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. ------------------------------------------------------------------------------- Jul 13 13:16:07 ..... Started STAR run Jul 13 13:16:07 ... Starting to generate Genome files Jul 13 13:16:47 ... starting to sort Suffix Array. This may take a long time... Jul 13 13:16:52 ... sorting Suffix Array chunks and saving them to disk... Jul 13 13:38:52 ... loading chunks from disk, packing SA... Jul 13 13:39:22 ... Finished generating suffix array Jul 13 13:39:22 ... Generating Suffix Array index Jul 13 13:41:03 ... Completed Suffix Array index Jul 13 13:41:03 ..... Processing annotations GTF Jul 13 13:41:14 ..... Inserting junctions into the genome indices Jul 13 13:47:32 ... writing Genome to disk ... Jul 13 13:47:37 ... writing Suffix Array to disk ... Jul 13 13:47:56 ... writing SAindex to disk Jul 13 13:48:00 ..... Finished successfully Creating new reference folder at /share/data/umw_biocore/genome_data/cellranger/zebrafish/GRCz11_v4.1.3/GRCz11_v4.1.3 ...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/zebrafish/GRCz11_v4.1.3/GRCz11_v4.1.3 ... ------------------------------------------------------------ Sender: LSF System Subject: Job 7697268: in cluster Done Job was submitted from host by user in cluster at Sat Jul 13 13:13:23 2019. Job was executed on host(s) , in queue , as user in cluster at Sat Jul 13 13:13:26 2019. was used as the home directory. was used as the working directory. Started at Sat Jul 13 13:13:26 2019. Terminated at Sat Jul 13 13:48:04 2019. Results reported at Sat Jul 13 13:48:04 2019. Your job looked like: ------------------------------------------------------------ # LSBATCH: User input module load cellranger/3.0.2 && cd /share/data/umw_biocore/genome_data/cellranger/zebrafish/GRCz11_v4.1.3 && cellranger mkref --genome=GRCz11_v4.1.3 --fasta=danRer11.primary.fa --genes=cuffmerge_v4.1.3.validated.gtf --ref-version=1.0.0 ------------------------------------------------------------ Successfully completed. Resource usage summary: CPU time : 2011.32 sec. Max Memory : 18667 MB Average Memory : 11190.55 MB Total Requested Memory : 20048.00 MB Delta Memory : 1381.00 MB Max Swap : - Max Processes : 6 Max Threads : 15 Run time : 2077 sec. Turnaround time : 2081 sec. The output (if any) is above this job summary.