vg giraffe unavailable perf events issue
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Entering edit mode
16 months ago
Suyeon • 0

Hi,

I'm trying to map WGS reads to genome graph using vg giraffe. And I got a warning related to "perf events" while mapping reads.

Can I ignore this warning? Here is the log for my execution.

Preparing Indexes
Loading Minimizer Index
Loading GBZ
Loading Distance Index v2
Paging in Distance Index v2
Initializing MinimizerMapper
Loading and initialization: 52.6884 seconds
Of which Distance Index v2 paging: 0.101052 seconds
Mapping reads to "-" (GAM)
--watchdog-timeout 10
--max-multimaps 1
--hit-cap 10
--hard-hit-cap 500
--score-fraction 0.9
--max-min 500
--num-bp-per-min 1000
--distance-limit 200
--max-extensions 800
--max-alignments 8
--cluster-score 50
--pad-cluster-score 20
--cluster-coverage 0.3
--extension-score 1
--extension-set 20
--rescue-attempts 15
--max-fragment-length 2000
--paired-distance-limit 2
--rescue-subgraph-size 4
--rescue-seed-limit 100
--chaining-cluster-distance 100
--precluster-connection-coverage-threshold 0.3
--min-precluster-connections 10
--max-precluster-connections 50
--max-lookback-bases 100
--min-lookback-items 1
--lookback-item-hard-cap 15
--chain-score-threshold 100
--min-chains 1
--chain-min-score 100
--max-chain-connection 100
--max-tail-length 100
--max-dp-cells 16777216
--rescue-algorithm dozeu
Not counting CPU instructions because perf events are unavailable: Permission denied
Using fragment length estimate: 298.086 +/- 55.3073

Thank you, Sue

vg • 473 views
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Entering edit mode

Yes, you can feel free to ignore that I believe as it is just performance information

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