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Log of PLASS assembly
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| assemble data/clean_reads/concatenated//pacman_forward.fastq.gz data/clean_reads/concatenated//pacman_reverse.fastq.gz /mnt/lustre/scratch/aobiol/Experiments/PACMAN/plass/pacman_coassembly.faa tmp | |
| MMseqs Version: 5d03cce371dc51c23652a251550c33fd0358690d | |
| Substitution matrix nucl:nucleotide.out,aa:blosum62.out | |
| Rescore mode 3 | |
| Allow wrapped scoring false | |
| Remove hits by seq. id. and coverage false | |
| E-value threshold 1e-05 | |
| Coverage threshold 0 | |
| Add backtrace false | |
| Coverage mode 0 | |
| Seq. id. threshold 0.9 | |
| Min alignment length 0 | |
| Seq. id. mode 0 | |
| Include identical seq. id. false | |
| Sort results 0 | |
| Preload mode 0 | |
| Threads 48 | |
| Compressed 0 | |
| Verbosity 3 | |
| Alphabet size 13 | |
| k-mers per sequence 60 | |
| Spaced k-mers 0 | |
| Spaced k-mer pattern | |
| Scale k-mers per sequence nucl:0.200,aa:0.000 | |
| Adjust k-mer length false | |
| Mask residues 0 | |
| Mask lower case residues 0 | |
| k-mer length 14 | |
| Max sequence length 65535 | |
| Shift hash 67 | |
| Split memory limit 0 | |
| Include only extendable true | |
| Skip repeating k-mers true | |
| Min codons in orf 45 | |
| Max codons in length 32734 | |
| Max orf gaps 2147483647 | |
| Contig start mode 2 | |
| Contig end mode 2 | |
| Orf start mode 1 | |
| Forward frames 1,2,3 | |
| Reverse frames 1,2,3 | |
| Translation table 1 | |
| Translate orf 0 | |
| Use all table starts false | |
| Offset of numeric ids 0 | |
| Create lookup 0 | |
| Protein Filter Threshold 0.2 | |
| Filter Proteins 1 | |
| Search iterations 12 | |
| Delete temporary files incremental 1 | |
| Remove temporary files false | |
| MPI runner | |
| Database type 0 | |
| Shuffle input database true | |
| Createdb mode 0 | |
| Write lookup file 1 | |
| Path tmp does not exist or is not a directory. | |
| Created directory tmp | |
| PAIRED END MODE | |
| mergereads data/clean_reads/concatenated//pacman_forward.fastq.gz data/clean_reads/concatenated//pacman_reverse.fastq.gz /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/nucl_reads -v 3 | |
| Start merging reads. | |
| Time for merging to nucl_reads: 0h 1m 29s 889ms | |
| Time for merging to nucl_reads_h: 0h 1m 22s 208ms | |
| Done. | |
| Time for processing: 0h 45m 6s 200ms | |
| Tmp /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp folder does not exist or is not a directory. | |
| Create dir /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp | |
| assembledb /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/nucl_reads /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp --rescore-mode 3 -e 1e-05 -c 0 --min-seq-id 0.9 --alph-size 13 --kmer-per-seq 60 --spaced-kmer-mode 0 --mask 0 -k 14 --include-only-extendable 1 --ignore-multi-kmer 1 --min-length 45 --num-iterations 12 | |
| extractorfs /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/nucl_reads /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/nucl_6f_start --min-length 20 --max-length 45 --max-gaps 0 --contig-start-mode 1 --contig-end-mode 0 --orf-start-mode 0 --forward-frames 1,2,3 --reverse-frames 1,2,3 --translation-table 1 --translate 0 --use-all-table-starts 0 --id-offset 0 --create-lookup 0 --threads 48 --compressed 0 -v 3 | |
| [=================================================================] 413.89M 4m 21s 939ms | |
| Time for merging to nucl_6f_start_h: 0h 0m 31s 471ms | |
| Time for merging to nucl_6f_start: 0h 0m 39s 0ms | |
| Time for processing: 0h 6m 24s 482ms | |
| translatenucs /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/nucl_6f_start /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/aa_6f_start --translation-table 1 --add-orf-stop 1 -v 3 --compressed 0 --threads 48 | |
| [=================================================================] 56.95M 27s 31ms | |
| Time for merging to aa_6f_start: 0h 0m 31s 362ms | |
| Time for processing: 0h 1m 3s 725ms | |
| extractorfs /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/nucl_reads /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/nucl_6f_long --min-length 45 --max-length 32734 --max-gaps 0 --contig-start-mode 2 --contig-end-mode 2 --orf-start-mode 0 --forward-frames 1,2,3 --reverse-frames 1,2,3 --translation-table 1 --translate 0 --use-all-table-starts 0 --id-offset 0 --create-lookup 0 --threads 48 --compressed 0 -v 3 | |
| [=================================================================] 413.89M 8m 11s 331ms | |
| Time for merging to nucl_6f_long_h: 0h 3m 58s 114ms | |
| Time for merging to nucl_6f_long: 0h 6m 5s 178ms | |
| Time for processing: 0h 20m 43s 217ms | |
| translatenucs /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/nucl_6f_long /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/aa_6f_long --translation-table 1 --add-orf-stop 1 -v 3 --compressed 0 --threads 48 | |
| [=================================================================] 327.65M 3m 21s 207ms | |
| Time for merging to aa_6f_long: 0h 3m 58s 115ms | |
| Time for processing: 0h 7m 45s 624ms | |
| concatdbs /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/aa_6f_long /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/aa_6f_start /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/aa_6f_start_long -v 3 | |
| [=================================================================] 327.65M 4m 18s 305ms | |
| [=================================================================] 56.95M 4m 55s 845ms | |
| Time for merging to aa_6f_start_long: 0h 2m 25s 871ms | |
| Time for processing: 0h 8m 52s 976ms | |
| concatdbs /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/nucl_6f_long_h /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/nucl_6f_start_h /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/aa_6f_start_long_h -v 3 | |
| [=================================================================] 327.65M 1m 53s 726ms | |
| [=================================================================] 56.95M 2m 18s 526ms | |
| Time for merging to aa_6f_start_long_h: 0h 1m 23s 763ms | |
| Time for processing: 0h 4m 51s 148ms | |
