Mercurial > repos > bgruening > diamond

diff test-data/diamond_log.txt @ 20:0729ae1533e5 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 62db819c1db857d3fba94dc4e290ee0f50f7928d
author iuc
date Mon, 03 Feb 2025 16:00:43 +0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/diamond_log.txt	Mon Feb 03 16:00:43 2025 +0000
@@ -0,0 +1,261 @@
+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