comparison test-data/diamond.log @ 27:7591bce96601 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee

27:7591bce96601

diamond blastp --quiet --threads 1 --db ./database --query /tmp/tmpxfb7idqd/files/e/4/f/dataset_e4f75201-863d-4397-8ca7-7c0b79593e9d.dat --no-self-hits --outfmt 0 --out /tmp/tmpxfb7idqd/job_working_directory/000/3/outputs/dataset_0fb25f52-9d9b-4592-a709-7e516f37daa1.dat --compress 0 --algo 0 --matrix BLOSUM62 --comp-based-stats 1 --masking 1 --max-target-seqs 25 --evalue 0.001 --id 0 --query-cover 0 --subject-cover 0 --block-size 2.0 --motif-masking 0 --log
diamond v2.0.15.153
#CPU threads: 1
Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)
CPU features detected: ssse3 popcnt sse4.1 avx2
Runtime dispatch: disabled
L3 cache size: 8388608
MAX_SHAPE_LEN=19 SEQ_MASK STRICT_BAND
Temporary directory: /tmp/tmpxfb7idqd/job_working_directory/000/3/outputs
#Target sequences to report alignments for: 25
DP fields: 1
Opening the database...  [0s]
Database: ./database.dmnd (type: Diamond database, sequences: 2, letters: 568)
Block size = 2000000000
Opening the input file...  [0s]
Opening the output file...  [0s]
Loading query sequences...  [0s]
Sequences = 2, letters = 566, average length = 283
Masking queries...  [0s]
Current RSS: 6.8 MB, Peak RSS: 6.8 MB
Algorithm: Double-indexed
Shape configuration: 111101110111,111011010010111
Building query histograms...  [0s]
Allocating buffers...  [0s]
Current RSS: 6.9 MB, Peak RSS: 6.9 MB
Loading reference sequences...  [0s]
Sequences = 2, letters = 568, average length = 284
Current RSS: 6.9 MB, Peak RSS: 6.9 MB
Masking reference...  [0s]
Masked letters: 0
Initializing temporary storage... Async_buffer() 2,1
 [0s]
Building reference histograms...  [0s]
Allocating buffers...  [0s]
Current RSS: 6.9 MB, Peak RSS: 7.0 MB
Processing query block 1, reference block 1/1, shape 1/2, index chunk 1/4.
Building reference seed array...  [0s]
Building query seed array...  [0s]
Indexed query seeds = 97875695011120/566 (17292525620339.22%), reference seeds = 0/568 (0.00%)
Soft masked letters = 0/566 (0.00%), 0/568 (0.00%)
Computing hash join...  [0s]
Masking low complexity seeds...  [0s]
Masked seeds: 0/57 (0.00%)
Masked positions (query): 0/566 (0.00%)
Masked positions (target): 0/568 (0.00%)
Searching alignments...  [0s]
Processing query block 1, reference block 1/1, shape 1/2, index chunk 2/4.
Building reference seed array...  [0s]
Building query seed array...  [0s]
Indexed query seeds = 2560271741526742528/566 (452344830658435072.00%), reference seeds = 0/568 (0.00%)
Soft masked letters = 0/566 (0.00%), 0/568 (0.00%)
Computing hash join...  [0s]
Masking low complexity seeds...  [0s]
Masked seeds: 0/57 (0.00%)
Masked positions (query): 0/566 (0.00%)
Masked positions (target): 0/568 (0.00%)
Searching alignments...  [0s]
Processing query block 1, reference block 1/1, shape 1/2, index chunk 3/4.
Building reference seed array...  [0s]
Building query seed array...  [0s]
Indexed query seeds = 2560271741526742528/566 (452344830658435072.00%), reference seeds = 0/568 (0.00%)
Soft masked letters = 0/566 (0.00%), 0/568 (0.00%)
Computing hash join...  [0s]
Masking low complexity seeds...  [0s]
Masked seeds: 0/65 (0.00%)
Masked positions (query): 0/566 (0.00%)
Masked positions (target): 0/568 (0.00%)
Searching alignments...  [0s]
Processing query block 1, reference block 1/1, shape 1/2, index chunk 4/4.
Building reference seed array...  [0s]
Building query seed array...  [0s]
Indexed query seeds = 129/566 (22.79%), reference seeds = 107/568 (18.84%)
Soft masked letters = 0/566 (0.00%), 0/568 (0.00%)
Computing hash join...  [0s]
Masking low complexity seeds...  [0s]
Masked seeds: 0/60 (0.00%)
Masked positions (query): 0/566 (0.00%)
Masked positions (target): 0/568 (0.00%)
Searching alignments...  [0s]
Current RSS: 9.1 MB, Peak RSS: 9.2 MB
Processing query block 1, reference block 1/1, shape 2/2, index chunk 1/4.