| STEP: 0 | |
| kmermatcher /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/aa_6f_start_long /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/pref_0 --sub-mat nucl:nucleotide.out,aa:blosum62.out --alph-size 13 --min-seq-id 0.9 --kmer-per-seq 60 --spaced-kmer-mode 0 --kmer-per-seq-scale nucl:0.200,aa:0.000 --adjust-kmer-len 0 --mask 0 --mask-lower-case 0 --cov-mode 0 -k 14 -c 0 --max-seq-len 65535 --hash-shift 67 --split-memory-limit 0 --include-only-extendable 1 --ignore-multi-kmer 1 --threads 48 --compressed 0 -v 3 | |
| kmermatcher /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/aa_6f_start_long /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/pref_0 --sub-mat nucl:nucleotide.out,aa:blosum62.out --alph-size 13 --min-seq-id 0.9 --kmer-per-seq 60 --spaced-kmer-mode 0 --kmer-per-seq-scale nucl:0.200,aa:0.000 --adjust-kmer-len 0 --mask 0 --mask-lower-case 0 --cov-mode 0 -k 14 -c 0 --max-seq-len 65535 --hash-shift 67 --split-memory-limit 0 --include-only-extendable 1 --ignore-multi-kmer 1 --threads 48 --compressed 0 -v 3 | |
| Database size: 384600802 type: Aminoacid | |
| Reduced amino acid alphabet: (A S T) (C) (D B N) (E Q Z) (F Y) (G) (H) (I V) (K R) (L J M) (P) (W) (X) | |
| Generate k-mers list for 1 split | |
| [=================================================================] 384.60M 4m 3s 224ms | |
| Sort kmer 0h 2m 41s 203ms | |
| Sort by rep. sequence 0h 0m 45s 182ms | |
| Time for fill: 0h 1m 44s 165ms | |
| Time for merging to pref_0: 0h 0m 0s 6ms | |
| Time for processing: 0h 14m 44s 711ms | |
| rescorediagonal /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/aa_6f_start_long /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/aa_6f_start_long /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/pref_0 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/aln_0 --sub-mat nucl:nucleotide.out,aa:blosum62.out --rescore-mode 3 --wrapped-scoring 0 --filter-hits 0 -e 1e-05 -c 0 -a 0 --cov-mode 0 --min-seq-id 0.9 --min-aln-len 0 --seq-id-mode 0 --add-self-matches 0 --sort-results 0 --db-load-mode 0 --threads 48 --compressed 0 -v 3 | |
| [=================================================================] 384.60M 4m 3s 315ms | |
| Time for merging to aln_0: 0h 4m 52s 466ms | |
| Time for processing: 0h 13m 35s 287ms | |
| findassemblystart /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/aa_6f_start_long /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/aln_0 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/corrected_seqs --threads 48 -v 3 | |
| [=================================================================] 384.60M 1m 19s 841ms | |
| Time for merging to corrected_seqs: 0h 4m 56s 730ms | |
| Time for processing: 0h 9m 13s 897ms | |
| kmermatcher /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/corrected_seqs /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/pref_corrected_0 --sub-mat nucl:nucleotide.out,aa:blosum62.out --alph-size 13 --min-seq-id 0.9 --kmer-per-seq 60 --spaced-kmer-mode 0 --kmer-per-seq-scale nucl:0.200,aa:0.000 --adjust-kmer-len 0 --mask 0 --mask-lower-case 0 --cov-mode 0 -k 14 -c 0 --max-seq-len 65535 --hash-shift 67 --split-memory-limit 0 --include-only-extendable 1 --ignore-multi-kmer 1 --threads 48 --compressed 0 -v 3 | |
| kmermatcher /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/corrected_seqs /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/pref_corrected_0 --sub-mat nucl:nucleotide.out,aa:blosum62.out --alph-size 13 --min-seq-id 0.9 --kmer-per-seq 60 --spaced-kmer-mode 0 --kmer-per-seq-scale nucl:0.200,aa:0.000 --adjust-kmer-len 0 --mask 0 --mask-lower-case 0 --cov-mode 0 -k 14 -c 0 --max-seq-len 65535 --hash-shift 67 --split-memory-limit 0 --include-only-extendable 1 --ignore-multi-kmer 1 --threads 48 --compressed 0 -v 3 | |
| Database size: 384600802 type: Aminoacid | |
| Reduced amino acid alphabet: (A S T) (C) (D B N) (E Q Z) (F Y) (G) (H) (I V) (K R) (L J M) (P) (W) (X) | |
| Generate k-mers list for 1 split | |
| [=================================================================] 384.60M 2m 12s 635ms | |
| Sort kmer 0h 2m 36s 227ms | |
| Sort by rep. sequence 0h 0m 43s 362ms | |
| Time for fill: 0h 1m 30s 741ms | |
| Time for merging to pref_corrected_0: 0h 0m 0s 8ms | |
| Time for processing: 0h 12m 3s 748ms | |
| rmdb /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/pref_0 | |
| Time for processing: 0h 0m 0s 2ms | |
| rescorediagonal /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/corrected_seqs /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/corrected_seqs /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/pref_corrected_0 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/aln_corrected_0 --sub-mat nucl:nucleotide.out,aa:blosum62.out --rescore-mode 3 --wrapped-scoring 0 --filter-hits 0 -e 1e-05 -c 0 -a 0 --cov-mode 0 --min-seq-id 0.9 --min-aln-len 0 --seq-id-mode 0 --add-self-matches 0 --sort-results 0 --db-load-mode 0 --threads 48 --compressed 0 -v 3 | |
| [=================================================================] 384.60M 47m 31s 475ms | |
| Time for merging to aln_corrected_0: 0h 4m 13s 47ms | |
| Time for processing: 0h 53m 47s 650ms | |
| rmdb /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/aln_0 | |
| Time for processing: 0h 0m 0s 572ms | |
| assembleresults /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/corrected_seqs /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/aln_corrected_0 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_0 --min-seq-id 0.9 --max-seq-len 65535 --threads 48 -v 3 --rescore-mode 3 | |
| Compute assembly. | |
| [=================================================================] 384.60M 2m 13s 139ms | |
| Time for merging to assembly_0: 0h 5m 47s 284ms | |
| Done. | |
| Time for processing: 0h 11m 39s 984ms | |
| rmdb /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/corrected_seqs | |
| Time for processing: 0h 0m 5s 242ms | |
| STEP: 1 | |
