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. ------------------------------------------------------------------------------- May 12 10:32:06 ..... Started STAR run May 12 10:32:06 ... Starting to generate Genome files May 12 10:32:41 ... starting to sort Suffix Array. This may take a long time... May 12 10:32:45 ... sorting Suffix Array chunks and saving them to disk... May 12 10:50:36 ... loading chunks from disk, packing SA... May 12 10:51:09 ... Finished generating suffix array May 12 10:51:09 ... Generating Suffix Array index May 12 10:52:43 ... Completed Suffix Array index May 12 10:52:43 ..... Processing annotations GTF May 12 10:52:52 ..... Inserting junctions into the genome indices May 12 10:58:25 ... writing Genome to disk ... May 12 10:58:30 ... writing Suffix Array to disk ... May 12 10:58:48 ... writing SAindex to disk May 12 10:58:52 ..... Finished successfully Creating new reference folder at /share/data/umw_biocore/genome_data/cellranger/zebrafish/GRCz11_v4.3/GRCz11_v4.3 ...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_v4.3/GRCz11_v4.3 ... ------------------------------------------------------------ Sender: LSF System Subject: Job 6839904: in cluster Done Job was submitted from host by user in cluster at Tue May 12 10:29:56 2020 Job was executed on host(s) , in queue , as user in cluster at Tue May 12 10:29:56 2020 was used as the home directory. was used as the working directory. Started at Tue May 12 10:29:56 2020 Terminated at Tue May 12 10:58:53 2020 Results reported at Tue May 12 10:58:53 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 && cellranger mkref --genome=GRCz11_v4.3 --fasta=danRer11.primary.fa --genes=V4.3.validated.gtf --ref-version=1.0.0 ------------------------------------------------------------ Successfully completed. Resource usage summary: CPU time : 1669.29 sec. Max Memory : 18718 MB Average Memory : 11085.10 MB Total Requested Memory : 20048.00 MB Delta Memory : 1330.00 MB Max Swap : - Max Processes : 6 Max Threads : 15 Run time : 1740 sec. Turnaround time : 1737 sec. The output (if any) is above this job summary.