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$ mmseqs search queryDB sequenceDB resultDB tmp search queryDB sequenceDB resultDB tmp
MMseqs Version: GITDIR-NOTFOUND Substitution matrix nucl:nucleotide.out,aa:blosum62.out Add backtrace false Alignment mode 2 Alignment mode 0 Allow wrapped scoring false E-value threshold 0.001 Seq. id. threshold 0 Min alignment length 0 Seq. id. mode 0 Alternative alignments 0 Coverage threshold 0 Coverage mode 0 Max sequence length 65535 Compositional bias 1 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 Realign hits false Realign score bias -0.2 Realign max seqs 2147483647 Gap open cost nucl:5,aa:11 Gap extension cost nucl:2,aa:1 Zdrop 40 Threads 40 Compressed 0 Verbosity 3 Seed substitution matrix nucl:nucleotide.out,aa:VTML80.out Sensitivity 5.7 k-mer length 0 k-score 2147483647 Alphabet size nucl:5,aa:21 Max results per query 300 Split database 0 Split mode 2 Split memory limit 0 Diagonal scoring true 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 Rescore mode 0 Remove hits by seq. id. and coverage false Sort results 0 Mask profile 1 Profile E-value threshold 0.1 Global sequence weighting false Allow deletions 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 Min codons in orf 30 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 Add orf stop false Overlap between sequences 0 Sequence split mode 1 Header split mode 0 Chain overlapping alignments 0 Merge query 1 Search type 0 Search iterations 1 Start sensitivity 4 Search steps 1 Exhaustive search mode false Filter results during exhaustive search 0 Strand selection 1 LCA search mode false Disk space limit 0 MPI runner Force restart with latest tmp false Remove temporary files false
prefilter queryDB sequenceDB tmp/837003320692135749/pref_0 --sub-mat nucl:nucleotide.out,aa:blosum62.out --seed-sub-mat nucl:nucleotide.out,aa:VTML80.out -k 0 --k-score 2147483647 --alph-size nucl:5,aa:21 --max-seq-len 65535 --max-seqs 300 --split 0 --split-mode 2 --split-memory-limit 0 -c 0 --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 40 --compressed 0 -v 3 -s 5.7
Query database size: 1 type: Aminoacid Target split mode. Searching through 5 splits Estimated memory consumption: 297G Target database size: 358983966 type: Aminoacid Process prefiltering step 1 of 5
Index table k-mer threshold: 122 at k-mer size 7 Index table: counting k-mers tmp/837003320692135749/blastp.sh: line 99: 35385 Killed $RUNNER "$MMSEQS" prefilter "$INPUT" "$TARGET" "$TMP_PATH/pref_$STEP" $PREFILTER_PAR -s "$SENS" Error: Prefilter died
$ mmseqs search queryDB sequenceDB resultDB tmp
Please make sure to also post the complete output of MMseqs. You can use gist.github.com for large output.
Doing a seach of one sequence in the queryDB aginst a larger DB of amino acid sequences.
Include as many relevant details about the environment you experienced the bug in.
The text was updated successfully, but these errors were encountered:
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Expected Behavior
Current Behavior
$ mmseqs search queryDB sequenceDB resultDB tmp
search queryDB sequenceDB resultDB tmp
MMseqs Version: GITDIR-NOTFOUND
Substitution matrix nucl:nucleotide.out,aa:blosum62.out
Add backtrace false
Alignment mode 2
Alignment mode 0
Allow wrapped scoring false
E-value threshold 0.001
Seq. id. threshold 0
Min alignment length 0
Seq. id. mode 0
Alternative alignments 0
Coverage threshold 0
Coverage mode 0
Max sequence length 65535
Compositional bias 1
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
Realign hits false
Realign score bias -0.2
Realign max seqs 2147483647
Gap open cost nucl:5,aa:11
Gap extension cost nucl:2,aa:1
Zdrop 40
Threads 40
Compressed 0
Verbosity 3
Seed substitution matrix nucl:nucleotide.out,aa:VTML80.out
Sensitivity 5.7
k-mer length 0
k-score 2147483647
Alphabet size nucl:5,aa:21
Max results per query 300
Split database 0
Split mode 2
Split memory limit 0
Diagonal scoring true
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
Rescore mode 0
Remove hits by seq. id. and coverage false
Sort results 0
Mask profile 1
Profile E-value threshold 0.1
Global sequence weighting false
Allow deletions 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
Min codons in orf 30
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
Add orf stop false
Overlap between sequences 0
Sequence split mode 1
Header split mode 0
Chain overlapping alignments 0
Merge query 1
Search type 0
Search iterations 1
Start sensitivity 4
Search steps 1
Exhaustive search mode false
Filter results during exhaustive search 0
Strand selection 1
LCA search mode false
Disk space limit 0
MPI runner
Force restart with latest tmp false
Remove temporary files false
prefilter queryDB sequenceDB tmp/837003320692135749/pref_0 --sub-mat nucl:nucleotide.out,aa:blosum62.out --seed-sub-mat nucl:nucleotide.out,aa:VTML80.out -k 0 --k-score 2147483647 --alph-size nucl:5,aa:21 --max-seq-len 65535 --max-seqs 300 --split 0 --split-mode 2 --split-memory-limit 0 -c 0 --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 40 --compressed 0 -v 3 -s 5.7
Query database size: 1 type: Aminoacid
Target split mode. Searching through 5 splits
Estimated memory consumption: 297G
Target database size: 358983966 type: Aminoacid
Process prefiltering step 1 of 5
Index table k-mer threshold: 122 at k-mer size 7
Index table: counting k-mers
tmp/837003320692135749/blastp.sh: line 99: 35385 Killed $RUNNER "$MMSEQS" prefilter "$INPUT" "$TARGET" "$TMP_PATH/pref_$STEP" $PREFILTER_PAR -s "$SENS"
Error: Prefilter died
Steps to Reproduce (for bugs)
$ mmseqs search queryDB sequenceDB resultDB tmp
MMseqs Output (for bugs)
Please make sure to also post the complete output of MMseqs. You can use gist.github.com for large output.
Context
Doing a seach of one sequence in the queryDB aginst a larger DB of amino acid sequences.
Your Environment
Include as many relevant details about the environment you experienced the bug in.
Architecture: x86_64
CPU op-mode(s): 32-bit, 64-bit
Byte Order: Little Endian
CPU(s): 40
On-line CPU(s) list: 0-39
Thread(s) per core: 1
Core(s) per socket: 20
Socket(s): 2
NUMA node(s): 2
Vendor ID: GenuineIntel
CPU family: 6
Model: 85
Model name: Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz
Stepping: 4
CPU MHz: 2400.000
BogoMIPS: 4800.00
Virtualization: VT-x
L1d cache: 32K
L1i cache: 32K
L2 cache: 1024K
L3 cache: 28160K
NUMA node0 CPU(s): 0-19
NUMA node1 CPU(s): 20-39
Flags: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc art arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 sdbg fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch epb cat_l3 cdp_l3 invpcid_single intel_ppin ssbd mba rsb_ctxsw ibrs ibpb stibp tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid rtm cqm mpx rdt_a avx512f avx512dq rdseed adx smap clflushopt clwb intel_pt avx512cd avx512bw avx512vl xsaveopt xsavec xgetbv1 cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local dtherm ida arat pln pts pku ospke md_clear spec_ctrl intel_stibp flush_l1d arch_capabilities
The text was updated successfully, but these errors were encountered: