Closed kad-ecoli closed 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
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
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
Why was there an 'Could not move result to resultDB' error code even though the "resultDB" and "resultDB.index" file was correctly generated?
Thank you for analyzing the problem. This helps me a lot. I changed the shebang line to bash.
Your run worked just fine. The output is "debug" output which occures becaues of the -x parameter at the shebang line. "#!/bin/bash -ex"
I removed this flag and updated the tar file. You can download it here http://github.com/soedinglab/mmseqs2/raw/master/mmseqs-static.tar.gz
No feedback. I assume its fixed now.
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"