diamoand error

[moshi4]

diamoand error

[moshi4]

It seems that the error is occurring at the first processing stage of FastDTLmapper, which estimates the ortholog group by OrthoFinder. The error is caused by the fact that diamond (v2.0.5), which is embedded in OrthoFinder, is not working properly.

I will give you v2.0.5 and the latest v2.0.15 of the diamond executable binary, so could you please check if the following command works in your environment?

./diamond_v2.0.5 makedb --in test.faa -d test_v2.0.5
./diamond_v2.0.15 makedb --in test.faa -d test_v2.0.15

If only diamond (v2.0.15) seems to work properly in your environment, I would like to replace v2.0.5 with v2.0.15 and release a new FastDTLmapper to resolve the cause of the error.

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diamond_run_test.zip

• diamond_v2.0.5
• diamond_v2.0.15
• test.faa

[suresh2014]

hi
thanks for prompt response
for me diamond_v2.0.15 working nicely

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terminal output

(base) pbl2-ec@pbl2:/diamond_run_test$ ./diamond_v2.0.5 makedb --in test.faa -d test_v2.0.5
terminate called after throwing an instance of 'std::runtime_error'
what(): CPU does not support POPCNT. Please compile the software from source.
Aborted (core dumped)
(base) pbl2-ec@pbl2:/diamond_run_test$ ./diamond_v2.0.15 makedb --in test.faa -d test_v2.0.15
diamond v2.0.15.153 (C) Max Planck Society for the Advancement of Science
Documentation, support and updates available at http://www.diamondsearch.org
Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021)

#CPU threads: 2
Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)
Database input file: test.faa
Opening the database file... [0s]
Loading sequences... [0.002s]
Masking sequences... [0.018s]
Writing sequences... [0s]
Hashing sequences... [0s]
Loading sequences... [0s]
Writing trailer... [0s]
Closing the input file... [0s]
Closing the database file... [0s]

Database sequences 686
Database letters 229919
Database hash 4f9ac375ba759867838d956b6530044c
Total time 0.023000s
(base) pbl2-ec@pbl2:~/diamond_run_test$

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[moshi4]

I have released new FastDTLmapper v0.3.4 which replaces diamond with v2.0.15, please try it.

[suresh2014]

its working ..cool .. thanks