| kmermatcher /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_0 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/pref_1 --sub-mat nucl:nucleotide.out,aa:blosum62.out --alph-size 13 --min-seq-id 0.9 --kmer-per-seq 60 --spaced-kmer-mode 0 --kmer-per-seq-scale nucl:0.200,aa:0.000 --adjust-kmer-len 0 --mask 0 --mask-lower-case 0 --cov-mode 0 -k 14 -c 0 --max-seq-len 65535 --hash-shift 68 --split-memory-limit 0 --include-only-extendable 1 --ignore-multi-kmer 1 --threads 48 --compressed 0 -v 3 | |
| kmermatcher /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_0 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/pref_1 --sub-mat nucl:nucleotide.out,aa:blosum62.out --alph-size 13 --min-seq-id 0.9 --kmer-per-seq 60 --spaced-kmer-mode 0 --kmer-per-seq-scale nucl:0.200,aa:0.000 --adjust-kmer-len 0 --mask 0 --mask-lower-case 0 --cov-mode 0 -k 14 -c 0 --max-seq-len 65535 --hash-shift 68 --split-memory-limit 0 --include-only-extendable 1 --ignore-multi-kmer 1 --threads 48 --compressed 0 -v 3 | |
| Database size: 384600802 type: Aminoacid | |
| Reduced amino acid alphabet: (A S T) (C) (D B N) (E Q Z) (F Y) (G) (H) (I V) (K R) (L J M) (P) (W) (X) | |
| Generate k-mers list for 1 split | |
| [=================================================================] 384.60M 2m 51s 134ms | |
| Sort kmer 0h 2m 41s 884ms | |
| Sort by rep. sequence 0h 0m 19s 922ms | |
| Time for fill: 0h 1m 41s 851ms | |
| Time for merging to pref_1: 0h 0m 0s 6ms | |
| Time for processing: 0h 12m 53s 233ms | |
| rmdb /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/pref_corrected_0 | |
| Time for processing: 0h 0m 0s 97ms | |
| rescorediagonal /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_0 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_0 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/pref_1 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/aln_1 --sub-mat nucl:nucleotide.out,aa:blosum62.out --rescore-mode 3 --wrapped-scoring 0 --filter-hits 0 -e 1e-05 -c 0 -a 0 --cov-mode 0 --min-seq-id 0.9 --min-aln-len 0 --seq-id-mode 0 --add-self-matches 0 --sort-results 0 --db-load-mode 0 --threads 48 --compressed 0 -v 3 | |
| [=================================================================] 384.60M 4m 47s 149ms | |
| Time for merging to aln_1: 0h 3m 52s 87ms | |
| Time for processing: 0h 12m 21s 977ms | |
| rmdb /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/aln_corrected_0 | |
| Time for processing: 0h 0m 0s 145ms | |
| assembleresults /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_0 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/aln_1 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_1 --min-seq-id 0.9 --max-seq-len 65535 --threads 48 -v 3 --rescore-mode 3 | |
| Compute assembly. | |
| [=================================================================] 384.60M 1m 26s 777ms | |
| Time for merging to assembly_1: 0h 5m 56s 200ms | |
| Done. | |
| Time for processing: 0h 9m 20s 371ms | |
| rmdb /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_0 | |
| Time for processing: 0h 0m 7s 16ms | |
| STEP: 2 | |
| kmermatcher /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_1 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/pref_2 --sub-mat nucl:nucleotide.out,aa:blosum62.out --alph-size 13 --min-seq-id 0.9 --kmer-per-seq 60 --spaced-kmer-mode 0 --kmer-per-seq-scale nucl:0.200,aa:0.000 --adjust-kmer-len 0 --mask 0 --mask-lower-case 0 --cov-mode 0 -k 14 -c 0 --max-seq-len 65535 --hash-shift 68 --split-memory-limit 0 --include-only-extendable 1 --ignore-multi-kmer 1 --threads 48 --compressed 0 -v 3 | |
| kmermatcher /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_1 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/pref_2 --sub-mat nucl:nucleotide.out,aa:blosum62.out --alph-size 13 --min-seq-id 0.9 --kmer-per-seq 60 --spaced-kmer-mode 0 --kmer-per-seq-scale nucl:0.200,aa:0.000 --adjust-kmer-len 0 --mask 0 --mask-lower-case 0 --cov-mode 0 -k 14 -c 0 --max-seq-len 65535 --hash-shift 68 --split-memory-limit 0 --include-only-extendable 1 --ignore-multi-kmer 1 --threads 48 --compressed 0 -v 3 | |
| Database size: 384600802 type: Aminoacid | |
| Reduced amino acid alphabet: (A S T) (C) (D B N) (E Q Z) (F Y) (G) (H) (I V) (K R) (L J M) (P) (W) (X) | |
| Generate k-mers list for 1 split | |
| [=================================================================] 384.60M 3m 58s 493ms | |
| Sort kmer 0h 2m 43s 24ms | |
| Sort by rep. sequence 0h 0m 14s 56ms | |
| Time for fill: 0h 1m 21s 810ms | |
| Time for merging to pref_2: 0h 0m 0s 8ms | |
| Time for processing: 0h 13m 7s 719ms | |
| rmdb /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/pref_1 | |
| Time for processing: 0h 0m 0s 2ms | |
| rescorediagonal /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_1 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_1 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/pref_2 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/aln_2 --sub-mat nucl:nucleotide.out,aa:blosum62.out --rescore-mode 3 --wrapped-scoring 0 --filter-hits 0 -e 1e-05 -c 0 -a 0 --cov-mode 0 --min-seq-id 0.9 --min-aln-len 0 --seq-id-mode 0 --add-self-matches 0 --sort-results 0 --db-load-mode 0 --threads 48 --compressed 0 -v 3 | |
| [=================================================================] 384.60M 3m 9s 291ms | |
| Time for merging to aln_2: 0h 3m 23s 399ms | |
| Time for processing: 0h 9m 8s 257ms | |
| rmdb /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/aln_1 | |
| Time for processing: 0h 0m 0s 24ms | |
| assembleresults /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_1 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/aln_2 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_2 --min-seq-id 0.9 --max-seq-len 65535 --threads 48 -v 3 --rescore-mode 3 | |
| Compute assembly. | |
| [=================================================================] 384.60M 1m 19s 205ms | |
| Time for merging to assembly_2: 0h 4m 43s 201ms | |
| Done. | |
| Time for processing: 0h 7m 29s 466ms | |
| rmdb /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_1 | |
| Time for processing: 0h 0m 0s 2ms | |
| STEP: 3 | |
