singularity singularity-3.4.0 is located under /share/pkg/singularity/singularity-3.4.0 cellranger-atac mkref (1.2.0) Copyright (c) 2019 10x Genomics, Inc. All rights reserved. ------------------------------------------------------------------------------- Non-standard genome name detected, building custom reference... >>> Creating reference for GRCz11_v4.3.2 <<< Creating new reference folder at /share/data/umw_biocore/dnext_data/genome_data_other/cellrangeratac/zebrafish/GRCz11_v4.3.2/GRCz11_v4.3.2 Copying original fasta file into reference folder... done Generating samtools index... done Generating pyfasta indexes... Number of contigs: 998 Total genome size: 1373475517 done Copying original gene annotation file into reference folder... done Writing TSS and transcripts bed file... Parsed 81819 unique TSS and 95543 unique transcripts. done Generating bwa index (may take over an hour for a 3Gb genome)... [bwa_index] Pack FASTA... 8.69 sec [bwa_index] Construct BWT for the packed sequence... [BWTIncCreate] textLength=2746951034, availableWord=205285296 [BWTIncConstructFromPacked] 10 iterations done. 99999994 characters processed. [BWTIncConstructFromPacked] 20 iterations done. 199999994 characters processed. [BWTIncConstructFromPacked] 30 iterations done. 299999994 characters processed. [BWTIncConstructFromPacked] 40 iterations done. 399999994 characters processed. [BWTIncConstructFromPacked] 50 iterations done. 499999994 characters processed. [BWTIncConstructFromPacked] 60 iterations done. 599999994 characters processed. [BWTIncConstructFromPacked] 70 iterations done. 699999994 characters processed. [BWTIncConstructFromPacked] 80 iterations done. 799999994 characters processed. [BWTIncConstructFromPacked] 90 iterations done. 899999994 characters processed. [BWTIncConstructFromPacked] 100 iterations done. 999999994 characters processed. [BWTIncConstructFromPacked] 110 iterations done. 1099999994 characters processed. [BWTIncConstructFromPacked] 120 iterations done. 1199999994 characters processed. [BWTIncConstructFromPacked] 130 iterations done. 1299999994 characters processed. [BWTIncConstructFromPacked] 140 iterations done. 1399999994 characters processed. [BWTIncConstructFromPacked] 150 iterations done. 1499999994 characters processed. [BWTIncConstructFromPacked] 160 iterations done. 1599999994 characters processed. [BWTIncConstructFromPacked] 170 iterations done. 1699999994 characters processed. [BWTIncConstructFromPacked] 180 iterations done. 1799999994 characters processed. [BWTIncConstructFromPacked] 190 iterations done. 1899999994 characters processed. [BWTIncConstructFromPacked] 200 iterations done. 1999999994 characters processed. [BWTIncConstructFromPacked] 210 iterations done. 2099494330 characters processed. [BWTIncConstructFromPacked] 220 iterations done. 2190602426 characters processed. [BWTIncConstructFromPacked] 230 iterations done. 2271575530 characters processed. [BWTIncConstructFromPacked] 240 iterations done. 2343540618 characters processed. [BWTIncConstructFromPacked] 250 iterations done. 2407499370 characters processed. [BWTIncConstructFromPacked] 260 iterations done. 2464342042 characters processed. [BWTIncConstructFromPacked] 270 iterations done. 2514859930 characters processed. [BWTIncConstructFromPacked] 280 iterations done. 2559756378 characters processed. [BWTIncConstructFromPacked] 290 iterations done. 2599656394 characters processed. [BWTIncConstructFromPacked] 300 iterations done. 2635115610 characters processed. [BWTIncConstructFromPacked] 310 iterations done. 2666627818 characters processed. [BWTIncConstructFromPacked] 320 iterations done. 2694631930 characters processed. [BWTIncConstructFromPacked] 330 iterations done. 2719518026 characters processed. [BWTIncConstructFromPacked] 340 iterations done. 2741632810 characters processed. [bwt_gen] Finished constructing BWT in 343 iterations. [bwa_index] 861.30 seconds elapse. [bwa_index] Update BWT... 6.25 sec [bwa_index] Pack forward-only FASTA... 