#yaml used project: test1noflter sequence_files: file1: name: /media/lab/Lab10TB/Project1/00_Fastq/downloadtest/correcteddemerge/reads_for_zUMIs.R1.fastq.gz base_definition: - UMI(9-13) file2: name: /media/lab/Lab10TB/Project1/00_Fastq/downloadtest/correcteddemerge/reads_for_zUMIs.R2.fastq.gz base_definition: - cDNA(1-47) file3: name: /media/lab/Lab10TB/Project1/00_Fastq/downloadtest/correcteddemerge/reads_for_zUMIs.index.fastq.gz base_definition: - BC(1-8) reference: STAR_index: /media/lab/Lab/GRCh38genome/nogtf/a GTF_file: /media/lab/Lab/GRCh38genome/Homo_sapiens.GRCh38.gtf additional_STAR_params: '' additional_files: ~ out_dir: /media/lab/Lab10TB/Project1/00_Fastq/downloadtest/correcteddemerge/output num_threads: 10 mem_limit: 20 filter_cutoffs: BC_filter: num_bases: 1 phred: ~ UMI_filter: num_bases: 1 phred: ~ barcodes: barcode_num: ~ barcode_file: /media/lab/Lab10TB/Project1/00_Fastq/downloadtest/correcteddemerge/reads_for_zUMIs.expected_barcodes.txt automatic: no BarcodeBinning: 0 nReadsperCell: 100 counting_opts: introns: yes downsampling: '0' strand: 1 Ham_Dist: 0 velocyto: no primaryHit: yes twoPass: yes make_stats: yes which_Stage: Filtering samtools_exec: samtools pigz_exec: pigz STAR_exec: STAR Rscript_exec: Rscript zUMIs_directory: /media/lab/Lab/software/zUMIs-main ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Using miniconda environment for zUMIs! note: internal executables will be used instead of those specified in the YAML file! You provided these parameters: YAML file: test.yaml zUMIs directory: /media/lab/Lab/software/zUMIs-main STAR executable STAR samtools executable samtools pigz executable pigz Rscript executable Rscript RAM limit: 20 zUMIs version 2.9.7 Thu 07 Apr 2022 02:37:43 PM IST WARNING: The STAR version used for mapping is 2.7.10a and the STAR index was created using the version 2.7.4a. This may lead to an error while mapping. If you encounter any errors at the mapping stage, please make sure to create the STAR index using STAR 2.7.10a. Filtering... Fri 08 Apr 2022 02:27:35 AM IST [1] " reads were assigned to barcodes that do not correspond to intact cells." Warning message: In gsum(n) : The sum of an integer column for a group was more than type 'integer' can hold so the result has been coerced to 'numeric' automatically for convenience. Mapping... [1] "2022-04-08 02:27:37 IST" [1] "STAR --readFilesCommand samtools view -@ 2 --outSAMmultNmax 1 --outFilterMultimapNmax 50 --outSAMunmapped Within --outSAMtype BAM Unsorted --quantMode TranscriptomeSAM --genomeDir /media/lab/Lab/GRCh38genome/nogtf/a --sjdbGTFfile /media/lab/Lab/GRCh38genome/Homo_sapiens.GRCh38.gtf --runThreadN 8 --sjdbOverhang 46 --readFilesType SAM SE " STAR --readFilesCommand samtools view -@ 2 --outSAMmultNmax 1 --outFilterMultimapNmax 50 --outSAMunmapped Within --outSAMtype BAM Unsorted --quantMode TranscriptomeSAM --genomeDir /media/lab/Lab/GRCh38genome/nogtf/a --sjdbGTFfile /media/lab/Lab/GRCh38genome/Homo_sapiens.GRCh38.gtf --runThreadN 8 --sjdbOverhang 46 --readFilesType SAM SE --twopassMode Basic --readFilesIn /media/lab/Lab10TB/Project1/00_Fastq/downloadtest/correcteddemerge/output/zUMIs_output/.tmpMerge//test1noflter.test1noflteraa.filtered.tagged.bam,/media/lab/Lab10TB/Project1/00_Fastq/downloadtest/correcteddemerge/output/zUMIs_output/.tmpMerge//test1noflter.test1noflterab.filtered.tagged.bam,/media/lab/Lab10TB/Project1/00_Fastq/downloadtest/correcteddemerge/output/zUMIs_output/.tmpMerge//test1noflter.test1noflterac.filtered.tagged.bam,/media/lab/Lab10TB/Project1/00_Fastq/downloadtest/correcteddemerge/output/zUMIs_output/.tmpMerge//test1noflter.test1noflterad.filtered.tagged.bam,/media/lab/Lab10TB/Project1/00_Fastq/downloadtest/correcteddemerge/output/zUMIs_output/.tmpMerge//test1noflter.test1noflterae.filtered.tagged.bam,/media/lab/Lab10TB/Project1/00_Fastq/downloadtest/correcteddemerge/output/zUMIs_output/.tmpMerge//test1noflter.test1noflteraf.filtered.tagged.bam,/media/lab/Lab10TB/Project1/00_Fastq/downloadtest/correcteddemerge/output/zUMIs_output/.tmpMerge//test1noflter.test1noflterag.filtered.tagged.bam,/media/lab/Lab10TB/Project1/00_Fastq/downloadtest/correcteddemerge/output/zUMIs_output/.tmpMerge//test1noflter.test1noflterah.filtered.tagged.bam,/media/lab/Lab10TB/Project1/00_Fastq/downloadtest/correcteddemerge/output/zUMIs_output/.tmpMerge//test1noflter.test1noflterai.filtered.tagged.bam,/media/lab/Lab10TB/Project1/00_Fastq/downloadtest/correcteddemerge/output/zUMIs_output/.tmpMerge//test1noflter.test1noflteraj.filtered.tagged.bam --outFileNamePrefix /media/lab/Lab10TB/Project1/00_Fastq/downloadtest/correcteddemerge/output/test1noflter.filtered.tagged. STAR version: 2.7.10a compiled: 2022-01-14T18:50:00-05:00 :/home/dobin/data/STAR/STARcode/STAR.master/source Apr 08 02:27:44 ..... started STAR run Apr 08 02:27:45 ..... loading genome Apr 08 02:30:29 ..... processing annotations GTF Apr 08 02:30:44 ..... inserting junctions into the genome indices Apr 08 02:32:48 ..... started 1st pass mapping EXITING because of fatal error: buffer size for SJ output is too small Solution: increase input parameter --limitOutSJcollapsed Apr 08 04:36:50 ...... FATAL ERROR, exiting Fri 08 Apr 2022 04:36:56 AM IST Counting... [1] "2022-04-08 04:37:05 IST" [1] "9e+07 Reads per chunk" [1] "Loading reference annotation from:" [1] "/media/lab/Lab10TB/Project1/00_Fastq/downloadtest/correcteddemerge/output/test1noflter.final_annot.gtf" Error in gsub("SN:", "", chr) : object 'chr' not found Calls: .makeSAF ... .chromLengthFilter -> [ -> [.data.table -> eval -> eval -> gsub In addition: Warning message: In data.table::fread(bread, col.names = c("chr", "len"), header = F) : File '/tmp/RtmpAViMjD/file46e6a70d01f58' has size 0. Returning a NULL data.table. Execution halted Fri 08 Apr 2022 04:37:24 AM IST Loading required package: yaml Loading required package: Matrix [1] "loomR found" Error in gzfile(file, "rb") : cannot open the connection Calls: rds_to_loom -> readRDS -> gzfile In addition: Warning message: In gzfile(file, "rb") : cannot open compressed file '/media/lab/Lab10TB/Project1/00_Fastq/downloadtest/correcteddemerge/output/zUMIs_output/expression/test1noflter.dgecounts.rds', probable reason 'No such file or directory' Execution halted Fri 08 Apr 2022 04:37:26 AM IST Descriptive statistics... [1] "I am loading useful packages for plotting..." [1] "2022-04-08 04:37:26 IST" Error in gzfile(file, "rb") : cannot open the connection Calls: readRDS -> gzfile In addition: Warning message: In gzfile(file, "rb") : cannot open compressed file '/media/lab/Lab10TB/Project1/00_Fastq/downloadtest/correcteddemerge/output/zUMIs_output/expression/test1noflter.dgecounts.rds', probable reason 'No such file or directory' Execution halted Fri 08 Apr 2022 04:37:29 AM IST