| kmermatcher /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_2 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/pref_3 --sub-mat nucl:nucleotide.out,aa:blosum62.out --alph-size 13 --min-seq-id 0.9 --kmer-per-seq 60 --spaced-kmer-mode 0 --kmer-per-seq-scale nucl:0.200,aa:0.000 --adjust-kmer-len 0 --mask 0 --mask-lower-case 0 --cov-mode 0 -k 14 -c 0 --max-seq-len 65535 --hash-shift 69 --split-memory-limit 0 --include-only-extendable 1 --ignore-multi-kmer 1 --threads 48 --compressed 0 -v 3 | |
| kmermatcher /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_2 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/pref_3 --sub-mat nucl:nucleotide.out,aa:blosum62.out --alph-size 13 --min-seq-id 0.9 --kmer-per-seq 60 --spaced-kmer-mode 0 --kmer-per-seq-scale nucl:0.200,aa:0.000 --adjust-kmer-len 0 --mask 0 --mask-lower-case 0 --cov-mode 0 -k 14 -c 0 --max-seq-len 65535 --hash-shift 69 --split-memory-limit 0 --include-only-extendable 1 --ignore-multi-kmer 1 --threads 48 --compressed 0 -v 3 | |
| Database size: 384600802 type: Aminoacid | |
| Reduced amino acid alphabet: (A S T) (C) (D B N) (E Q Z) (F Y) (G) (H) (I V) (K R) (L J M) (P) (W) (X) | |
| Generate k-mers list for 1 split | |
| [=================================================================] 384.60M 3m 10s 972ms | |
| Sort kmer 0h 2m 45s 19ms | |
| Sort by rep. sequence 0h 0m 12s 511ms | |
| Time for fill: 0h 2m 1s 672ms | |
| Time for merging to pref_3: 0h 0m 0s 5ms | |
| Time for processing: 0h 13m 42s 150ms | |
| rmdb /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/pref_2 | |
| Time for processing: 0h 0m 0s 2ms | |
| rescorediagonal /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_2 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_2 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/pref_3 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/aln_3 --sub-mat nucl:nucleotide.out,aa:blosum62.out --rescore-mode 3 --wrapped-scoring 0 --filter-hits 0 -e 1e-05 -c 0 -a 0 --cov-mode 0 --min-seq-id 0.9 --min-aln-len 0 --seq-id-mode 0 --add-self-matches 0 --sort-results 0 --db-load-mode 0 --threads 48 --compressed 0 -v 3 | |
| [=================================================================] 384.60M 5m 26s 120ms | |
| Time for merging to aln_3: 0h 4m 7s 414ms | |
| Time for processing: 0h 15m 6s 705ms | |
| rmdb /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/aln_2 | |
| Time for processing: 0h 0m 0s 34ms | |
| assembleresults /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_2 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/aln_3 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_3 --min-seq-id 0.9 --max-seq-len 65535 --threads 48 -v 3 --rescore-mode 3 | |
| Compute assembly. | |
| [=================================================================] 384.60M 15m 2s 637ms | |
| Time for merging to assembly_3: 0h 5m 34s 706ms | |
| Done. | |
| Time for processing: 0h 22m 40s 934ms | |
| rmdb /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_2 | |
| Time for processing: 0h 0m 2s 401ms | |
| STEP: 4 | |
| kmermatcher /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_3 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/pref_4 --sub-mat nucl:nucleotide.out,aa:blosum62.out --alph-size 13 --min-seq-id 0.9 --kmer-per-seq 60 --spaced-kmer-mode 0 --kmer-per-seq-scale nucl:0.200,aa:0.000 --adjust-kmer-len 0 --mask 0 --mask-lower-case 0 --cov-mode 0 -k 14 -c 0 --max-seq-len 65535 --hash-shift 69 --split-memory-limit 0 --include-only-extendable 1 --ignore-multi-kmer 1 --threads 48 --compressed 0 -v 3 | |
| kmermatcher /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_3 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/pref_4 --sub-mat nucl:nucleotide.out,aa:blosum62.out --alph-size 13 --min-seq-id 0.9 --kmer-per-seq 60 --spaced-kmer-mode 0 --kmer-per-seq-scale nucl:0.200,aa:0.000 --adjust-kmer-len 0 --mask 0 --mask-lower-case 0 --cov-mode 0 -k 14 -c 0 --max-seq-len 65535 --hash-shift 69 --split-memory-limit 0 --include-only-extendable 1 --ignore-multi-kmer 1 --threads 48 --compressed 0 -v 3 | |
| Database size: 384600802 type: Aminoacid | |
| Reduced amino acid alphabet: (A S T) (C) (D B N) (E Q Z) (F Y) (G) (H) (I V) (K R) (L J M) (P) (W) (X) | |
| Generate k-mers list for 1 split | |
| [=================================================================] 384.60M 4m 28s 144ms | |
| Sort kmer 0h 2m 47s 469ms | |
| Sort by rep. sequence 0h 0m 11s 597ms | |
| Time for fill: 0h 1m 22s 751ms | |
| Time for merging to pref_4: 0h 0m 0s 7ms | |
| Time for processing: 0h 13m 45s 135ms | |
| rmdb /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/pref_3 | |
| Time for processing: 0h 0m 0s 2ms | |
| rescorediagonal /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_3 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_3 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/pref_4 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/aln_4 --sub-mat nucl:nucleotide.out,aa:blosum62.out --rescore-mode 3 --wrapped-scoring 0 --filter-hits 0 -e 1e-05 -c 0 -a 0 --cov-mode 0 --min-seq-id 0.9 --min-aln-len 0 --seq-id-mode 0 --add-self-matches 0 --sort-results 0 --db-load-mode 0 --threads 48 --compressed 0 -v 3 | |
| [=================================================================] 384.60M 2m 58s 837ms | |
| Time for merging to aln_4: 0h 3m 13s 343ms | |
| Time for processing: 0h 12m 49s 741ms | |
| rmdb /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/aln_3 | |
| Time for processing: 0h 0m 0s 17ms | |
| assembleresults /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_3 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/aln_4 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_4 --min-seq-id 0.9 --max-seq-len 65535 --threads 48 -v 3 --rescore-mode 3 | |
| Compute assembly. | |
| [=================================================================] 384.60M 1m 55s 561ms | |
| Time for merging to assembly_4: 0h 4m 57s 438ms | |
| Done. | |
| Time for processing: 0h 8m 46s 149ms | |
| rmdb /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_3 | |
| Time for processing: 0h 0m 6s 2ms | |
| STEP: 5 | |
| kmermatcher /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_4 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/pref_5 --sub-mat nucl:nucleotide.out,aa:blosum62.out --alph-size 13 --min-seq-id 0.9 --kmer-per-seq 60 --spaced-kmer-mode 0 --kmer-per-seq-scale nucl:0.200,aa:0.000 --adjust-kmer-len 0 --mask 0 --mask-lower-case 0 --cov-mode 0 -k 14 -c 0 --max-seq-len 65535 --hash-shift 70 --split-memory-limit 0 --include-only-extendable 1 --ignore-multi-kmer 1 --threads 48 --compressed 0 -v 3 | |
