view test-data/diamond_log.txt @ 12:60f307965815 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 62db819c1db857d3fba94dc4e290ee0f50f7928d

diamond blastx --quiet --threads 1 --db ./database --query /tmp/tmpb7mnrgbk/files/0/b/a/dataset_0bafd694-5276-4809-9258-1d272c89c442.dat --query-gencode 1 --strand both --min-orf 1 --outfmt 6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore --out /tmp/tmpb7mnrgbk/job_working_directory/000/34/outputs/dataset_9356bfe1-71ff-4289-b524-b07b2006b561.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 --soft-masking 0 --index-chunks 4 --file-buffer-size 67108864 --log
#CPU threads: 1
Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)
CPU features detected: ssse3 popcnt sse4.1 avx2
L3 cache size: 12582912
MAX_SHAPE_LEN=19 SEQ_MASK STRICT_BAND
Temporary directory: /tmp/tmpb7mnrgbk/job_working_directory/000/34/outputs
#Target sequences to report alignments for: 25
DP fields: 510
Opening the database...  [0s]
Database: ./database (type: Diamond database, sequences: 2, letters: 568)
Block size = 2000000000
Current RSS: 6.5 MB, Peak RSS: 6.5 MB
Opening the input file...  [0s]
Opening the output file...  [0s]
Current RSS: 6.6 MB, Peak RSS: 6.6 MB
Loading query sequences... Sequences = 6, letters = 1694, average length = 282
 [0s]
Sequences = 6, letters = 1694, average length = 282
Masking queries...  [0s]
Current RSS: 7.1 MB, Peak RSS: 7.1 MB
Seed partition bits = 8
Algorithm: Double-indexed
Shape configuration: 111101110111,111011010010111
Building query histograms...  [0s]
Current RSS: 7.1 MB, Peak RSS: 7.1 MB
Seeking in database...  [0s]
Loading reference sequences... Sequences = 2, letters = 568, average length = 284
 [0s]
Current RSS: 7.1 MB, Peak RSS: 7.1 MB
Masking reference...  [0s]
Masked letters: 0
Initializing temporary storage... Async_buffer() 1
 [0s]
Building reference histograms...  [0s]
Allocating buffers...  [0s]
Current RSS: 7.4 MB, Peak RSS: 7.4 MB
Processing query block 1, reference block 1/1, shape 1/2, index chunk 1/4.
Building reference seed array...  [0s]
Current RSS: 7.4 MB, Peak RSS: 7.4 MB
Building query seed array...  [0s]
Current RSS: 7.4 MB, Peak RSS: 7.4 MB
Indexed query seeds = 301/1694 (17.77%), reference seeds = 87/568 (15.32%)
Soft masked letters = 0/1694 (0.00%), 0/568 (0.00%)
Computing hash join...  [0s]
Current RSS: 7.2 MB, Peak RSS: 7.4 MB
Masking low complexity seeds...  [0s]
Masked seeds: 0/53 (0.00%)
Masked positions (query): 0/1694 (0.00%)
Masked positions (target): 0/568 (0.00%)
Current RSS: 7.4 MB, Peak RSS: 7.4 MB
Searching alignments...  [0s]
Current RSS: 8.6 MB, Peak RSS: 9.5 MB
Deallocating memory...  [0s]
Current RSS: 7.6 MB, Peak RSS: 9.5 MB
Processing query block 1, reference block 1/1, shape 1/2, index chunk 2/4.
Building reference seed array...  [0s]
Current RSS: 7.6 MB, Peak RSS: 9.5 MB
Building query seed array...  [0s]
Current RSS: 7.6 MB, Peak RSS: 9.5 MB
Indexed query seeds = 286/1694 (16.88%), reference seeds = 120/568 (21.13%)
Soft masked letters = 0/1694 (0.00%), 0/568 (0.00%)
Computing hash join...  [0s]
Current RSS: 7.6 MB, Peak RSS: 9.5 MB
Masking low complexity seeds...  [0s]
Masked seeds: 0/71 (0.00%)
Masked positions (query): 0/1694 (0.00%)
Masked positions (target): 0/568 (0.00%)
Current RSS: 7.6 MB, Peak RSS: 9.5 MB
Searching alignments...  [0s]
Current RSS: 9.4 MB, Peak RSS: 9.5 MB
Deallocating memory...  [0s]
Current RSS: 9.4 MB, Peak RSS: 9.5 MB
Processing query block 1, reference block 1/1, shape 1/2, index chunk 3/4.
