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problems when running HGT-Finder #3

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Paymentzhong opened this issue Sep 18, 2019 · 2 comments
Open

problems when running HGT-Finder #3

Paymentzhong opened this issue Sep 18, 2019 · 2 comments

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@Paymentzhong
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Hello, I met some problems when I was running HGT-Finder,it would be very helpful if you could
give me some clues to fix it, thank you in advance!
image
here is the command:
./HGTFinder -d DK001.nr.diamond.m8 -s self_revised_peps.fa.diamond -t 498257 -o HGT -r 0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9 -p 0.1 -q 0.01
When I ran HGT-finder,it keeps outputting "Could not find tax lineage for taxID: -1 " and the output files are empty, no matter how I changed the R value and Q value, the problem did not fix, and the website http://cys.bios.niu.edu/HGTFinder/ is not available any more, so I could not read the program's example and see what's going wrong
looking forward to your reply! thank you

@Tinyman392
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Hey there,

can you confirm that the taxonomic IDs for all your protein sequences as well as your query genome are in the nodes.dmp, names.dmp, and nr.tax file? If not, they'll need to be added in and the nr.hdb file recreated using the DBFormatter tool.

@JianjiaDTU
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When I run the HGT, it reports the error:
Reading in tax DB...terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
/opt/gridengine/default/spool/cngb-compute-m17-2/job_scripts/279579: line 6: 58994 Aborted

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3 participants