text clusterupdate_39ee37f97ab065a3763ee10b834b3e6e25aae491.log
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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以上是关于text clusterupdate_39ee37f97ab065a3763ee10b834b3e6e25aae491.log的主要内容，如果未能解决你的问题，请参考以下文章
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