text cl_updt.o1889

Posted 2021-04-29

+ 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_20190430/mg_gtdb_db_052019 /vol/attached/gtdb/mg_gtdb_update_20190430/mg_gtdb_db_052019_clu /vol/attached/gtdb/mg_gtdb_update_20190430/tmp --min-seq-id 0.3 -s 5 --cov-mode 0 -c 0.8 --split 10
diffseqdbs /vol/scratch/gtdb/marine_hmp_db_03112017 /vol/scratch/gtdb/mg_gtdb_orfs_db /vol/attached/gtdb/mg_gtdb_update_20190430/tmp/removedSeqs /vol/attached/gtdb/mg_gtdb_update_20190430/tmp/mappingSeqs /vol/attached/gtdb/mg_gtdb_update_20190430/tmp/newSeqs --use-seq-id 0 --threads 28 --compressed 0 -v 3 

Time for processing: 0h 48m 25s 579ms
===================================================
=== Update the new sequences with the old keys ====
===================================================
===================================================
====== Filter out the new from old sequences ======
===================================================
createsubdb /vol/attached/gtdb/mg_gtdb_update_20190430/tmp/newSeqs /vol/attached/gtdb/mg_gtdb_update_20190430/mg_gtdb_db_052019 /vol/attached/gtdb/mg_gtdb_update_20190430/tmp/NEWDB.newSeqs 

Time for merging files: 0h 0m 15s 750ms
Time for processing: 0h 3m 38s 404ms
===================================================
======= Extract representative sequences ==========
===================================================
result2repseq /vol/scratch/gtdb/marine_hmp_db_03112017 /vol/scratch/gtdb/marine_hmp_db_03112017_clu /vol/attached/gtdb/mg_gtdb_update_20190430/tmp/OLDDB.repSeq 

Start computing representative sequences.
[=================================================================] 32.47M 46s 401ms

Time for merging files: 0h 0m 26s 450ms
Time for processing: 0h 1m 55s 877ms
===================================================
======== Search the new sequences against =========
========= previous (rep seq of) clusters ==========
===================================================
MPI Init
Rank: 0 Size: 10
prefilter /vol/attached/gtdb/mg_gtdb_update_20190430/tmp/NEWDB.newSeqs /vol/attached/gtdb/mg_gtdb_update_20190430/tmp/OLDDB.repSeq /vol/attached/gtdb/mg_gtdb_update_20190430/tmp/search/1938064807414409353/pref_0 --sub-mat blosum62.out --seed-sub-mat VTML80.out -k 0 --k-score 2147483647 --alph-size 21 --max-seq-len 65535 --max-seqs 300 --split 10 --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 --threads 28 --compressed 0 -v 3 -s 5.0 

Using 28 threads.
Query sequence type not implemented!
-------------------------------------------------------
Primary job  terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.
-------------------------------------------------------
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:

  Process name: [[35320,1],9]
  Exit code:    1
--------------------------------------------------------------------------
Error: Prefilter died
Error: Search died