Building reference seed array...  [0s]
Current RSS: 9.4 MB, Peak RSS: 9.5 MB
Building query seed array...  [0s]
Current RSS: 9.4 MB, Peak RSS: 9.5 MB
Indexed query seeds = 296/1694 (17.47%), reference seeds = 98/568 (17.25%)
Soft masked letters = 0/1694 (0.00%), 0/568 (0.00%)
Computing hash join...  [0s]
Current RSS: 9.4 MB, Peak RSS: 9.5 MB
Masking low complexity seeds...  [0s]
Masked seeds: 0/54 (0.00%)
Masked positions (query): 0/1694 (0.00%)
Masked positions (target): 0/568 (0.00%)
Current RSS: 9.4 MB, Peak RSS: 9.5 MB
Searching alignments...  [0s]
Current RSS: 9.4 MB, Peak RSS: 9.5 MB
Deallocating memory...  [0s]
Current RSS: 9.4 MB, Peak RSS: 9.5 MB
Processing query block 1, reference block 1/1, shape 1/2, index chunk 4/4.
Building reference seed array...  [0s]
Current RSS: 9.4 MB, Peak RSS: 9.5 MB
Building query seed array...  [0s]
Current RSS: 9.4 MB, Peak RSS: 9.5 MB
Indexed query seeds = 307/1694 (18.12%), reference seeds = 109/568 (19.19%)
Soft masked letters = 0/1694 (0.00%), 0/568 (0.00%)
Computing hash join...  [0s]
Current RSS: 9.4 MB, Peak RSS: 9.5 MB
Masking low complexity seeds...  [0s]
Masked seeds: 0/61 (0.00%)
Masked positions (query): 0/1694 (0.00%)
Masked positions (target): 0/568 (0.00%)
Current RSS: 9.4 MB, Peak RSS: 9.5 MB
Searching alignments...  [0s]
Current RSS: 9.4 MB, Peak RSS: 9.5 MB
Deallocating memory...  [0s]
Current RSS: 9.4 MB, Peak RSS: 9.5 MB
Current RSS: 9.4 MB, Peak RSS: 9.5 MB
Processing query block 1, reference block 1/1, shape 2/2, index chunk 1/4.
Building reference seed array...  [0s]
Current RSS: 9.4 MB, Peak RSS: 9.5 MB
Building query seed array...  [0s]
Current RSS: 9.4 MB, Peak RSS: 9.5 MB
Indexed query seeds = 301/1694 (17.77%), reference seeds = 92/568 (16.20%)
Soft masked letters = 0/1694 (0.00%), 0/568 (0.00%)
Computing hash join...  [0s]
Current RSS: 9.4 MB, Peak RSS: 9.5 MB
Masking low complexity seeds...  [0s]
Masked seeds: 0/51 (0.00%)
Masked positions (query): 0/1694 (0.00%)
Masked positions (target): 0/568 (0.00%)
Current RSS: 9.4 MB, Peak RSS: 9.5 MB
Searching alignments...  [0s]
Current RSS: 9.4 MB, Peak RSS: 9.5 MB
Deallocating memory...  [0s]
Current RSS: 9.4 MB, Peak RSS: 9.5 MB
Processing query block 1, reference block 1/1, shape 2/2, index chunk 2/4.
Building reference seed array...  [0s]
Current RSS: 9.4 MB, Peak RSS: 9.5 MB
Building query seed array...  [0s]
Current RSS: 9.4 MB, Peak RSS: 9.5 MB
Indexed query seeds = 283/1694 (16.71%), reference seeds = 95/568 (16.73%)
Soft masked letters = 0/1694 (0.00%), 0/568 (0.00%)
Computing hash join...  [0s]
Current RSS: 9.4 MB, Peak RSS: 9.5 MB
Masking low complexity seeds...  [0s]
Masked seeds: 0/55 (0.00%)
Masked positions (query): 0/1694 (0.00%)
Masked positions (target): 0/568 (0.00%)
Current RSS: 9.4 MB, Peak RSS: 9.5 MB
Searching alignments...  [0s]
Current RSS: 9.4 MB, Peak RSS: 9.5 MB
Deallocating memory...  [0s]
Current RSS: 9.4 MB, Peak RSS: 9.5 MB
Processing query block 1, reference block 1/1, shape 2/2, index chunk 3/4.
Building reference seed array...  [0s]
Current RSS: 9.4 MB, Peak RSS: 9.5 MB
Building query seed array...  [0s]
Current RSS: 9.4 MB, Peak RSS: 9.5 MB
Indexed query seeds = 266/1694 (15.70%), reference seeds = 93/568 (16.37%)
Soft masked letters = 0/1694 (0.00%), 0/568 (0.00%)
Computing hash join...  [0s]
Current RSS: 9.4 MB, Peak RSS: 9.5 MB
Masking low complexity seeds...  [0s]
Masked seeds: 0/56 (0.00%)
Masked positions (query): 0/1694 (0.00%)
Masked positions (target): 0/568 (0.00%)
Current RSS: 9.4 MB, Peak RSS: 9.5 MB
Searching alignments...  [0s]
Current RSS: 9.4 MB, Peak RSS: 9.5 MB
Deallocating memory...  [0s]
Current RSS: 9.4 MB, Peak RSS: 9.5 MB
Processing query block 1, reference block 1/1, shape 2/2, index chunk 4/4.
