Created
April 29, 2019 20:19
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| + set -e | |
| + MMSEQS=/vol/attached/opt/MPI/MMseqs2/bin/mmseqs | |
| + DIR=/vol/attached/gtdb | |
| + SDIR=/vol/scratch/gtdb | |
| + export 'OMPI_MCA_btl=^openib' | |
| + OMPI_MCA_btl='^openib' | |
| + export OMP_NUM_THREADS=28 | |
| + OMP_NUM_THREADS=28 | |
| + RUNNER='mpirun --mca btl_tcp_if_include ens3 -n 10 --map-by ppr:1:node --bind-to none ' | |
| + /vol/attached/opt/MPI/MMseqs2/bin/mmseqs clusterupdate /vol/scratch/gtdb/marine_hmp_db_03112017 /vol/scratch/gtdb/mg_gtdb_orfs_db /vol/scratch/gtdb/marine_hmp_db_03112017_clu /vol/attached/gtdb/mg_gtdb_update/mg_gtdb_db_052019 /vol/attached/gtdb/mg_gtdb_update/mg_gtdb_db_0520 | |
| 19_clu /vol/attached/gtdb/mg_gtdb_update/tmp --local-tmp /vol/scratch/gtdb/ --min-seq-id 0.3 -s 5 --cov-mode 0 -c 0.8 --threads 28 | |
| clusterupdate /vol/scratch/gtdb/marine_hmp_db_03112017 /vol/scratch/gtdb/mg_gtdb_orfs_db /vol/scratch/gtdb/marine_hmp_db_03112017_clu /vol/attached/gtdb/mg_gtdb_update/mg_gtdb_db_052019 /vol/attached/gtdb/mg_gtdb_update/mg_gtdb_db_052019_clu /vol/attached/gtdb/mg_gtdb_update/tm | |
| p --local-tmp /vol/scratch/gtdb/ --min-seq-id 0.3 -s 5 --cov-mode 0 -c 0.8 --threads 28 | |
| MMseqs Version: 39ee37f97ab065a3763ee10b834b3e6e25aae491-MPI | |
| Substitution matrix blosum62.out | |
| Add backtrace false | |
| Alignment mode 0 | |
| E-value threshold 0.001 | |
| Seq. id. threshold 0.3 | |
| Min. alignment length 0 | |
| Seq. id. mode 0 | |
| Alternative alignments 0 | |
| Coverage threshold 0.8 | |
| Coverage mode 0 | |
| Max sequence length 65535 | |
| Compositional bias 1 | |
| Realign hits false | |
| Max reject 2147483647 | |
| Max accept 2147483647 | |
| Include identical seq. id. false | |
| Preload mode 0 | |
| Pseudo count a 1 | |
| Pseudo count b 1.5 | |
| Score bias 0 | |
| Gap open cost 11 | |
| Gap extension cost 1 | |
| Threads 28 | |
| Compressed 0 | |
| Verbosity 3 | |
| Seed substitution matrix VTML80.out | |
| Sensitivity 5 | |
| K-mer size 0 | |
| K-score 2147483647 | |
| Alphabet size 21 | |
| Previous max results per query | |
| Split database 0 | |
| Split mode 2 | |
| Split memory limit 0 | |
| Diagonal scoring 1 | |
| Exact k-mer matching 0 | |
| Mask residues 1 | |
| Mask lower case residues 0 | |
| Minimum diagonal score 15 | |
| Spaced k-mers 1 | |
| Spaced k-mer pattern | |
| Local temporary path /vol/scratch/gtdb/ | |
| Rescore mode 0 | |
| Remove hits by seq. id. and coverage false | |
| Sort results 0 | |
| Global diagonal rescoring false | |
| Mask profile 1 | |
| Profile e-value threshold 0.001 | |
| Use global sequence weighting false | |
| Filter MSA 1 | |
| Maximum seq. id. threshold 0.9 | |
| Minimum seq. id. 0 | |
| Minimum score per column -20 | |
| Minimum coverage 0 | |
| Select N most diverse seqs 1000 | |
| Omit consensus false | |
| Min codons in orf 30 | |
| Max codons in length 32734 | |
| Max orf gaps 2147483647 | |
| Contig start mode 2 | |
| Contig end mode 2 [1/9890] | |
| Orf start mode 1 | |
| Forward frames 1,2,3 | |
| Reverse frames 1,2,3 | |
| Translation table 1 | |
| Use all table starts false | |
| Offset of numeric ids 0 | |
| Add orf stop false | |
| Chain overlapping alignments 0 | |
| Merge query 1 | |
| Search type 0 | |
| Number search iterations 1 | |
| Start sensitivity 4 | |
| Search steps 1 | |
| Run a seq-profile search in slice mode false | |
| Strand selection 1 | |
| Disk space limit 0 | |
| MPI runner mpirun --mca btl_tcp_if_include ens3 -n 10 --map-by ppr:1:node --bind-to none | |
| Force restart with latest tmp false | |
| Remove temporary files false | |
| Cluster mode 0 | |
| Max depth connected component 1000 | |
| Similarity type 2 | |
| =================================================== | |
| === Update the new sequences with the old keys ==== | |
| =================================================== | |
| =================================================== | |
| ====== Filter out the new from old sequences ====== | |
| =================================================== | |
| =================================================== | |
| ======= Extract representative sequences ========== | |
| =================================================== | |
| =================================================== | |
| ======== Search the new sequences against ========= | |
| ========= previous (rep seq of) clusters ========== | |
| =================================================== | |
| MPI Init | |
| Rank: 0 Size: 10 | |
| prefilter /vol/attached/gtdb/mg_gtdb_update/tmp/NEWDB.newSeqs /vol/attached/gtdb/mg_gtdb_update/tmp/OLDDB.repSeq /vol/attached/gtdb/mg_gtdb_update/tmp/search/7773636450665169409/pref_0 --sub-mat blosum62.out --seed-sub-mat VTML80.out -k 0 --k-score 2147483647 --alph-size 21 --m | |
| ax-seq-len 65535 --max-seqs 300 --split 0 --split-mode 2 --split-memory-limit 0 -c 0.8 --cov-mode 0 --comp-bias-corr 1 --diag-score 1 --exact-kmer-matching 0 --mask 1 --mask-lower-case 0 --min-ungapped-score 15 --add-self-matches 0 --spaced-kmer-mode 1 --db-load-mode 0 --pca 1 | |
| --pcb 1.5 --local-tmp /vol/scratch/gtdb/ --threads 28 --compressed 0 -v 3 -s 5.0 | |
| Using 28 threads. | |
| Estimated memory consumption 77751 MB | |
| Target database size: 32465074 type: Aminoacid | |
| Index table k-mer threshold: 130 at k-mer size 7 | |
| Index table: counting k-mers | |
| [=================================================================] 32.47M 52s 1ms | |
| Index table: Masked residues: 74030343 | |
| Index table: fill |
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