Closed shump2 closed 3 years ago
Other users have reported this issue before. Sorry you will have to use Python 2 instead of Python 3.
I have reformatted the custom database and it is now working smoothly!!!
I have reformatted the custom database and it is now working smoothly!!!
May I ask what you @shump2 did to get this working for your database? I am getting a similar python error with what appears to me to be a properly formaetted database/taxonomy file.
Louis
Hi, I have built a custom ncbi nt database and generated the associated taxonomy file. I successfully completed the test.fasta data on this database without issue. However, with my own data, I am getting the following error (note that I am using python3 and blast 2.12.0) :
**
The blast search runs fine but I noticed that the blastn aligment fails and outputs the above error and I am wondering what could be the issue:
The test.fasta.blastn output that works:
seq1 AE000782.1 100.000 470 0 0 1 470 1790478 1790009 0.0 869 470 minus 2178400 470 seq1 NR_074334.1 100.000 470 0 0 1 470 1 470 0.0 869 470 plus 1492 470 seq1 CP006577.1 99.787 470 1 0 1 470 1952565 1952096 0.0 863 467 minus 2316287 470 seq1 AB819341.1 99.786 468 1 0 3 470 1 468 0.0 859 465 plus 1487 470 seq1 EU573153.1 99.574 469 2 0 2 470 1 469 0.0 856 463 plus 934 470 seq1 FN356383.1 99.147 469 4 0 2 470 1 469 0.0 845 457 plus 1463 470 seq1 FN356382.1 99.147 469 4 0 2 470 1 469 0.0 845 457 plus 1465 470 seq1 FN356380.1 99.147 469 4 0 2 470 1 469 0.0 845 457 plus 1434 470 seq1 FN356423.1 98.934 469 5 0 2 470 1 469 0.0 839 454 plus 886 470 seq1 JF789483.1 99.563 458 0 2 15 470 1 458 0.0 833 451 plus 1328 470
My data blastn file that produces the error:
seq102 KX069362.1 100.000 471 0 0 1 471 188 658 0.0 815 441 plus 658 471 seq102 KX069361.1 100.000 471 0 0 1 471 188 658 0.0 815 441 plus 658 471 seq102 KF644040.1 100.000 471 0 0 1 471 188 658 0.0 815 441 plus 658 471 seq102 KF643756.1 99.788 471 1 0 1 471 188 658 0.0 809 438 plus 658 471 seq102 KF643376.1 99.788 471 1 0 1 471 188 658 0.0 809 438 plus 658 471 seq102 KF643271.1 99.788 471 1 0 1 471 188 658 0.0 809 438 plus 658 471 seq102 KF643895.1 100.000 465 0 0 1 465 188 652 0.0 804 435 plus 652 471 seq102 AB238459.1 99.363 471 3 0 1 471 188 658 0.0 798 432 plus 658 471 seq102 KF644122.1 100.000 419 0 0 1 419 188 606 0.0 774 419 plus 645 471 seq102 KF643711.1 100.000 419 0 0 1 419 188 606 0.0 774 419 plus 643 471
Using parameters -x and attempting -a muscle generates the errors regardless. I have got this to work in the past but recently I cannot get past this above erros. I would appreciate any advice on this matter. P