You provided these parameters: YAML file: ./N706-PBMC-CD34CD45-1-5-chip2.yaml zUMIs directory: /home/mbassal/tools/zUMIs2.3 STAR executable STAR samtools executable samtools pigz executable pigz Rscript executable Rscript RAM limit: 0 zUMIs version 2.3.0b Filtering... Mapping... Mar 05 01:05:29 ..... started STAR run Mar 05 01:05:29 ..... loading genome Mar 05 01:05:49 ..... processing annotations GTF Mar 05 01:06:01 ..... inserting junctions into the genome indices Mar 05 01:08:31 ..... started 1st pass mapping Mar 05 01:42:39 ..... finished 1st pass mapping Mar 05 01:42:40 ..... inserting junctions into the genome indices Mar 05 01:46:51 ..... started mapping Mar 05 02:46:05 ..... finished successfully Counting... [1] "2019-03-05 02:46:18 EST" [1] "1537441 barcodes detected." [1] " reads were assigned to barcodes that do not correspond to intact cells." [1] "Inf Reads per chunk" [1] "Loading reference annotation from:" [1] "/mnt/md0/genomes/human_STAR_index/Homo_sapiens.GRCh38.dna_sm.primary_assembly_ucsc_refseq.gtf" [1] "Annotation loaded!" [1] "Assigning reads to features (ex)" ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ Rsubread 1.32.2 //========================== featureCounts setting ===========================\\ || || || Input files : 1 BAM file || || S N706-PBMC-CD34CD45-1-5-chip2.filtered.tagg ... || || || || Annotation : R data.frame || || Assignment details : .featureCounts.bam || || (Note that files are saved to the output directory) || || || || Dir for temp files : . || || Threads : 30 || || Level : meta-feature level || || Paired-end : yes || || Multimapping reads : counted || || Multiple alignments : primary alignment only || || Multi-overlapping reads : not counted || || Min overlapping bases : 1 || || || || Chimeric reads : not counted || || Both ends mapped : not required || || || \\===================== http://subread.sourceforge.net/ ======================// //================================= Running ==================================\\ || || || Load annotation file .Rsubread_UserProvidedAnnotation_pid2456 ... || || Features : 380895 || || Meta-features : 37444 || || Chromosomes/contigs : 249 || || || || Process BAM file N706-PBMC-CD34CD45-1-5-chip2.filtered.tagged.Aligned. ... || || Single-end reads are included. || || Strand specific : reversely stranded || || Assign alignments to features... || || Total alignments : 368616248 || || Successfully assigned alignments : 8774535 (2.4%) || || Running time : 3.33 minutes || || || || || \\===================== http://subread.sourceforge.net/ ======================// [1] "Assigning reads to features (in)" ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ Rsubread 1.32.2 //========================== featureCounts setting ===========================\\ || || || Input files : 1 BAM file || || S N706-PBMC-CD34CD45-1-5-chip2.filtered.tagg ... || || || || Annotation : R data.frame || || Assignment details : .featureCounts.bam || || (Note that files are saved to the output directory) || || || || Dir for temp files : . || || Threads : 30 || || Level : meta-feature level || || Paired-end : yes || || Multimapping reads : counted || || Multiple alignments : primary alignment only || || Multi-overlapping reads : not counted || || Min overlapping bases : 1 || || || || Chimeric reads : not counted || || Both ends mapped : not required || || || \\===================== http://subread.sourceforge.net/ ======================// //================================= Running ==================================\\ || || || Load annotation file .Rsubread_UserProvidedAnnotation_pid2456 ... || || Features : 266361 || || Meta-features : 31035 || || Chromosomes/contigs : 243 || || || || Process BAM file N706-PBMC-CD34CD45-1-5-chip2.filtered.tagged.Aligned. ... || || Single-end reads are included. || || Strand specific : reversely stranded || || Assign alignments to features... || || Total alignments : 368616248 || || Successfully assigned alignments : 35479639 (9.6%) || || Running time : 3.17 minutes || || || || || \\===================== http://subread.sourceforge.net/ ======================// [bam_sort_core] merging from 210 files... [bam_sort_core] merging from 210 files... [1] "Here are the detected subsampling options:" [1] "Automatic downsampling" [1] "Working on barcode chunk 1 out of 1" [1] "Processing 1537441 barcodes in this chunk..." Initialising 30 core cluster. Initialising 30 core cluster. Initialising 30 core cluster. Initialising 30 core cluster. Initialising 30 core cluster. Initialising 30 core cluster. There were 12 warnings (use warnings() to see them) [1] "2019-03-05 23:05:54 EST" [1] "I am done!! Look what I produced.../mnt/md0/MB/analyses/biorad/my_analysis/zumi_processed/PBMC-CD34CD45-1-5-chip2/zUMIs_output/" used (Mb) gc trigger (Mb) max used (Mb) Ncells 11228108 599.7 36584338 1953.9 39248761 2096.2 Vcells 629523154 4802.9 1740436169 13278.5 3393060619 25887.0 Descriptive statistics... [1] "I am loading useful packages for plotting..." [1] "2019-03-05 23:05:59 EST" Error in if (any(i < 0L)) { : missing value where TRUE/FALSE needed Calls: ... as -> .class1 -> .TM.repl.i.mat -> [<- -> [<- -> int2i In addition: Warning message: In int2i(as.integer(i), n) : NAs introduced by coercion to integer range Execution halted