| kmermatcher /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_4 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/pref_5 --sub-mat nucl:nucleotide.out,aa:blosum62.out --alph-size 13 --min-seq-id 0.9 --kmer-per-seq 60 --spaced-kmer-mode 0 --kmer-per-seq-scale nucl:0.200,aa:0.000 --adjust-kmer-len 0 --mask 0 --mask-lower-case 0 --cov-mode 0 -k 14 -c 0 --max-seq-len 65535 --hash-shift 70 --split-memory-limit 0 --include-only-extendable 1 --ignore-multi-kmer 1 --threads 48 --compressed 0 -v 3 | |
| Database size: 384600802 type: Aminoacid | |
| Reduced amino acid alphabet: (A S T) (C) (D B N) (E Q Z) (F Y) (G) (H) (I V) (K R) (L J M) (P) (W) (X) | |
| Generate k-mers list for 1 split | |
| [=================================================================] 384.60M 3m 12s 904ms | |
| Sort kmer 0h 2m 48s 346ms | |
| Sort by rep. sequence 0h 0m 11s 74ms | |
| Time for fill: 0h 2m 7s 635ms | |
| Time for merging to pref_5: 0h 0m 0s 6ms | |
| Time for processing: 0h 13m 49s 689ms | |
| rmdb /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/pref_4 | |
| Time for processing: 0h 0m 0s 2ms | |
| rescorediagonal /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_4 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_4 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/pref_5 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/aln_5 --sub-mat nucl:nucleotide.out,aa:blosum62.out --rescore-mode 3 --wrapped-scoring 0 --filter-hits 0 -e 1e-05 -c 0 -a 0 --cov-mode 0 --min-seq-id 0.9 --min-aln-len 0 --seq-id-mode 0 --add-self-matches 0 --sort-results 0 --db-load-mode 0 --threads 48 --compressed 0 -v 3 | |
| [=================================================================] 384.60M 3m 21s 823ms | |
| Time for merging to aln_5: 0h 3m 27s 701ms | |
| Time for processing: 0h 11m 45s 196ms | |
| rmdb /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/aln_4 | |
| Time for processing: 0h 0m 0s 15ms | |
| assembleresults /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_4 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/aln_5 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_5 --min-seq-id 0.9 --max-seq-len 65535 --threads 48 -v 3 --rescore-mode 3 | |
| Compute assembly. | |
| [=================================================================] 384.60M 1m 13s 388ms | |
| Time for merging to assembly_5: 0h 5m 10s 183ms | |
| Done. | |
| Time for processing: 0h 9m 15s 200ms | |
| rmdb /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_4 | |
| Time for processing: 0h 0m 5s 476ms | |
| STEP: 6 | |
| kmermatcher /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_5 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/pref_6 --sub-mat nucl:nucleotide.out,aa:blosum62.out --alph-size 13 --min-seq-id 0.9 --kmer-per-seq 60 --spaced-kmer-mode 0 --kmer-per-seq-scale nucl:0.200,aa:0.000 --adjust-kmer-len 0 --mask 0 --mask-lower-case 0 --cov-mode 0 -k 14 -c 0 --max-seq-len 65535 --hash-shift 70 --split-memory-limit 0 --include-only-extendable 1 --ignore-multi-kmer 1 --threads 48 --compressed 0 -v 3 | |
| kmermatcher /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_5 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/pref_6 --sub-mat nucl:nucleotide.out,aa:blosum62.out --alph-size 13 --min-seq-id 0.9 --kmer-per-seq 60 --spaced-kmer-mode 0 --kmer-per-seq-scale nucl:0.200,aa:0.000 --adjust-kmer-len 0 --mask 0 --mask-lower-case 0 --cov-mode 0 -k 14 -c 0 --max-seq-len 65535 --hash-shift 70 --split-memory-limit 0 --include-only-extendable 1 --ignore-multi-kmer 1 --threads 48 --compressed 0 -v 3 | |
| Database size: 384600802 type: Aminoacid | |
| Reduced amino acid alphabet: (A S T) (C) (D B N) (E Q Z) (F Y) (G) (H) (I V) (K R) (L J M) (P) (W) (X) | |
| Not enough memory to process at once need to split | |
| [=================================================================] 384.60M 2m 40s 841ms | |
| Process file into 1 parts | |
| Generate k-mers list for 1 split | |
| [=================================================================] 384.60M 3m 23s 17ms | |
| Sort kmer 0h 2m 49s 841ms | |
| Sort by rep. sequence 0h 0m 10s 434ms | |
| Merge splits ... Time for fill: 0h 2m 47s 559ms | |
| Time for merging to pref_6: 0h 0m 0s 4ms | |
| Time for processing: 0h 17m 34s 495ms | |
| rmdb /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/pref_5 | |
| Time for processing: 0h 0m 0s 1ms | |
| rescorediagonal /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_5 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_5 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/pref_6 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/aln_6 --sub-mat nucl:nucleotide.out,aa:blosum62.out --rescore-mode 3 --wrapped-scoring 0 --filter-hits 0 -e 1e-05 -c 0 -a 0 --cov-mode 0 --min-seq-id 0.9 --min-aln-len 0 --seq-id-mode 0 --add-self-matches 0 --sort-results 0 --db-load-mode 0 --threads 48 --compressed 0 -v 3 | |
| [=================================================================] 384.60M 2m 59s 661ms | |
| Time for merging to aln_6: 0h 3m 18s 354ms | |
| Time for processing: 0h 12m 7s 760ms | |
| rmdb /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/aln_5 | |
| Time for processing: 0h 0m 0s 15ms | |
| assembleresults /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_5 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/aln_6 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_6 --min-seq-id 0.9 --max-seq-len 65535 --threads 48 -v 3 --rescore-mode 3 | |
| Compute assembly. | |
| [=================================================================] 384.60M 2m 10s 233ms | |
| Time for merging to assembly_6: 0h 5m 32s 411ms | |
| Done. | |
| Time for processing: 0h 10m 19s 616ms | |
| rmdb /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_5 | |
| Time for processing: 0h 0m 5s 722ms | |
| STEP: 7 | |
