate=19.5k reads per second || | || 41% completed, 0.0 mins elapsed, rate=19.4k reads per second || | || 47% completed, 0.1 mins elapsed, rate=19.1k reads per second || | || 54% completed, 0.1 mins elapsed, rate=18.9k reads per second || | || 61% completed, 0.1 mins elapsed, rate=18.9k reads per second || | || 70% completed, 0.1 mins elapsed, rate=13.2k reads per second || | || 73% completed, 0.1 mins elapsed, rate=13.3k reads per second || | || 76% completed, 0.1 mins elapsed, rate=13.3k reads per second || | || 80% completed, 0.1 mins elapsed, rate=13.4k reads per second || | || 83% completed, 0.1 mins elapsed, rate=13.4k reads per second || | || 86% completed, 0.1 mins elapsed, rate=13.5k reads per second || | || 90% completed, 0.1 mins elapsed, rate=13.5k reads per second || | || 93% completed, 0.1 mins elapsed, rate=13.6k reads per second || | || 96% completed, 0.1 mins elapsed, rate=13.6k reads per second || | || || | || Completed successfully. || | || || | \\============================================================================// | //================================= Summary ==================================\\ | || || | || Processed : 85430 reads || | || Mapped : 84722 reads (99.2%), wherein || | || Uniquely mapped : 81914 || | || Multi-mapping : 2808 || | || || | || Not mapped : 708 || | || || | || Indels : 1366 || | || || | || Running time : 0.1 minutes || | || || | \\===================== http://subread.sourceforge.net/ ======================// | [1] "Detecting barcodes" | [1] "Assigning reads to exons" | add gff3 annotation: mm10_MT19_gff3_gz.gff3 | unique map to exon:51428 | ambiguous map to multiple exon:2090 | map to intron:14503 | not mapped:16701 | unaligned:708 | [1] "De-multiplexing data" | [1] "Counting genes" | [1] "Performing QC" | [1] "organism/gene_id_type not provided. make a guess: mmusculus_gene_ensembl / ensembl_gene_id" | [1] "spikeNames(sce)==NULL, no spike-in information." | [1] "the following QC metrics not find in colData from sce:" | [1] "non_ERCC_percent" | null device | 1 | [1] "Removing outliers" | [1] "Creating report" | | | | 0% | |.. | 2% | inline R code fragments | | |... | 5% | label: unnamed-chunk-1 (with options) | List of 3 | $ warning: logi FALSE | $ echo : logi FALSE | $ message: logi FALSE | | |..... | 7% | inline R code fragments | | |...... | 10% | label: unnamed-chunk-2 (with options) | List of 2 | $ warning: logi FALSE | $ message: logi FALSE | | |........ | 12% | ordinary text without R code | | |......... | 14% | label: unnamed-chunk-3 | | |........... | 17% | ordinary text without R code | | |............ | 19% | label: unnamed-chunk-4 | | |.............. | 21% | ordinary text without R code | | |............... | 24% | label: unnamed-chunk-5 | | |................. | 26% | ordinary text without R code | | |................... | 29% | label: unnamed-chunk-6 | | |.................... | 31% | inline R code fragments | | |...................... | 33% | label: unnamed-chunk-7 | Dataset Job Standard Error: | Warning message: | In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : | OS reports request to set locale to "en_US.UTF-8" cannot be honored | `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. | `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. | `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. | `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. | processing file: report.Rmd | Quitting from lines 147-152 (report.Rmd) | Error: Please install xml2 package | -------------------------------------- | 10 - scPipe on data 4, data 3, and others: RData file (HID - NAME) | Dataset State: | error | Dataset Blurb: | error | Dataset Info: | [1] "Trimming barcodes" | pass QC: 85430 | removed_have_N: 0 | removed_low_qual: 0 | [1] "Building genome index" | ========== _____ _ _ ____ _____ ______ _____ | ===== / ____| | | | _ \| __ \| ____| /\ | __ \ | Peek: | *Peek unavilable.