cellranger 3.0.2 is located under /share/pkg/cellranger/3.0.2 /share/pkg/cellranger/3.0.2/cellranger-cs/3.0.2/bin cellranger mkref (3.0.2) Copyright (c) 2019 10x Genomics, Inc. All rights reserved. ------------------------------------------------------------------------------- Mar 13 15:31:01 ..... Started STAR run Mar 13 15:31:01 ... Starting to generate Genome files Mar 13 15:32:23 ... starting to sort Suffix Array. This may take a long time... Mar 13 15:32:30 ... sorting Suffix Array chunks and saving them to disk... Mar 13 16:18:23 ... loading chunks from disk, packing SA... Mar 13 16:20:17 ... Finished generating suffix array Mar 13 16:20:17 ... Generating Suffix Array index Mar 13 16:22:16 ... Completed Suffix Array index Mar 13 16:22:16 ..... Processing annotations GTF Mar 13 16:22:29 ..... Inserting junctions into the genome indices Mar 13 16:26:56 ... writing Genome to disk ... Mar 13 16:27:10 ... writing Suffix Array to disk ... Mar 13 16:27:50 ... writing SAindex to disk Mar 13 16:27:57 ..... Finished successfully Creating new reference folder at /share/data/umw_biocore/genome_data/cellranger/human/hg38_gencode_v28/hg38_gencode_v28 ...done Writing genome FASTA file into reference folder... ...done Computing hash of genome FASTA file... ...done Indexing genome FASTA file... ...done Writing genes GTF file into reference folder... ...done Computing hash of genes GTF file... ...done Writing genes index file into reference folder (may take over 10 minutes for a 3Gb genome)... ...done Writing genome metadata JSON file into reference folder... ...done Generating STAR genome index (may take over 8 core hours for a 3Gb genome)... ...done. >>> Reference successfully created! <<< You can now specify this reference on the command line: cellranger --transcriptome=/share/data/umw_biocore/genome_data/cellranger/human/hg38_gencode_v28/hg38_gencode_v28 ... ------------------------------------------------------------ Sender: LSF System Subject: Job 2721864: in cluster Done Job was submitted from host by user in cluster at Fri Mar 13 15:24:31 2020. Job was executed on host(s) <2*c40b16>, in queue , as user in cluster at Fri Mar 13 15:24:33 2020. was used as the home directory. was used as the working directory. Started at Fri Mar 13 15:24:33 2020. Terminated at Fri Mar 13 16:28:00 2020. Results reported at Fri Mar 13 16:28:00 2020. Your job looked like: ------------------------------------------------------------ # LSBATCH: User input module load cellranger/3.0.2 && cd /share/data/umw_biocore/genome_data/cellranger/human/hg38_gencode_v28 && cellranger mkref --genome=hg38_gencode_v28 --fasta=hg38.fa --genes=gencode.v28.basic.annotation.filtered.gtf --ref-version=3.0.2 ------------------------------------------------------------ Successfully completed. Resource usage summary: CPU time : 3468.96 sec. Max Memory : 18787 MB Average Memory : 12451.37 MB Total Requested Memory : 40096.00 MB Delta Memory : 21309.00 MB Max Swap : - Max Processes : 6 Max Threads : 15 Run time : 3804 sec. Turnaround time : 3809 sec. The output (if any) is above this job summary.