| kmermatcher /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_6 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/pref_7 --sub-mat nucl:nucleotide.out,aa:blosum62.out --alph-size 13 --min-seq-id 0.9 --kmer-per-seq 60 --spaced-kmer-mode 0 --kmer-per-seq-scale nucl:0.200,aa:0.000 --adjust-kmer-len 0 --mask 0 --mask-lower-case 0 --cov-mode 0 -k 14 -c 0 --max-seq-len 65535 --hash-shift 71 --split-memory-limit 0 --include-only-extendable 1 --ignore-multi-kmer 1 --threads 48 --compressed 0 -v 3 | |
| kmermatcher /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_6 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/pref_7 --sub-mat nucl:nucleotide.out,aa:blosum62.out --alph-size 13 --min-seq-id 0.9 --kmer-per-seq 60 --spaced-kmer-mode 0 --kmer-per-seq-scale nucl:0.200,aa:0.000 --adjust-kmer-len 0 --mask 0 --mask-lower-case 0 --cov-mode 0 -k 14 -c 0 --max-seq-len 65535 --hash-shift 71 --split-memory-limit 0 --include-only-extendable 1 --ignore-multi-kmer 1 --threads 48 --compressed 0 -v 3 | |
| Database size: 384600802 type: Aminoacid | |
| Reduced amino acid alphabet: (A S T) (C) (D B N) (E Q Z) (F Y) (G) (H) (I V) (K R) (L J M) (P) (W) (X) | |
| Not enough memory to process at once need to split | |
| [=================================================================] 384.60M 2m 30s 723ms | |
| Process file into 1 parts | |
| Generate k-mers list for 1 split | |
| [=================================================================] 384.60M 3m 25s 882ms | |
| Sort kmer 0h 2m 49s 642ms | |
| Sort by rep. sequence 0h 0m 10s 86ms | |
| Merge splits ... Time for fill: 0h 2m 37s 593ms | |
| Time for merging to pref_7: 0h 0m 0s 4ms | |
| Time for processing: 0h 17m 8s 303ms | |
| rmdb /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/pref_6 | |
| Time for processing: 0h 0m 0s 1ms | |
| rescorediagonal /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_6 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_6 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/pref_7 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/aln_7 --sub-mat nucl:nucleotide.out,aa:blosum62.out --rescore-mode 3 --wrapped-scoring 0 --filter-hits 0 -e 1e-05 -c 0 -a 0 --cov-mode 0 --min-seq-id 0.9 --min-aln-len 0 --seq-id-mode 0 --add-self-matches 0 --sort-results 0 --db-load-mode 0 --threads 48 --compressed 0 -v 3 | |
| [=================================================================] 384.60M 4m 17s 60ms | |
| Time for merging to aln_7: 0h 3m 52s 979ms | |
| Time for processing: 0h 10m 55s 309ms | |
| rmdb /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/aln_6 | |
| Time for processing: 0h 0m 0s 220ms | |
| assembleresults /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_6 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/aln_7 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_7 --min-seq-id 0.9 --max-seq-len 65535 --threads 48 -v 3 --rescore-mode 3 | |
| Compute assembly. | |
| [=================================================================] 384.60M 2h 46m 55s 335ms | |
| Time for merging to assembly_7: 0h 5m 50s 113ms | |
| Done. | |
| Time for processing: 2h 54m 33s 851ms | |
| rmdb /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_6 | |
| Time for processing: 0h 0m 7s 805ms | |
| STEP: 8 | |
| kmermatcher /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_7 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/pref_8 --sub-mat nucl:nucleotide.out,aa:blosum62.out --alph-size 13 --min-seq-id 0.9 --kmer-per-seq 60 --spaced-kmer-mode 0 --kmer-per-seq-scale nucl:0.200,aa:0.000 --adjust-kmer-len 0 --mask 0 --mask-lower-case 0 --cov-mode 0 -k 14 -c 0 --max-seq-len 65535 --hash-shift 71 --split-memory-limit 0 --include-only-extendable 1 --ignore-multi-kmer 1 --threads 48 --compressed 0 -v 3 | |
| kmermatcher /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_7 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/pref_8 --sub-mat nucl:nucleotide.out,aa:blosum62.out --alph-size 13 --min-seq-id 0.9 --kmer-per-seq 60 --spaced-kmer-mode 0 --kmer-per-seq-scale nucl:0.200,aa:0.000 --adjust-kmer-len 0 --mask 0 --mask-lower-case 0 --cov-mode 0 -k 14 -c 0 --max-seq-len 65535 --hash-shift 71 --split-memory-limit 0 --include-only-extendable 1 --ignore-multi-kmer 1 --threads 48 --compressed 0 -v 3 | |
| Database size: 384600802 type: Aminoacid | |
| Reduced amino acid alphabet: (A S T) (C) (D B N) (E Q Z) (F Y) (G) (H) (I V) (K R) (L J M) (P) (W) (X) | |
| Not enough memory to process at once need to split | |
| [=================================================================] 384.60M 2m 33s 297ms | |
| Process file into 2 parts | |
| Generate k-mers list for 1 split | |
| [=================================================================] 384.60M 3m 39s 606ms | |
| Sort kmer 0h 2m 50s 760ms | |
| Sort by rep. sequence 0h 0m 9s 694ms | |
| Generate k-mers list for 2 split | |
| [=================================================================] 384.60M 10m 54s 32ms | |
| Sort kmer 0h 0m 0s 268ms | |
| Sort by rep. sequence 0h 0m 0s 43ms | |
| Merge splits ... Time for fill: 0h 2m 48s 760ms | |
| Time for merging to pref_8: 0h 0m 0s 12ms | |
| Time for processing: 0h 28m 47s 284ms | |
| rmdb /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/pref_7 | |
| Time for processing: 0h 0m 0s 252ms | |
| rescorediagonal /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_7 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_7 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/pref_8 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/aln_8 --sub-mat nucl:nucleotide.out,aa:blosum62.out --rescore-mode 3 --wrapped-scoring 0 --filter-hits 0 -e 1e-05 -c 0 -a 0 --cov-mode 0 --min-seq-id 0.9 --min-aln-len 0 --seq-id-mode 0 --add-self-matches 0 --sort-results 0 --db-load-mode 0 --threads 48 --compressed 0 -v 3 | |
| [=================================================================] 384.60M 3m 14s 806ms | |
| Time for merging to aln_8: 0h 3m 52s 28ms | |
| Time for processing: 0h 11m 23s 588ms | |
| rmdb /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/aln_7 | |
| Time for processing: 0h 0m 0s 474ms | |
| assembleresults /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_7 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/aln_8 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_8 --min-seq-id 0.9 --max-seq-len 65535 --threads 48 -v 3 --rescore-mode 3 | |
