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 mkgtf (3.0.2) Copyright (c) 2019 10x Genomics, Inc. All rights reserved. ------------------------------------------------------------------------------- Input file does not exist: /share/data/umw_biocore/genome_data/cellranger/zebrafish/GRCz11_v4.2.1/V4.3.gtf ------------------------------------------------------------ Sender: LSF System Subject: Job 6839891: in cluster Exited Job was submitted from host by user in cluster at Tue May 12 10:27:23 2020 Job was executed on host(s) , in queue , as user in cluster at Tue May 12 10:27:24 2020 was used as the home directory. was used as the working directory. Started at Tue May 12 10:27:24 2020 Terminated at Tue May 12 10:27:51 2020 Results reported at Tue May 12 10:27:51 2020 Your job looked like: ------------------------------------------------------------ # LSBATCH: User input module load cellranger/3.0.2 && cd /share/data/umw_biocore/genome_data/cellranger/zebrafish/GRCz11_v4.2.1 && cellranger mkgtf V4.3.gtf V4.3.validated.gtf ------------------------------------------------------------ Exited with exit code 1. Resource usage summary: CPU time : 1.81 sec. Max Memory : 34 MB Average Memory : 27.25 MB Total Requested Memory : 20048.00 MB Delta Memory : 20014.00 MB Max Swap : - Max Processes : 5 Max Threads : 6 Run time : 31 sec. Turnaround time : 28 sec. The output (if any) is above this job summary. 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 mkgtf (3.0.2) Copyright (c) 2019 10x Genomics, Inc. All rights reserved. ------------------------------------------------------------------------------- Writing new genes GTF file (may take 10 minutes for a 1GB input GTF file)... ...done ------------------------------------------------------------ Sender: LSF System Subject: Job 6839902: in cluster Done Job was submitted from host by user in cluster at Tue May 12 10:28:37 2020 Job was executed on host(s) , in queue , as user in cluster at Tue May 12 10:28:37 2020 was used as the home directory. was used as the working directory. Started at Tue May 12 10:28:37 2020 Terminated at Tue May 12 10:29:08 2020 Results reported at Tue May 12 10:29:08 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 mkgtf V4.3.gtf V4.3.validated.gtf ------------------------------------------------------------ Successfully completed. Resource usage summary: CPU time : 25.35 sec. Max Memory : 53 MB Average Memory : 43.00 MB Total Requested Memory : 20048.00 MB Delta Memory : 19995.00 MB Max Swap : - Max Processes : 5 Max Threads : 14 Run time : 45 sec. Turnaround time : 31 sec. The output (if any) is above this job summary.