Closed alexander-nord closed 7 years ago
Could you post the whole log?
It looks like the prefilter step failed for some reason and the next step is now complaining about that.
Here's the full output (filepaths slightly redacted, for readability):
$ mmseqs search Candidates_db trans_small_db Trials/mmseqs/Candidates_to_Small mmseqs_tmp/ -v 3 Program call: Candidates_db trans_small_db Trials/mmseqs/Candidates_to_Small mmseqs_tmp/ -v 3
MMseqs Version: 8bd3de3e35c91c0723517a964efc3223682c3bb5 Sub Matrix blosum62.out Add backtrace false Alignment mode 0 E-value threshold 0.001 Seq. Id Threshold 0 Coverage threshold 0 Max. sequence length 32000 Max. results per query 300 Compositional bias 1 Profile false Realign hit false Max Reject 2147483647 Max Accept 2147483647 Include identical Seq. Id. false Threads 1 Verbosity 3 Sensitivity 4 K-mer size 0 K-score 2147483647 Alphabet size 21 Offset result 0 Split DB 0 Split mode 2 Diagonal Scoring 1 Minimum Diagonal score 15 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 Number search iterations 1 Start sensitivity 4 sensitivity step size 1 Sets the MPI runner
[pwd] [pwd] Program call: Candidates_db trans_small_db [pwd]/mmseqs_tmp/pref_4 --sub-mat blosum62.out -k 0 --k-score 2147483647 --alph-size 21 --max-seq-len 32000 --max-seqs 300 --offset-result 0 --split 0 --split-mode 2 -c 0 --comp-bias-corr 1 --diag-score 1 --min-ungapped-score 15 --spaced-kmer-mode 1 --threads 1 -v 3 -s 4
MMseqs Version: 8bd3de3e35c91c0723517a964efc3223682c3bb5 Sub Matrix blosum62.out Sensitivity 4 K-mer size 0 K-score 2147483647 Alphabet size 21 Max. sequence length 32000 Profile false Max. results per query 300 Offset result 0 Split DB 0 Split mode 2 Coverage threshold 0 Compositional bias 1 Diagonal Scoring 1 Minimum Diagonal score 15 Include identical Seq. Id. false Spaced Kmer 1 Threads 1 Verbosity 3
Initialising data structures...
Cound not find precomputed index. Compute index. Query database: Candidates_db(size=6144) Target database: trans_small_db(size=137914) Use kmer size 6 and split 1 using split mode 0 Needed memory (1556507147 byte) of total memory (4294967296 byte) Substitution matrices... Time for init: 0 h 0 m 7s
Process prefiltering step 0 of 1
[pwd]/mmseqs_tmp/pref_4_tmp_0.0: File exists Program call: Candidates_db trans_small_db [pwd]/mmseqs_tmp/pref_4 [pwd]/mmseqs_tmp/aln_4 --sub-mat blosum62.out --alignment-mode 0 -e 0.001 --min-seq-id 0 -c 0 --max-seq-len 32000 --max-seqs 300 --comp-bias-corr 1 --max-rejected 2147483647 --max-accept 2147483647 --threads 1 -v 3
MMseqs Version: 8bd3de3e35c91c0723517a964efc3223682c3bb5 Sub Matrix blosum62.out Add backtrace false Alignment mode 0 E-value threshold 0.001 Seq. Id Threshold 0 Coverage threshold 0 Max. sequence length 32000 Max. results per query 300 Compositional bias 1 Profile false Realign hit false Max Reject 2147483647 Max Accept 2147483647 Include identical Seq. Id. false Threads 1 Verbosity 3
Init data structures... Compute score only. Could not open data file [pwd]/mmseqs_tmp/pref_4! mv: rename [pwd]/mmseqs_tmp/aln_4 to Trials/mmseqs/Candidates_to_Small: No such file or directory
The prefilter results from the previous run are obscuring the real error. Could you empty the tmp folder and start again?
This part: "[pwd]/mmseqs_tmp/pref_4_tmp_0.0: File exists"
Ah! I had assumed that the new run would overwrite the existing files. I just removed and remade the temporary directory and things are running smoothly.
Thanks for the help!
No problem. I know that the errors are not very clear. We'll try to improve that. :)
I've been trying to perform some basic tests with MMSeqs2 and have encountered an issue where I repeated get the following error message:
The "[path_to_dir]/mmseqs_tmp/" directory contains two temporary files (pref_4.index_tmp_0.0 and pref_4_tmp_0.0) along with a blastp.sh script.
I'm not using any advanced options for my search, and both input databases are (as far as I can see) formatted correctly. Maybe I'm overlooking something embarrassingly simple?
Thanks!