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. ------------------------------------------------------------------------------- Oct 30 13:00:27 ..... Started STAR run Oct 30 13:00:27 ... Starting to generate Genome files Oct 30 13:01:08 ... starting to sort Suffix Array. This may take a long time... Oct 30 13:01:13 ... sorting Suffix Array chunks and saving them to disk... Oct 30 13:28:16 ... loading chunks from disk, packing SA... Oct 30 13:28:38 ... Finished generating suffix array Oct 30 13:28:38 ... Generating Suffix Array index Oct 30 13:31:06 ... Completed Suffix Array index Oct 30 13:31:06 ..... Processing annotations GTF Oct 30 13:31:16 ..... Inserting junctions into the genome indices Oct 30 13:39:56 ... writing Genome to disk ... Oct 30 13:40:02 ... writing Suffix Array to disk ... Oct 30 13:40:22 ... writing SAindex to disk Oct 30 13:40:26 ..... Finished successfully Creating new reference folder at /share/data/umw_biocore/dnext_data/genome_data_other/cellranger/zebrafish/GRCz11_v4.3.2_new/GRCz11_v4.3.2 ...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/dnext_data/genome_data_other/cellranger/zebrafish/GRCz11_v4.3.2_new/GRCz11_v4.3.2 ... ------------------------------------------------------------ Sender: LSF System Subject: Job 869935: in cluster Done Job was submitted from host by user in cluster at Fri Oct 30 12:57:59 2020 Job was executed on host(s) , in queue , as user in cluster at Fri Oct 30 12:58:01 2020 was used as the home directory. was used as the working directory. Started at Fri Oct 30 12:58:01 2020 Terminated at Fri Oct 30 13:40:30 2020 Results reported at Fri Oct 30 13:40:30 2020 Your job looked like: ------------------------------------------------------------ # LSBATCH: User input module load cellranger/3.0.2 && cd /share/data/umw_biocore/genome_data/cellranger/zebrafish/GRCz11_v4.3.2_new && cellranger mkref --genome=GRCz11_v4.3.2 --fasta=danRer11.primary.fa --genes=V4.3.2.validated.gtf --ref-version=1.0.0 ------------------------------------------------------------ Successfully completed. Resource usage summary: CPU time : 2487.20 sec. Max Memory : 19007 MB Average Memory : 11388.48 MB Total Requested Memory : 20048.00 MB Delta Memory : 1041.00 MB Max Swap : - Max Processes : 6 Max Threads : 15 Run time : 2560 sec. Turnaround time : 2551 sec. The output (if any) is above this job summary.