kad-ecoli
commented
8 years ago After I fix the above mentioned bug, my output is like this: $ mmseqs search queryDB targetDB resultDB tmp --use-index
Program call: queryDB targetDB resultDB tmp --use-index
MMseqs Version: ef19bf40b8f6f5151d5ecbab42cfcb903facb907 Sub Matrix /home/zcx/Program/MMseqs/2.0/data/blosum62.out Alignment mode 0 E-value threshold 0.001 Coverage threshold 0 Detect fragments false Compositional bias 1 Seq. Id Threshold 0 Max. sequence length 32000 Max. results per query 300 Max Reject 2147483647 Include identical Seq. Id. false Nucleotide false Profile false Add backtrace false Realign hit false Threads 32 Verbosity 3 Sensitivity 4 K-mer size 7 K-score 2147483647 Alphabet size 21 Split DB 0 Split mode 2 Search mode 2 Diagonal Scoring 1 Minimum Diagonal score 30 Spaced Kmer 1 Profile e-value threshold 0.001 Use global sequence weighting false Maximum sequence identity threshold 0.9 Minimum seq. id. 0 Minimum score per column -20 Minimum coverage 0 Select n most diverse seqs 100 Pseudo count a 1 Pseudo count b 1.5 First sequence as respresentative false Number search iterations 1 Start sensitivity 4 Sensitivity step size 1 Use index true Sets the MPI runner
- '[' -z /home/zcx/Program/MMseqs/2.0 ']'
- '[' 4 -ne 4 ']'
- '[' '!' -f queryDB ']'
- '[' '!' -f targetDB ']'
- '[' -f resultDB ']'
- '[' '!' -d tmp ']'
- export OMP_PROC_BIND=TRUE
- OMP_PROC_BIND=TRUE ++ dirname queryDB
- cd . ++ basename queryDB
- QUERY_FILE=queryDB ++ pwd
- ABS_QUERY=/home/zcx/Program/MMseqs/2.0/test/queryDB
- cd - /home/zcx/Program/MMseqs/2.0/test
- cd tmp ++ pwd
- TMP_PATH=/home/zcx/Program/MMseqs/2.0/test/tmp
- cd - /home/zcx/Program/MMseqs/2.0/test
- INPUT=queryDB
- TARGET=targetDB
- SENS=4
- '[' 4 -le 4 ']'
- notExists /home/zcx/Program/MMseqs/2.0/test/tmp/pref_4
- '[' '!' -f /home/zcx/Program/MMseqs/2.0/test/tmp/pref_4 ']'
- mmseqs prefilter queryDB targetDB.sk7 /home/zcx/Program/MMseqs/2.0/test/tmp/pref_4 --sub-mat /home/zcx/Program/MMseqs/2.0/data/blosum62.out -k 7 --k-score 2147483647 --alph-size 21 --max-seq-len 32000 --max-seqs 300 --split 0 --split-mode 2 --search-mode 2 --comp-bias-corr 1 --diag-score 1 --min-diag-score 30 --spaced-kmer-mode 1 --threads 32 -v 3 -s 4 Program call: queryDB targetDB.sk7 /home/zcx/Program/MMseqs/2.0/test/tmp/pref_4 --sub-mat /home/zcx/Program/MMseqs/2.0/data/blosum62.out -k 7 --k-score 2147483647 --alph-size 21 --max-seq-len 32000 --max-seqs 300 --split 0 --split-mode 2 --search-mode 2 --comp-bias-corr 1 --diag-score 1 --min-diag-score 30 --spaced-kmer-mode 1 --threads 32 -v 3 -s 4
MMseqs Version: ef19bf40b8f6f5151d5ecbab42cfcb903facb907 Sub Matrix /home/zcx/Program/MMseqs/2.0/data/blosum62.out Sensitivity 4 K-mer size 7 K-score 2147483647 Alphabet size 21 Max. sequence length 32000 Profile false Nucleotide false Max. results per query 300 Split DB 0 Split mode 2 Search mode 2 Compositional bias 1 Diagonal Scoring 1 Minimum Diagonal score 30 Include identical Seq. Id. false Spaced Kmer 1 Threads 32 Verbosity 3
Initialising data structures... Using 32 threads.
Index version: 774909490 KmerSize: 7 AlphabetSize: 21 Skip: 0 Split: 1 Type: 1 Spaced: 1 Query database: queryDB(size=246) Target database: targetDB.sk7(size=10000) Needed memory (14434761936 byte) of total memory (270462795776 byte) Substitution matrices... Time for init: 0 h 0 m 3s
Process prefiltering step 0 of 1
Index version: 774909490
KmerSize: 7
AlphabetSize: 21
Skip: 0
Split: 1
Type: 1
Spaced: 1
Copy 1650981 Entries (9905886 byte)
Setup Sizes
Read IndexTable ... Done
k-mer similarity threshold: 115
k-mer match probability: 0
qStarting prefiltering scores calculation (step 0 of 1) Query db start 0 to 246 Target db start 0 to 10000
736 k-mers per position. 448 DB matches per sequence. 553 Double diagonal matches per sequence. 0 Overflows . 25 sequences passed prefiltering per query sequence. Median result list size: 21 5 sequences with 0 size result lists.
Time for prefiltering scores calculation: 0 h 2 m 8s Time for merging files: 0 h 0 m 0 s
Overall time for prefiltering run: 0 h 2 m 22s
- checkReturnCode 'Prefilter died'
- '[' 0 -ne 0 ']'
- notExists /home/zcx/Program/MMseqs/2.0/test/tmp/aln_4
- '[' '!' -f /home/zcx/Program/MMseqs/2.0/test/tmp/aln_4 ']'
- mmseqs alignment queryDB targetDB /home/zcx/Program/MMseqs/2.0/test/tmp/pref_4 /home/zcx/Program/MMseqs/2.0/test/tmp/aln_4 --sub-mat /home/zcx/Program/MMseqs/2.0/data/blosum62.out --alignment-mode 0 -e 0.001 -c 0 --comp-bias-corr 1 --min-seq-id 0 --max-seq-len 32000 --max-seqs 300 --max-rejected 2147483647 --threads 32 -v 3 Program call: queryDB targetDB /home/zcx/Program/MMseqs/2.0/test/tmp/pref_4 /home/zcx/Program/MMseqs/2.0/test/tmp/aln_4 --sub-mat /home/zcx/Program/MMseqs/2.0/data/blosum62.out --alignment-mode 0 -e 0.001 -c 0 --comp-bias-corr 1 --min-seq-id 0 --max-seq-len 32000 --max-seqs 300 --max-rejected 2147483647 --threads 32 -v 3
MMseqs Version: ef19bf40b8f6f5151d5ecbab42cfcb903facb907 Sub Matrix /home/zcx/Program/MMseqs/2.0/data/blosum62.out Alignment mode 0 E-value threshold 0.001 Coverage threshold 0 Detect fragments false Compositional bias 1 Seq. Id Threshold 0 Max. sequence length 32000 Max. results per query 300 Max Reject 2147483647 Include identical Seq. Id. false Nucleotide false Profile false Add backtrace false Realign hit false Threads 32 Verbosity 3
Init data structures... Compute score only. Using 32 threads. Calculation of Smith-Waterman alignments. Time for merging files: 0 h 0 m 0 s
All sequences processed.
6287 alignments calculated. 6203 sequence pairs passed the thresholds (0.986639 of overall calculated). 25.2154 hits per query sequence. Time for alignments calculation: 0 h 0 m 1s
- checkReturnCode 'Alignment died'
- '[' 0 -ne 0 ']'
- '[' 4 -gt 4 ']'
- NEXTINPUT=/home/zcx/Program/MMseqs/2.0/test/tmp/input_step4
- '[' 4 -lt 4 ']'
- let SENS=SENS+SENS_STEP_SIZE
- INPUT=/home/zcx/Program/MMseqs/2.0/test/tmp/input_step4
- '[' 5 -le 4 ']'
- mv -f /home/zcx/Program/MMseqs/2.0/test/tmp/aln_4 resultDB
- mv -f /home/zcx/Program/MMseqs/2.0/test/tmp/aln_4.index resultDB.index
- checkReturnCode 'Could not move result to resultDB'
- '[' 0 -ne 0 ']'
- '[' -n '' ']'
Why was there an 'Could not move result to resultDB' error code even though the "resultDB" and "resultDB.index" file was correctly generated?