* | Dataset Job Standard Output: | [1] "Trimming barcodes" | pass QC: 85430 | removed_have_N: 0 | removed_low_qual: 0 | [1] "Building genome index" | ========== _____ _ _ ____ _____ ______ _____ | ===== / ____| | | | _ \| __ \| ____| /\ | __ \ | ===== | (___ | | | | |_) | |__) | |__ / \ | | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ | Rsubread 1.28.1 | //=========================== indexBuilder setting ===========================\\ | || || | || Index name : ./mm10_MT19_fa_gz.fasta_index || | || Index space : base-space || | || Memory : 8000 Mbytes || | || Repeat threshold : 100 repeats || | || Distance to next subread : 3 || | || || | || Input files : 1 file in total || | || o mm10_MT19_fa_gz || | || || | \\===================== http://subread.sourceforge.net/ ======================// | //================================= Running ==================================\\ | || || | || Check the integrity of provided reference sequences ... || | || No format issues were found || | || Scan uninformative subreads in reference sequences ... || | || 8%, 0 mins elapsed, rate=1162.8k bps/s, total=7m || | || 16%, 0 mins elapsed, rate=2219.9k bps/s, total=7m || | || 24%, 0 mins elapsed, rate=3190.8k bps/s, total=7m || | || 33%, 0 mins elapsed, rate=4084.0k bps/s, total=7m || | || 41%, 0 mins elapsed, rate=4908.3k bps/s, total=7m || | || 49%, 0 mins elapsed, rate=5477.1k bps/s, total=7m || | || 58%, 0 mins elapsed, rate=5902.7k bps/s, total=7m || | || 66%, 0 mins elapsed, rate=6310.1k bps/s, total=7m || | || 74%, 0 mins elapsed, rate=6668.1k bps/s, total=7m || | || 83%, 0 mins elapsed, rate=6985.1k bps/s, total=7m || | || 91%, 0 mins elapsed, rate=7243.3k bps/s, total=7m || | || 14 uninformative subreads were found. || | || These subreads were excluded from index building. || | || Build the index... || | || 8%, 0 mins elapsed, rate=14293.9k bps/s, total=7m || | || 16%, 0 mins elapsed, rate=13953.6k bps/s, total=7m || | || 24%, 0 mins elapsed, rate=14178.7k bps/s, total=7m || | || 33%, 0 mins elapsed, rate=14207.3k bps/s, total=7m || | || 41%, 0 mins elapsed, rate=14155.8k bps/s, total=7m || | || 49%, 0 mins elapsed, rate=6697.7k bps/s, total=7m || | || 58%, 0 mins elapsed, rate=4014.1k bps/s, total=7m || | || 66%, 0 mins elapsed, rate=3414.7k bps/s, total=7m || | || 74%, 0 mins elapsed, rate=3239.8k bps/s, total=7m || | || 83%, 0 mins elapsed, rate=3167.8k bps/s, total=7m || | || 91%, 0 mins elapsed, rate=3199.3k bps/s, total=7m || | || Save current index block... || | || [ 0.0% finished ] || | || [ 10.0% finished ] || | || [ 20.0% finished ] || | || [ 30.0% finished ] || | || [ 40.0% finished ] || | || [ 50.0% finished ] || | || [ 60.0% finished ] || | || [ 70.0% finished ] || | || [ 80.0% finished ] || | || [ 90.0% finished ] || | || [ 100.0% finished ] || | || || | || Total running time: 0.1 minutes. || | || Index ./mm10_MT19_fa_gz.fasta_index was successfully built! || | || || | \\===================== http://subread.sourceforge.net/ ======================// | [1] "Aligning reads to genome" | ========== _____ _ _ ____ _____ ______ _____ | ===== / ____| | | | _ \| __ \| ____| /\ | __ \ | ===== | (___ | | | | |_) | |__) | |__ / \ | | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ | Rsubread 1.28.1 | //========================== subread-align setting ===========================\\ | || || | || Function : Read alignment (RNA-Seq) || | || Input file : ./combined.fastq || | || Output file : ./aligned.bam (BAM) || | || Index name : ./mm10_MT19_fa_gz.fasta_index || | || || | || ------------------------------------ || | || || | || Threads : 1 || | || Phred offset : 33 || | || Min votes : 3 / 10 || | || Maximum allowed mismatches : 3 || | || Maximum allowed indel bases : 5 || | || # of best alignments reported : 1 || | || Unique mapping : no || | || || | \\===================== http://subread.sourceforge.net/ ======================// | //================= Running (30-Jan-2020 09:28:29, pid=230) ==================\\ | || || | || The input file contains base space reads. || | || The range of Phred scores observed in the data is [14,36] || | || Load the 1-th index block... || | || 7% completed, 0.0 mins elapsed, rate=19.5k reads per second || | || 14% completed, 0.0 mins elapsed, rate=19.4k reads per second || | || 21% completed, 0.0 mins elapsed, rate=19.4k reads per second || | || 27% completed, 0.0 mins elapsed, rate=19.4k reads per second || | || 34% completed, 0.0 mins elapsed, rate=19.5k reads per second || | || 41% completed, 0.0 mins elapsed, rate=19.4k reads per second || | || 47% completed, 0.1 mins elapsed, rate=19.1k reads per second || | || 54% completed, 