some error in building kraken2 database
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8 weeks ago
Art1ess • 0

I am building the database of kraken2. The previous add-to-library used my custom taxID and wrote names.dmp and nodes.dmp myself.

When running kraken2-build --build --db., the following prompt appears:

Creating sequence ID to taxonomy ID map (step 1)...
Sequence ID to taxonomy ID map already present, skipping map creation.
Estimating required capacity (step 2)...
Estimated hash table requirement: 21298865004 bytes
Capacity estimation complete. [11m0.264s]
Building database files (step 3)...
Taxonomy parsed and converted.
CHT created with 13 bits reserved for taxid.
Completed processing of 0 sequences, 0 bp
Writing data to disk... complete.
Database files completed. [2m59.229s]
Database construction complete. [Total: 14m0.492s]

Obviously, running kraken2 after the build is complete does not produce the correct results:

U CL100096888L1C013R048_557162/1 unclassified (taxid 0) 100 A:29 0:12 A:29
U CL100096888L1C012R064_96906/1 unclassified (taxid 0) 100 0:20 A:31 0:19
U CL100096888L1C004R035_314813/1 unclassified (taxid 0) 100 A:70
U CL100096888L1C017R037_497775/1 unclassified (taxid 0) 100 A:29 0:10 A:31
U CL100096888L1C012R006_314272/1 unclassified (taxid 0) 100 0:70
U CL100096888L1C017R067_125180/1 unclassified (taxid 0) 100 A:59 0:11
U CL100096888L1C017R067_147919/1 unclassified (taxid 0) 100 A:59 0:11
U CL100096888L1C003R044_122470/1 unclassified (taxid 0) 100 0:7 A:52 0:4 A:7
U CL100096888L1C009R091_47094/1 unclassified (taxid 0) 100 0:70
U CL100096888L1C011R005_253537/1 unclassified (taxid 0) 100 0:70
metagenome kraken2 • 481 views
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Obviously, running kraken2 after the build is complete does not produce the correct results

What do you get instead? Error/no output? Have you looked at the log files?

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I have 2 files output, no error logs...

the .kreport file:

100.00  160136511       160136511       U       0       unclassified

head .result.kraken file:

U       CL100096888L1C013R048_557162/1  unclassified (taxid 0)  100     A:29 0:12 A:29

U       CL100096888L1C012R064_96906/1   unclassified (taxid 0)  100     0:20 A:31 0:19

U       CL100096888L1C004R035_314813/1  unclassified (taxid 0)  100     A:70

U       CL100096888L1C017R037_497775/1  unclassified (taxid 0)  100     A:29 0:10 A:31

U       CL100096888L1C012R006_314272/1  unclassified (taxid 0)  100     0:70

U       CL100096888L1C017R067_125180/1  unclassified (taxid 0)  100     A:59 0:11

U       CL100096888L1C017R067_147919/1  unclassified (taxid 0)  100     A:59 0:11

U       CL100096888L1C003R044_122470/1  unclassified (taxid 0)  100     0:7 A:52 0:4 A:7

U       CL100096888L1C009R091_47094/1   unclassified (taxid 0)  100     0:70

U       CL100096888L1C011R005_253537/1  unclassified (taxid 0)  100     0:70
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this is names.dmp:names.dmp and nodes.dmpnodes.dmp

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Were you able to fix this issue? I'm also trying to add external species to krakendb

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