4.97 sec [bwa_index] Construct SA from BWT and Occ... 303.00 sec [main] Version: 0.7.17-r1188 [main] CMD: bwa index /share/data/umw_biocore/dnext_data/genome_data_other/cellrangeratac/zebrafish/GRCz11_v4.3.2/GRCz11_v4.3.2/fasta/genome.fa [main] Real time: 1196.084 sec; CPU: 1184.051 sec done Copying original pfm file into reference folder... done Finishing up... >>> Reference successfully created! <<< ------------------------------------------------------------ Sender: LSF System Subject: Job 2025008: in cluster Done Job was submitted from host by user in cluster at Fri Dec 11 16:08:28 2020 Job was executed on host(s) <4*c39b14>, in queue , as user in cluster at Fri Dec 11 16:08:31 2020 <2*c39b12> was used as the home directory. was used as the working directory. Started at Fri Dec 11 16:08:31 2020 Terminated at Fri Dec 11 16:29:36 2020 Results reported at Fri Dec 11 16:29:36 2020 Your job looked like: ------------------------------------------------------------ # LSBATCH: User input module load singularity/singularity-3.4.0 && cd /share/data/umw_biocore/genome_data/cellrangeratac/zebrafish/GRCz11_v4.3.2 && singularity exec -B /share /project/umw_biocore/singularity/UMMS-Biocore-singularity-cellranger-v3.simg cellranger-atac mkref GRCz11_v4.3.2 --config config_primary.txt ------------------------------------------------------------ Successfully completed. Resource usage summary: CPU time : 1235.24 sec. Max Memory : 2065 MB Average Memory : 1021.76 MB Total Requested Memory : 120288.00 MB Delta Memory : 118223.00 MB Max Swap : - Max Processes : 8 Max Threads : 22 Run time : 1270 sec. Turnaround time : 1268 sec. The output (if any) is above this job summary. singularity singularity-3.4.0 is located under /share/pkg/singularity/singularity-3.4.0 cellranger-atac mkref (1.2.0) Copyright (c) 2019 10x Genomics, Inc. All rights reserved. ------------------------------------------------------------------------------- Non-standard genome name detected, building custom reference... >>> Creating reference for GRCz11_v4.3.2 <<< Destination reference folder already exists: /share/data/umw_biocore/dnext_data/genome_data_other/cellrangeratac/zebrafish/GRCz11_v4.3.2/GRCz11_v4.3.2 /share/data/umw_biocore/dnext_data/genome_data_other/cellrangeratac/zebrafish/GRCz11_v4.3.2/GRCz11_v4.3.2/fasta/genome.fa file already exists! Skip fetching from source... Generating samtools index... done Generating pyfasta indexes... Number of contigs: 998 Total genome size: 1373475517 done /share/data/umw_biocore/dnext_data/genome_data_other/cellrangeratac/zebrafish/GRCz11_v4.3.2/GRCz11_v4.3.2/genes/genes.gtf file already exists! Skip fetching from source... Writing TSS and transcripts bed file... /share/data/umw_biocore/dnext_data/genome_data_other/cellrangeratac/zebrafish/GRCz11_v4.3.2/GRCz11_v4.3.2/regions/tss.bed file already exists! Skip parsing from gene annotation... Parsed 81819 unique TSS. Parsed 95543 unique transcripts. done Generating bwa index (may take over an hour for a 3Gb genome)... [bwa_index] Pack FASTA... 8.41 sec [bwa_index] Construct BWT for the packed sequence... [BWTIncCreate] textLength=2746951034, availableWord=205285296 [BWTIncConstructFromPacked] 10 iterations done. 99999994 characters processed. [BWTIncConstructFromPacked] 20 iterations done. 199999994 characters processed. [BWTIncConstructFromPacked] 30 iterations done. 299999994 characters processed. [BWTIncConstructFromPacked] 40 iterations done. 399999994 characters processed. [BWTIncConstructFromPacked] 50 iterations done. 499999994 characters processed. [BWTIncConstructFromPacked] 60 iterations done. 599999994 characters processed. [BWTIncConstructFromPacked] 70 iterations done. 699999994 characters processed. [BWTIncConstructFromPacked] 80 iterations done. 799999994 characters processed. [BWTIncConstructFromPacked] 90 iterations done. 899999994 characters processed. [BWTIncConstructFromPacked] 100 iterations done. 999999994 characters processed. [BWTIncConstructFromPacked] 110 iterations done. 1099999994 characters processed. [BWTIncConstructFromPacked] 120 iterations done. 1199999994 characters processed. [BWTIncConstructFromPacked] 130 iterations done. 1299999994 characters processed. [BWTIncConstructFromPacked] 140 iterations done. 1399999994 characters processed. [BWTIncConstructFromPacked] 150 iterations done. 1499999994 characters processed. [BWTIncConstructFromPacked] 160 iterations done. 1599999994 characters processed. [BWTIncConstructFromPacked] 170 iterations done. 1699999994 characters processed. [BWTIncConstructFromPacked] 180 iterations done. 1799999994 characters processed. [BWTIncConstructFromPacked] 190 iterations done. 1899999994 characters processed. [BWTIncConstructFromPacked] 200 iterations done. 1999999994 characters processed. [BWTIncConstructFromPacked] 