0.1 mins elapsed, rate=18.9k reads per second || | || 61% completed, 0.1 mins elapsed, rate=18.9k reads per second || | || 70% completed, 0.1 mins elapsed, rate=13.2k reads per second || | || 73% completed, 0.1 mins elapsed, rate=13.3k reads per second || | || 76% completed, 0.1 mins elapsed, rate=13.3k reads per second || | || 80% completed, 0.1 mins elapsed, rate=13.4k reads per second || | || 83% completed, 0.1 mins elapsed, rate=13.4k reads per second || | || 86% completed, 0.1 mins elapsed, rate=13.5k reads per second || | || 90% completed, 0.1 mins elapsed, rate=13.5k reads per second || | || 93% completed, 0.1 mins elapsed, rate=13.6k reads per second || | || 96% completed, 0.1 mins elapsed, rate=13.6k reads per second || | || || | || Completed successfully. || | || || | \\============================================================================// | //================================= Summary ==================================\\ | || || | || Processed : 85430 reads || | || Mapped : 84722 reads (99.2%), wherein || | || Uniquely mapped : 81914 || | || Multi-mapping : 2808 || | || || | || Not mapped : 708 || | || || | || Indels : 1366 || | || || | || Running time : 0.1 minutes || | || || | \\===================== http://subread.sourceforge.net/ ======================// | [1] "Detecting barcodes" | [1] "Assigning reads to exons" | add gff3 annotation: mm10_MT19_gff3_gz.gff3 | unique map to exon:51428 | ambiguous map to multiple exon:2090 | map to intron:14503 | not mapped:16701 | unaligned:708 | [1] "De-multiplexing data" | [1] "Counting genes" | [1] "Performing QC" | [1] "organism/gene_id_type not provided. make a guess: mmusculus_gene_ensembl / ensembl_gene_id" | [1] "spikeNames(sce)==NULL, no spike-in information." | [1] "the following QC metrics not find in colData from sce:" | [1] "non_ERCC_percent" | null device | 1 | [1] "Removing outliers" | [1] "Creating report" | | | | 0% | |.. | 2% | inline R code fragments | | |... | 5% | label: unnamed-chunk-1 (with options) | List of 3 | $ warning: logi FALSE | $ echo : logi FALSE | $ message: logi FALSE | | |..... | 7% | inline R code fragments | | |...... | 10% | label: unnamed-chunk-2 (with options) | List of 2 | $ warning: logi FALSE | $ message: logi FALSE | | |........ | 12% | ordinary text without R code | | |......... | 14% | label: unnamed-chunk-3 | | |........... | 17% | ordinary text without R code | | |............ | 19% | label: unnamed-chunk-4 | | |.............. | 21% | ordinary text without R code | | |............... | 24% | label: unnamed-chunk-5 | | |................. | 26% | ordinary text without R code | | |................... | 29% | label: unnamed-chunk-6 | | |.................... | 31% | inline R code fragments | | |...................... | 33% | label: unnamed-chunk-7 | Dataset Job Standard Error: | Warning message: | In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") : | OS reports request to set locale to "en_US.UTF-8" cannot be honored | `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. | `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. | `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. | `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. | processing file: report.Rmd | Quitting from lines 147-152 (report.Rmd) | Error: Please install xml2 package | -------------------------------------- | Job 82ea1c58d22fbeef | State: | error | Update Time: | 2020-01-30T09:31:45.123969 | Create Time: | 2020-01-30T09:27:17.766642 | -------------------------------------- | Job 4c469a959b869c08 | State: | ok | Update Time: | 2020-01-30T09:27:11.455972 | Create Time: | 2020-01-30T09:27:04.680425 | -------------------------------------- | Job 8c559fb88d75a36b | State: | ok | Update Time: | 2020-01-30T09:27:02.716234 | Create Time: | 2020-01-30T09:26:58.092806 | -------------------------------------- | Job aa6cc630da5109fb | State: | ok | Update Time: | 2020-01-30T09:26:55.692257 | Create Time: | 2020-01-30T09:26:51.506336 | -------------------------------------- | Job 37f9ab3378d23774 | State: | ok | Update Time: | 2020-01-30T09:26:49.432773 | Create Time: | 2020-01-30T09:26:44.843867 | -------------------------------------- --------------------- >> end captured stdout << ----------------------

Overview

Tests