| Compute assembly. | |
| [=================================================================] 384.60M 3m 37s 234ms | |
| Time for merging to assembly_8: 0h 6m 21s 820ms | |
| Done. | |
| Time for processing: 0h 11m 58s 204ms | |
| rmdb /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_7 | |
| Time for processing: 0h 0m 0s 2ms | |
| STEP: 9 | |
| kmermatcher /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_8 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/pref_9 --sub-mat nucl:nucleotide.out,aa:blosum62.out --alph-size 13 --min-seq-id 0.9 --kmer-per-seq 60 --spaced-kmer-mode 0 --kmer-per-seq-scale nucl:0.200,aa:0.000 --adjust-kmer-len 0 --mask 0 --mask-lower-case 0 --cov-mode 0 -k 14 -c 0 --max-seq-len 65535 --hash-shift 72 --split-memory-limit 0 --include-only-extendable 1 --ignore-multi-kmer 1 --threads 48 --compressed 0 -v 3 | |
| kmermatcher /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_8 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/pref_9 --sub-mat nucl:nucleotide.out,aa:blosum62.out --alph-size 13 --min-seq-id 0.9 --kmer-per-seq 60 --spaced-kmer-mode 0 --kmer-per-seq-scale nucl:0.200,aa:0.000 --adjust-kmer-len 0 --mask 0 --mask-lower-case 0 --cov-mode 0 -k 14 -c 0 --max-seq-len 65535 --hash-shift 72 --split-memory-limit 0 --include-only-extendable 1 --ignore-multi-kmer 1 --threads 48 --compressed 0 -v 3 | |
| Database size: 384600802 type: Aminoacid | |
| Reduced amino acid alphabet: (A S T) (C) (D B N) (E Q Z) (F Y) (G) (H) (I V) (K R) (L J M) (P) (W) (X) | |
| Not enough memory to process at once need to split | |
| [=================================================================] 384.60M 2m 42s 433ms | |
| Process file into 2 parts | |
| Generate k-mers list for 1 split | |
| [=================================================================] 384.60M 4m 52s 990ms | |
| Sort kmer 0h 2m 51s 244ms | |
| Sort by rep. sequence 0h 0m 9s 399ms | |
| Generate k-mers list for 2 split | |
| [=================================================================] 384.60M 9m 19s 81ms | |
| Sort kmer 0h 0m 0s 876ms | |
| Sort by rep. sequence 0h 0m 0s 131ms | |
| Merge splits ... Time for fill: 0h 3m 10s 729ms | |
| Time for merging to pref_9: 0h 0m 0s 9ms | |
| Time for processing: 0h 29m 13s 256ms | |
| rmdb /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/pref_8 | |
| Time for processing: 0h 0m 0s 2ms | |
| rescorediagonal /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_8 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_8 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/pref_9 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/aln_9 --sub-mat nucl:nucleotide.out,aa:blosum62.out --rescore-mode 3 --wrapped-scoring 0 --filter-hits 0 -e 1e-05 -c 0 -a 0 --cov-mode 0 --min-seq-id 0.9 --min-aln-len 0 --seq-id-mode 0 --add-self-matches 0 --sort-results 0 --db-load-mode 0 --threads 48 --compressed 0 -v 3 | |
| [=================================================================] 384.60M 3m 36s 797ms | |
| Time for merging to aln_9: 0h 3m 46s 286ms | |
| Time for processing: 0h 10m 41s 421ms | |
| rmdb /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/aln_8 | |
| Time for processing: 0h 0m 0s 109ms | |
| assembleresults /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_8 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/aln_9 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_9 --min-seq-id 0.9 --max-seq-len 65535 --threads 48 -v 3 --rescore-mode 3 | |
| Compute assembly. | |
| [=================================================================] 384.60M 15m 7s 517ms | |
| Time for merging to assembly_9: 0h 4m 48s 692ms | |
| Done. | |
| Time for processing: 0h 21m 43s 409ms | |
| rmdb /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_8 | |
| Time for processing: 0h 0m 4s 723ms | |
| STEP: 10 | |
| kmermatcher /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_9 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/pref_10 --sub-mat nucl:nucleotide.out,aa:blosum62.out --alph-size 13 --min-seq-id 0.9 --kmer-per-seq 60 --spaced-kmer-mode 0 --kmer-per-seq-scale nucl:0.200,aa:0.000 --adjust-kmer-len 0 --mask 0 --mask-lower-case 0 --cov-mode 0 -k 14 -c 0 --max-seq-len 65535 --hash-shift 72 --split-memory-limit 0 --include-only-extendable 1 --ignore-multi-kmer 1 --threads 48 --compressed 0 -v 3 | |
| kmermatcher /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_9 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/pref_10 --sub-mat nucl:nucleotide.out,aa:blosum62.out --alph-size 13 --min-seq-id 0.9 --kmer-per-seq 60 --spaced-kmer-mode 0 --kmer-per-seq-scale nucl:0.200,aa:0.000 --adjust-kmer-len 0 --mask 0 --mask-lower-case 0 --cov-mode 0 -k 14 -c 0 --max-seq-len 65535 --hash-shift 72 --split-memory-limit 0 --include-only-extendable 1 --ignore-multi-kmer 1 --threads 48 --compressed 0 -v 3 | |
| Database size: 384600802 type: Aminoacid | |
| Reduced amino acid alphabet: (A S T) (C) (D B N) (E Q Z) (F Y) (G) (H) (I V) (K R) (L J M) (P) (W) (X) | |
| Not enough memory to process at once need to split | |
| [=================================================================] 384.60M 3m 44s 581ms | |
| Process file into 2 parts | |
| Generate k-mers list for 1 split | |
| [=================================================================] 384.60M 12m 41s 277ms | |
| Sort kmer 0h 2m 50s 897ms | |
| Sort by rep. sequence 0h 0m 9s 123ms | |
| Generate k-mers list for 2 split | |
| [=================================================================] 384.60M 12m 5s 533ms | |
| Sort kmer 0h 0m 1s 436ms | |
| Sort by rep. sequence 0h 0m 0s 216ms | |
| Merge splits ... Time for fill: 0h 3m 21s 522ms | |
| Time for merging to pref_10: 0h 0m 0s 7ms | |
| Time for processing: 0h 40m 28s 578ms | |
| rmdb /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/pref_9 | |
| Time for processing: 0h 0m 0s 5ms | |