210 iterations done. 2099494330 characters processed. [BWTIncConstructFromPacked] 220 iterations done. 2190602426 characters processed. [BWTIncConstructFromPacked] 230 iterations done. 2271575530 characters processed. [BWTIncConstructFromPacked] 240 iterations done. 2343540618 characters processed. [BWTIncConstructFromPacked] 250 iterations done. 2407499370 characters processed. [BWTIncConstructFromPacked] 260 iterations done. 2464342042 characters processed. [BWTIncConstructFromPacked] 270 iterations done. 2514859930 characters processed. [BWTIncConstructFromPacked] 280 iterations done. 2559756378 characters processed. [BWTIncConstructFromPacked] 290 iterations done. 2599656394 characters processed. [BWTIncConstructFromPacked] 300 iterations done. 2635115610 characters processed. [BWTIncConstructFromPacked] 310 iterations done. 2666627818 characters processed. [BWTIncConstructFromPacked] 320 iterations done. 2694631930 characters processed. [BWTIncConstructFromPacked] 330 iterations done. 2719518026 characters processed. [BWTIncConstructFromPacked] 340 iterations done. 2741632810 characters processed. [bwt_gen] Finished constructing BWT in 343 iterations. [bwa_index] 837.93 seconds elapse. [bwa_index] Update BWT... 5.93 sec [bwa_index] Pack forward-only FASTA... 4.96 sec [bwa_index] Construct SA from BWT and Occ... 302.61 sec [main] Version: 0.7.17-r1188 [main] CMD: bwa index /share/data/umw_biocore/dnext_data/genome_data_other/cellrangeratac/zebrafish/GRCz11_v4.3.2/GRCz11_v4.3.2/fasta/genome.fa [main] Real time: 1182.131 sec; CPU: 1159.679 sec done /share/data/umw_biocore/dnext_data/genome_data_other/cellrangeratac/zebrafish/GRCz11_v4.3.2/GRCz11_v4.3.2/regions/motifs.pfm file already exists! Skip fetching from source... Finishing up... >>> Reference successfully created! <<< ------------------------------------------------------------ Sender: LSF System Subject: Job 2026182: in cluster Done Job was submitted from host by user in cluster at Fri Dec 11 16:44:35 2020 Job was executed on host(s) <2*c39b14>, in queue , as user in cluster at Fri Dec 11 16:45:09 2020 <2*c40b03> <1*c40b07> <1*c40b13> was used as the home directory. was used as the working directory. Started at Fri Dec 11 16:45:09 2020 Terminated at Fri Dec 11 17:05:16 2020 Results reported at Fri Dec 11 17:05:16 2020 Your job looked like: ------------------------------------------------------------ # LSBATCH: User input module load singularity/singularity-3.4.0 && cd /share/data/umw_biocore/genome_data/cellrangeratac/zebrafish/GRCz11_v4.3.2 && singularity exec -B /share /project/umw_biocore/singularity/UMMS-Biocore-singularity-cellranger-v3.simg cellranger-atac mkref GRCz11_v4.3.2 --config config_primary.txt ------------------------------------------------------------ Successfully completed. Resource usage summary: CPU time : 1175.11 sec. Max Memory : 2046 MB Average Memory : 928.71 MB Total Requested Memory : 120288.00 MB Delta Memory : 118242.00 MB Max Swap : - Max Processes : 8 Max Threads : 22 Run time : 1216 sec. Turnaround time : 1241 sec. The output (if any) is above this job summary. singularity singularity-3.4.0 is located under /share/pkg/singularity/singularity-3.4.0 cellranger-atac mkref (1.2.0) Copyright (c) 2019 10x Genomics, Inc. All rights reserved. ------------------------------------------------------------------------------- Non-standard genome name detected, building custom reference... >>> Creating reference for GRCz11_v4.3.2 <<< Creating new reference folder at /share/data/umw_biocore/dnext_data/genome_data_other/cellrangeratac/zebrafish/GRCz11_v4.3.2/GRCz11_v4.3.2 Copying original fasta file into reference folder... done Generating samtools index... done Generating pyfasta indexes... Number of contigs: 998 Total genome size: 1373475517 done Copying original gene annotation file into reference folder... done Writing TSS and transcripts bed file... Parsed 81819 unique TSS and 95543 unique transcripts. done Generating bwa index (may take over an hour for a 3Gb genome)... [bwa_index] Pack FASTA... 