Building reference seed array...  [0s]
Current RSS: 9.4 MB, Peak RSS: 9.5 MB
Building query seed array...  [0s]
Current RSS: 9.4 MB, Peak RSS: 9.5 MB
Indexed query seeds = 305/1694 (18.00%), reference seeds = 113/568 (19.89%)
Soft masked letters = 0/1694 (0.00%), 0/568 (0.00%)
Computing hash join...  [0s]
Current RSS: 9.4 MB, Peak RSS: 9.5 MB
Masking low complexity seeds...  [0s]
Masked seeds: 0/68 (0.00%)
Masked positions (query): 0/1694 (0.00%)
Masked positions (target): 0/568 (0.00%)
Current RSS: 9.4 MB, Peak RSS: 9.5 MB
Searching alignments...  [0s]
Current RSS: 9.4 MB, Peak RSS: 9.5 MB
Deallocating memory...  [0s]
Current RSS: 9.4 MB, Peak RSS: 9.5 MB
Current RSS: 9.4 MB, Peak RSS: 9.5 MB
Deallocating buffers...  [0s]
Clearing query masking...  [0s]
Current RSS: 9.4 MB, Peak RSS: 9.5 MB
Computing alignments... Async_buffer.load() 21(2.93367e-07 GB, 2.38419e-07 GB on disk)
Loading trace points...  [0s]
Sorting trace points...  [0s]
Computing partition...  [0s]
Computing alignments...  [0s]
Deallocating buffers...  [0s]
Loading trace points...  [0s]
 [0.001s]
Deallocating reference...  [0s]
Loading reference sequences... Current RSS: 10.1 MB, Peak RSS: 10.1 MB
 [0s]
Deallocating buffers...  [0s]
Current RSS: 10.1 MB, Peak RSS: 10.1 MB
Deallocating queries...  [0s]
Current RSS: 10.1 MB, Peak RSS: 10.1 MB
Loading query sequences...  [0s]
Closing the input file...  [0s]
Closing the output file...  [0s]
Closing the database...  [0s]
Cleaning up...  [0s]
Current RSS: 10.1 MB, Peak RSS: 10.1 MB
Total time = 0.017s
Hits (filter stage 0) = 774
Hits (filter stage 1) = 774 (100 %)
Hits (filter stage 2) = 774 (100 %)
Hits (filter stage 3) = 21 (2.71318 %)
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
Target hits (stage 6) = 2
Swipe realignments    = 0
Matrix adjusts        = 0
Extensions (8 bit)    = 0
Extensions (16 bit)   = 4
Extensions (32 bit)   = 0
Overflows (8 bit)     = 0
Wasted (16 bit)       = 0
Effort (Extension)    = 8
Effort (Cells)        = 0
Cells (8 bit)         = 0
Cells (16 bit)        = 0
SWIPE tasks           = 2
SWIPE tasks (async)   = 0
Trivial aln           = 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) = 5e-06s (CPU)
Time (Sort targets by score) = 0s (CPU)
Time (Gapped filter)         = 0s (CPU)
Time (Matrix adjust)         = 0s (CPU)
Time (Chaining)              = 3.4e-05s (CPU)
Time (DP target sorting)     = 0s (CPU)
Time (Query profiles)        = 0s (CPU)
Time (Smith Waterman)        = 0.000352s (CPU)
Time (Anchored SWIPE Alloc)  = 0s (CPU)
Time (Anchored SWIPE Sort)   = 0s (CPU)
Time (Anchored SWIPE Add)    = 0s (CPU)
Time (Anchored SWIPE Output) = 0s (CPU)
Time (Anchored SWIPE)        = 0s (CPU)
Time (Smith Waterman TB)     = 0s (CPU)
Time (Smith Waterman-32)     = 0s (CPU)
Time (Traceback)             = 1.6e-05s (CPU)
Time (Target parallel)       = 0s (wall)
Time (Load seed hits)        = 0.000797s (wall)
Time (Sort seed hits)        = 2.8e-05s (wall)
Time (Extension)             = 0.000568s (wall)
Temporary disk space used (search): 2.38419e-07 GB
Reported 2 pairwise alignments, 2 HSPs.
1 queries aligned.
Current RSS: 10.1 MB, Peak RSS: 10.1 MB