singularity singularity-2.6.1 is located under /share/pkg/singularity/singularity-2.6.1 [33mWARNING: Non existent bind point (directory) in container: '/lsf' [0m[33mWARNING: Non existent bind point (directory) in container: '/farline' [0m[33mWARNING: Not mounting requested bind point (already mounted in container): /project [0m[33mWARNING: Not mounting requested bind point (already mounted in container): /share [0mWriting new genes GTF file (may take 10 minutes for a 1GB input GTF file)... ...done ------------------------------------------------------------ Sender: LSF System Subject: Job 9740053: in cluster Done Job was submitted from host by user in cluster at Mon May 24 14:56:03 2021 Job was executed on host(s) , in queue , as user in cluster at Mon May 24 14:56:10 2021 was used as the home directory. was used as the working directory. Started at Mon May 24 14:56:10 2021 Terminated at Mon May 24 14:57:19 2021 Results reported at Mon May 24 14:57:19 2021 Your job looked like: ------------------------------------------------------------ # LSBATCH: User input module load singularity/singularity-2.6.1 && cd /share/data/umw_biocore/genome_data/cellranger/zebrafish/GRCz11_v4.3.2_cellranger_v6 && singularity exec -B /project:/project -B /share:/share /share/data/umw_biocore/dnext_data/singularity/UMMS-Biocore-singularity-cellranger-v4.simg cellranger mkgtf V4.3.2.gtf V4.3.2.validated.gtf ------------------------------------------------------------ Successfully completed. Resource usage summary: CPU time : 47.70 sec. Max Memory : 28 MB Average Memory : 22.71 MB Total Requested Memory : 20048.00 MB Delta Memory : 20020.00 MB Max Swap : - Max Processes : 5 Max Threads : 6 Run time : 75 sec. Turnaround time : 76 sec. The output (if any) is above this job summary. singularity singularity-2.6.1 is located under /share/pkg/singularity/singularity-2.6.1 [33mWARNING: Non existent bind point (directory) in container: '/lsf' [0m[33mWARNING: Non existent bind point (directory) in container: '/farline' [0m[33mWARNING: Not mounting requested bind point (already mounted in container): /project [0m[33mWARNING: Not mounting requested bind point (already mounted in container): /share [0m['/usr/bin/cellranger-6.0.1/bin/rna/mkref', '--genome=GRCz11_v4.3.2', '--fasta=danRer11.primary.fa', '--genes=V4.3.2.validated.gtf', '--ref-version=1.0.0'] May 24 19:22:27 ..... started STAR run May 24 19:22:27 ... starting to generate Genome files May 24 19:23:11 ... starting to sort Suffix Array. This may take a long time... May 24 19:23:16 ... sorting Suffix Array chunks and saving them to disk... May 24 19:42:03 ... loading chunks from disk, packing SA... May 24 19:42:33 ... finished generating suffix array May 24 19:42:33 ... generating Suffix Array index May 24 19:44:08 ... completed Suffix Array index May 24 19:44:08 ..... processing annotations GTF May 24 19:44:19 ..... inserting junctions into the genome indices May 24 19:50:09 ... writing Genome to disk ... May 24 19:50:16 ... writing Suffix Array to disk ... May 24 19:50:37 ... writing SAindex to disk May 24 19:50:44 ..... finished successfully Creating new reference folder at /share/data/umw_biocore/dnext_data/genome_data_other/cellranger/zebrafish/GRCz11_v4.3.2_cellranger_v6/GRCz11_v4.3.2 ...done Writing genome FASTA file into reference folder... ...done Indexing genome FASTA file... ...done Writing genes GTF file into reference folder... ...done Generating STAR genome index (may take over 8 core hours for a 3Gb genome)... ...done. Writing genome metadata JSON file into reference folder... Computing hash of genome FASTA file... ...done Computing hash of genes GTF file... ...done ...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_cellranger_v6/GRCz11_v4.3.2 ... ------------------------------------------------------------ Sender: LSF System Subject: Job 9740087: in cluster Done Job was submitted from host by user in cluster at Mon May 24 15:21:09 2021 Job was executed on host(s) , in queue , as user in cluster at Mon May 24 15:21:14 2021 was used as the home directory. was used as the working directory. Started at Mon May 24 15:21:14 2021 Terminated at Mon May 24 15:50:50 2021 Results reported at Mon May 24 15:50:50 2021 Your job looked like: ------------------------------------------------------------ # LSBATCH: User input module load singularity/singularity-2.6.1 && cd /share/data/umw_biocore/genome_data/cellranger/zebrafish/GRCz11_v4.3.2_cellranger_v6 && singularity exec -B /project:/project -B /share:/share /share/data/umw_biocore/dnext_data/singularity/UMMS-Biocore-singularity-cellranger-v4.simg 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 : 1672.44 sec. Max Memory : 18753 MB Average Memory : 10713.68 MB Total Requested Memory : 20048.00 MB Delta Memory : 1295.00 MB Max Swap : - Max Processes : 6 Max Threads : 7 Run time : 1790 sec. Turnaround time : 1781 sec. The output (if any) is above this job summary.