7.77 sec [bwa_index] Construct BWT for the packed sequence... [BWTIncCreate] textLength=2746951034, availableWord=205285296 [BWTIncConstructFromPacked] 10 iterations done. 99999994 characters processed. [BWTIncConstructFromPacked] 20 iterations done. 199999994 characters processed. [BWTIncConstructFromPacked] 30 iterations done. 299999994 characters processed. [BWTIncConstructFromPacked] 40 iterations done. 399999994 characters processed. [BWTIncConstructFromPacked] 50 iterations done. 499999994 characters processed. [BWTIncConstructFromPacked] 60 iterations done. 599999994 characters processed. [BWTIncConstructFromPacked] 70 iterations done. 699999994 characters processed. [BWTIncConstructFromPacked] 80 iterations done. 799999994 characters processed. [BWTIncConstructFromPacked] 90 iterations done. 899999994 characters processed. [BWTIncConstructFromPacked] 100 iterations done. 999999994 characters processed. [BWTIncConstructFromPacked] 110 iterations done. 1099999994 characters processed. [BWTIncConstructFromPacked] 120 iterations done. 1199999994 characters processed. [BWTIncConstructFromPacked] 130 iterations done. 1299999994 characters processed. [BWTIncConstructFromPacked] 140 iterations done. 1399999994 characters processed. [BWTIncConstructFromPacked] 150 iterations done. 1499999994 characters processed. [BWTIncConstructFromPacked] 160 iterations done. 1599999994 characters processed. [BWTIncConstructFromPacked] 170 iterations done. 1699999994 characters processed. [BWTIncConstructFromPacked] 180 iterations done. 1799999994 characters processed. [BWTIncConstructFromPacked] 190 iterations done. 1899999994 characters processed. [BWTIncConstructFromPacked] 200 iterations done. 1999999994 characters processed. [BWTIncConstructFromPacked] 210 iterations done. 2099494330 characters processed. [BWTIncConstructFromPacked] 220 iterations done. 2190602426 characters processed. [BWTIncConstructFromPacked] 230 iterations done. 2271575530 characters processed. [BWTIncConstructFromPacked] 240 iterations done. 2343540618 characters processed. [BWTIncConstructFromPacked] 250 iterations done. 2407499370 characters processed. [BWTIncConstructFromPacked] 260 iterations done. 2464342042 characters processed. [BWTIncConstructFromPacked] 270 iterations done. 2514859930 characters processed. [BWTIncConstructFromPacked] 280 iterations done. 2559756378 characters processed. [BWTIncConstructFromPacked] 290 iterations done. 2599656394 characters processed. [BWTIncConstructFromPacked] 300 iterations done. 2635115610 characters processed. [BWTIncConstructFromPacked] 310 iterations done. 2666627818 characters processed. [BWTIncConstructFromPacked] 320 iterations done. 2694631930 characters processed. [BWTIncConstructFromPacked] 330 iterations done. 2719518026 characters processed. [BWTIncConstructFromPacked] 340 iterations done. 2741632810 characters processed. [bwt_gen] Finished constructing BWT in 343 iterations. [bwa_index] 745.49 seconds elapse. [bwa_index] Update BWT... 5.49 sec [bwa_index] Pack forward-only FASTA... 4.60 sec [bwa_index] Construct SA from BWT and Occ... 284.98 sec [main] Version: 0.7.17-r1188 [main] CMD: bwa index /share/data/umw_biocore/dnext_data/genome_data_other/cellrangeratac/zebrafish/GRCz11_v4.3.2/GRCz11_v4.3.2/fasta/genome.fa [main] Real time: 1060.143 sec; CPU: 1048.188 sec done Copying original pfm file into reference folder... done Finishing up... >>> Reference successfully created! <<< ------------------------------------------------------------ Sender: LSF System Subject: Job 2027693: in cluster Done Job was submitted from host by user in cluster at Fri Dec 11 17:21:35 2020 Job was executed on host(s) <6*c40b15>, in queue , as user in cluster at Fri Dec 11 17:21:36 2020 was used as the home directory. was used as the working directory. Started at Fri Dec 11 17:21:36 2020 Terminated at Fri Dec 11 17:40:18 2020 Results reported at Fri Dec 11 17:40:18 2020 Your job looked like: ------------------------------------------------------------ # LSBATCH: User input module load singularity/singularity-3.4.0 && cd /share/data/umw_biocore/genome_data/cellrangeratac/zebrafish/GRCz11_v4.3.2 && singularity exec -B /share /project/umw_biocore/singularity/UMMS-Biocore-singularity-cellranger-v3.simg cellranger-atac mkref GRCz11_v4.3.2 --config config_primary.txt ------------------------------------------------------------ Successfully completed. Resource usage summary: CPU time : 1093.77 sec. Max Memory : 2066 MB Average Memory : 1023.16 MB Total Requested Memory : 120288.00 MB Delta Memory : 118222.00 MB Max Swap : - Max Processes : 8 Max Threads : 23 Run time : 1134 sec. Turnaround time : 1123 sec. The output (if any) is above this job summary.