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Find HGT of de novo gene models #5

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AlexWanghaoming opened this issue Jul 25, 2020 · 0 comments
Open

Find HGT of de novo gene models #5

AlexWanghaoming opened this issue Jul 25, 2020 · 0 comments

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@AlexWanghaoming
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Hello developer,
When I run HGT-Finder with command:
HGTFinder -d accessory_protein.outfmt6.tbl -s accessory_self.outfmt6.tbl -t 5455 -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
The errors occured:
No X for query: CSIYN17586.t1
No X for query: CSIYN17587.t1
No X for query: CSIYN17588.t1
Could not find tax lineage for taxID: -1

My protein and ID are Denovo predicted by Augustus, nodes.dmp and namse.dmp are downloaded from NCBI taxonomy database, my nr.hdb are download from bcb.unl.edu/HGTFinder.
My proteins are blast against nr database with outfmt6 output like:
CASFJ16744.t1 CCF43630.1 65.7 271 75 1 64 316 5 275 5.6e-97 364.4 CASFJ16744.t1 XP_018150623.1 63.4 279 76 2 64 316 51 329 2.0e-94 355.9 CASFJ16744.t1 KZL64686.1 63.8 271 80 1 64 316 50 320 5.8e-94 354.4 CASFJ16744.t1 OHW89509.1 63.8 271 80 1 64 316 46 316 5.8e-94 354.4 CASFJ16744.t1 OHX00758.1 63.6 275 81 2 60 316 31 304 3.7e-93 351.7 CASFJ16744.t1 XP_002999875.1 57.9 271 96 1 64 316 52 322 1.7e-85 326.2 CASFJ16744.t1 KZL78271.1 58.7 271 94 1 64 316 63 333 7.1e-84 320.9 CASFJ16744.t1 CRK20179.1 56.5 271 100 1 64 316 57 327 2.3e-82 315.8 CASFJ16744.t1 KZL79688.1 57.2 271 98 1 64 316 51 321 2.3e-82 315.8 CASFJ16744.t1 KZL86415.1 62.3 252 77 1 83 316 88 339 3.9e-82 315.1

CASFJXXXXX is my customized gene ID.

I have tried to use DBFormatter to build db with prot.accession2taxid.gz, it is very slow and I gave up.
Could you please help me or provide me with some suggestions?
Thanks,
Alex

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