Building reference seed array...  [0s]
Building query seed array...  [0s]
Indexed query seeds = 97875695011120/566 (17292525620339.22%), reference seeds = 107/568 (18.84%)
Soft masked letters = 0/566 (0.00%), 0/568 (0.00%)
Computing hash join...  [0s]
Masking low complexity seeds...  [0s]
Masked seeds: 0/58 (0.00%)
Masked positions (query): 0/566 (0.00%)
Masked positions (target): 0/568 (0.00%)
Searching alignments...  [0s]
Processing query block 1, reference block 1/1, shape 2/2, index chunk 2/4.
Building reference seed array...  [0s]
Building query seed array...  [0s]
Indexed query seeds = 2560271741526742528/566 (452344830658435072.00%), reference seeds = 107/568 (18.84%)
Soft masked letters = 0/566 (0.00%), 0/568 (0.00%)
Computing hash join...  [0s]
Masking low complexity seeds...  [0s]
Masked seeds: 0/66 (0.00%)
Masked positions (query): 0/566 (0.00%)
Masked positions (target): 0/568 (0.00%)
Searching alignments...  [0s]
Processing query block 1, reference block 1/1, shape 2/2, index chunk 3/4.
Building reference seed array...  [0s]
Building query seed array...  [0s]
Indexed query seeds = 2560271741526742528/566 (452344830658435072.00%), reference seeds = 107/568 (18.84%)
Soft masked letters = 0/566 (0.00%), 0/568 (0.00%)
Computing hash join...  [0s]
Masking low complexity seeds...  [0s]
Masked seeds: 0/46 (0.00%)
Masked positions (query): 0/566 (0.00%)
Masked positions (target): 0/568 (0.00%)
Searching alignments...  [0s]
Processing query block 1, reference block 1/1, shape 2/2, index chunk 4/4.
Building reference seed array...  [0s]
Building query seed array...  [0s]
Indexed query seeds = 120/566 (21.20%), reference seeds = 102/568 (17.96%)
Soft masked letters = 0/566 (0.00%), 0/568 (0.00%)
Computing hash join...  [0s]
Masking low complexity seeds...  [0s]
Masked seeds: 0/60 (0.00%)
Masked positions (query): 0/566 (0.00%)
Masked positions (target): 0/568 (0.00%)
Searching alignments...  [0s]
Deallocating buffers...  [0s]
Clearing query masking...  [0s]
Computing alignments... Async_buffer.load() 17(2.37487e-07 GB, 1.4063e-07 GB on disk)
Loading trace points...  [0s]
Sorting trace points...  [0s]
Computing alignments...  [0.01s]
Deallocating buffers...  [0s]
Loading trace points...  [0s]
 [0.011s]
Deallocating reference...  [0s]
Loading reference sequences...  [0s]
Current RSS: 9.6 MB, Peak RSS: 9.6 MB
Deallocating buffers...  [0s]
Current RSS: 9.6 MB, Peak RSS: 9.6 MB
Deallocating queries...  [0s]
Loading query sequences...  [0s]
Closing the input file...  [0s]
Closing the output file...  [0s]
Cleaning up...  [0s]
Current RSS: 9.6 MB, Peak RSS: 9.6 MB
Total time = 0.093s
Hits (filter stage 0) = 774
Hits (filter stage 1) = 774 (100 %)
Hits (filter stage 2) = 774 (100 %)
Hits (filter stage 3) = 17 (2.19638 %)
Target hits (stage 0) = 2
Target hits (stage 1) = 0
Target hits (stage 2) = 2
Target hits (stage 3) = 2 (0 (0%) with CBS)
Target hits (stage 4) = 2
Target hits (stage 5) = 2
Swipe realignments    = 0
Matrix adjusts        = 0
Extensions (8 bit)    = 0
Extensions (16 bit)   = 4
Extensions (32 bit)   = 0
Hard queries          = 0
Gapped filter (targets) = 0
Gapped filter (hits) stage 1 = 0
Gapped filter (hits) stage 2 = 0
Time (Load seed hit targets) = 4e-06s (CPU)
Time (Sort targets by score) = 0s (CPU)
Time (Gapped filter)         = 0s (CPU)
Time (Matrix adjust)         = 0s (CPU)
Time (Chaining)              = 2e-05s (CPU)
Time (DP target sorting)     = 0s (CPU)
Time (Smith Waterman)        = 6.9e-05s (CPU)
Time (Smith Waterman TB)     = 0.0001s (CPU)
Time (Traceback)             = 8e-06s (CPU)
Time (Target parallel)       = 0s (wall)
Time (Load seed hits)        = 0.000495s (wall)
Time (Sort seed hits)        = 2.4e-05s (wall)
Time (Extension)             = 0.010185s (wall)
Temporary disk space used (search): 1.4063e-07 GB
Reported 2 pairwise alignments, 2 HSPs.
1 queries aligned.