| rescorediagonal /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_9 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_9 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/pref_10 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/aln_10 --sub-mat nucl:nucleotide.out,aa:blosum62.out --rescore-mode 3 --wrapped-scoring 0 --filter-hits 0 -e 1e-05 -c 0 -a 0 --cov-mode 0 --min-seq-id 0.9 --min-aln-len 0 --seq-id-mode 0 --add-self-matches 0 --sort-results 0 --db-load-mode 0 --threads 48 --compressed 0 -v 3 | |
| [=================================================================] 384.60M 3m 13s 384ms | |
| Time for merging to aln_10: 0h 4m 33s 234ms | |
| Time for processing: 0h 12m 33s 103ms | |
| rmdb /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/aln_9 | |
| Time for processing: 0h 0m 0s 41ms | |
| assembleresults /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_9 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/aln_10 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_10 --min-seq-id 0.9 --max-seq-len 65535 --threads 48 -v 3 --rescore-mode 3 | |
| Compute assembly. | |
| [=================================================================] 384.60M 16m 29s 333ms | |
| Time for merging to assembly_10: 0h 6m 35s 999ms | |
| Done. | |
| Time for processing: 0h 26m 26s 61ms | |
| rmdb /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_9 | |
| Time for processing: 0h 0m 13s 0ms | |
| STEP: 11 | |
| kmermatcher /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_10 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/pref_11 --sub-mat nucl:nucleotide.out,aa:blosum62.out --alph-size 13 --min-seq-id 0.9 --kmer-per-seq 60 --spaced-kmer-mode 0 --kmer-per-seq-scale nucl:0.200,aa:0.000 --adjust-kmer-len 0 --mask 0 --mask-lower-case 0 --cov-mode 0 -k 14 -c 0 --max-seq-len 65535 --hash-shift 73 --split-memory-limit 0 --include-only-extendable 1 --ignore-multi-kmer 1 --threads 48 --compressed 0 -v 3 | |
| kmermatcher /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_10 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/pref_11 --sub-mat nucl:nucleotide.out,aa:blosum62.out --alph-size 13 --min-seq-id 0.9 --kmer-per-seq 60 --spaced-kmer-mode 0 --kmer-per-seq-scale nucl:0.200,aa:0.000 --adjust-kmer-len 0 --mask 0 --mask-lower-case 0 --cov-mode 0 -k 14 -c 0 --max-seq-len 65535 --hash-shift 73 --split-memory-limit 0 --include-only-extendable 1 --ignore-multi-kmer 1 --threads 48 --compressed 0 -v 3 | |
| Database size: 384600802 type: Aminoacid | |
| Reduced amino acid alphabet: (A S T) (C) (D B N) (E Q Z) (F Y) (G) (H) (I V) (K R) (L J M) (P) (W) (X) | |
| Not enough memory to process at once need to split | |
| [=================================================================] 384.60M 2m 40s 204ms | |
| Process file into 2 parts | |
| Generate k-mers list for 1 split | |
| [=================================================================] 384.60M 4m 6s 819ms | |
| Sort kmer 0h 2m 50s 427ms | |
| Sort by rep. sequence 0h 0m 8s 688ms | |
| Generate k-mers list for 2 split | |
| [=================================================================] 384.60M 7m 39s 755ms | |
| Sort kmer 0h 0m 1s 979ms | |
| Sort by rep. sequence 0h 0m 0s 285ms | |
| Merge splits ... Time for fill: 0h 3m 5s 1ms | |
| Time for merging to pref_11: 0h 0m 0s 13ms | |
| Time for processing: 0h 26m 36s 836ms | |
| rmdb /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/pref_10 | |
| Time for processing: 0h 0m 0s 4ms | |
| rescorediagonal /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_10 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_10 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/pref_11 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/aln_11 --sub-mat nucl:nucleotide.out,aa:blosum62.out --rescore-mode 3 --wrapped-scoring 0 --filter-hits 0 -e 1e-05 -c 0 -a 0 --cov-mode 0 --min-seq-id 0.9 --min-aln-len 0 --seq-id-mode 0 --add-self-matches 0 --sort-results 0 --db-load-mode 0 --threads 48 --compressed 0 -v 3 | |
| [=================================================================] 384.60M 4m 25s 503ms | |
| Time for merging to aln_11: 0h 4m 35s 418ms | |
| Time for processing: 0h 12m 39s 833ms | |
| rmdb /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/aln_10 | |
| Time for processing: 0h 0m 0s 169ms | |
| assembleresults /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_10 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/aln_11 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_11 --min-seq-id 0.9 --max-seq-len 65535 --threads 48 -v 3 --rescore-mode 3 | |
| Compute assembly. | |
| [=================================================================] 384.60M 3h 14m 7s 960ms | |
| Time for merging to assembly_11: 0h 5m 2s 396ms | |
| Done. | |
| Time for processing: 3h 22m 17s 111ms | |
| rmdb /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_10 | |
| Time for processing: 0h 0m 9s 513ms | |
| filternoncoding /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_11 /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_11_filtered --protein-filter-threshold 0.2 --threads 48 -v 3 | |
| Sequence database: /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_11 | |
| Output file: /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_11_filtered | |
| Reduced amino acid alphabet: (A S T) (C P) (D B E K N Q R Z) (F H W Y) (G) (I J L M V) (X) | |
| Time for merging to assembly_11_filtered: 0h 4m 14s 346ms | |
| Time for processing: 0h 7m 31s 824ms | |
| createsubdb /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_11_filtered_only_assembled.index /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly_tmp/13961392140243453648/assembly_11_filtered /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly --subdb-mode 0 | |
| Time for merging to assembly: 0h 0m 12s 772ms | |
| Time for processing: 0h 1m 48s 24ms | |
| createhdb /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly -v 3 | |
| Time for merging to assembly_h: 0h 0m 12s 670ms | |
| Time for processing: 0h 0m 33s 708ms | |
| convert2fasta /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly.fasta -v 3 | |
| Start writing file to /mnt/lustre/bio/users/aobiol/Functional_experiments/tmp/8044499188605896415/assembly.fasta | |
| Time for processing: 0h 0m 50s 177ms |
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