martin-steinegger
when I run the mmseqs2 to search sequence, I encounter a an error at blastp.sh:
$ mmseqs createdb queryDB.fasta queryDB $ mmseqs createdb targetDB.fasta targetDB $ mmseqs createindex targetDB $ mkdir -p tmp/ $ mmseqs search queryDB targetDB resultDB tmp --use-index
Program call: queryDB targetDB resultDB tmp --use-index
MMseqs Version: ef19bf40b8f6f5151d5ecbab42cfcb903facb907 Sub Matrix /home/zcx/Program/MMseqs/2.0/data/blosum62.out Alignment mode 0 E-value threshold 0.001 Coverage threshold 0 Detect fragments false Compositional bias 1 Seq. Id Threshold 0 Max. sequence length 32000 Max. results per query 300 Max Reject 2147483647 Include identical Seq. Id. false Nucleotide false Profile false Add backtrace false Realign hit false Threads 32 Verbosity 3 Sensitivity 4 K-mer size 7 K-score 2147483647 Alphabet size 21 Split DB 0 Split mode 2 Search mode 2 Diagonal Scoring 1 Minimum Diagonal score 30 Spaced Kmer 1 Profile e-value threshold 0.001 Use global sequence weighting false Maximum sequence identity threshold 0.9 Minimum seq. id. 0 Minimum score per column -20 Minimum coverage 0 Select n most diverse seqs 100 Pseudo count a 1 Pseudo count b 1.5 First sequence as respresentative false Number search iterations 1 Start sensitivity 4 Sensitivity step size 1 Use index true Sets the MPI runner
MMseqs Version: ef19bf40b8f6f5151d5ecbab42cfcb903facb907 Sub Matrix /home/zcx/Program/MMseqs/2.0/data/blosum62.out Sensitivity 4 K-mer size 7 K-score 2147483647 Alphabet size 21 Max. sequence length 32000 Profile false Nucleotide false Max. results per query 300 Split DB 0 Split mode 2 Search mode 2 Compositional bias 1 Diagonal Scoring 1 Minimum Diagonal score 30 Include identical Seq. Id. false Spaced Kmer 1 Threads 32 Verbosity 3
Initialising data structures... Using 32 threads.
Index version: 774909490 KmerSize: 7 AlphabetSize: 21 Skip: 0 Split: 1 Type: 1 Spaced: 1 Query database: queryDB(size=246) Target database: targetDB.sk7(size=10000) Needed memory (14434761936 byte) of total memory (270462795776 byte) Substitution matrices... Time for init: 0 h 0 m 3s
Process prefiltering step 0 of 1
Index version: 774909490 KmerSize: 7 AlphabetSize: 21 Skip: 0 Split: 1 Type: 1 Spaced: 1 Copy 1650981 Entries (9905886 byte) Setup Sizes
Read IndexTable ... Done k-mer similarity threshold: 115 k-mer match probability: 0
Starting prefiltering scores calculation (step 0 of 1) Query db start 0 to 246 Target db start 0 to 10000
736 k-mers per position. 448 DB matches per sequence. 553 Double diagonal matches per sequence. 0 Overflows . 25 sequences passed prefiltering per query sequence. Median result list size: 21 5 sequences with 0 size result lists.
Time for prefiltering scores calculation: 0 h 2 m 18s Time for merging files: 0 h 0 m 0 s
Overall time for prefiltering run: 0 h 2 m 32s
MMseqs Version: ef19bf40b8f6f5151d5ecbab42cfcb903facb907 Sub Matrix /home/zcx/Program/MMseqs/2.0/data/blosum62.out Alignment mode 0 E-value threshold 0.001 Coverage threshold 0 Detect fragments false Compositional bias 1 Seq. Id Threshold 0 Max. sequence length 32000 Max. results per query 300 Max Reject 2147483647 Include identical Seq. Id. false Nucleotide false Profile false Add backtrace false Realign hit false Threads 32 Verbosity 3
Init data structures... Compute score only. Using 32 threads. Calculation of Smith-Waterman alignments. Time for merging files: 0 h 0 m 0 s
All sequences processed.
6287 alignments calculated. 6203 sequence pairs passed the thresholds (0.986639 of overall calculated). 25.2154 hits per query sequence. Time for alignments calculation: 0 h 0 m 1s
I am running MMseqs2 on Ubuntu 14.04 (trusty) x86-64. On Ubuntu and Debian, the default shell /bin/sh is dash, not bash. dash does not support "let". I recommend changing the first line of "blastp.sh" from "#!/bin/sh -ex" to "#!/bin/bash -ex"