I ran a test file (xxx.txt) containing fasta formatted sequences that I uploaded from my desktop. There are only <10 sequences in the file. I wanted to test this because I was having issues with running megaBLAST on a larger dataset collection. At any rate, I think there is something happening with this python script that is causing megaBLAST to fail with large or small files.
This was the error message:
File “/project/galaxy/galaxy-py3/galaxy-base/database/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/megablast_wrapper/fb2e0e1dac89/megablast_wrapper/megablast_wrapper.py”, line 68
print megablast_command
^
SyntaxError: Missing parentheses in call to ‘print’. Did you mean print(megablast_command)?
I also tried to upload a pic of the error screen, not sure if it made it…
This was the input file (for some reason it’s not seeing the >'s at the start of each sequence title, but they are on there):
A00129:980:H5TVGDSX2:4:1107:23547:158121:N:0:TGTCGCAT+AAGCTGAC
TAGTAGATTTAAAACGAAGGTCTTGGGGGGTGGTACTTCCCTCAATTCCAATAACCTAAAATAAAATTAAAATTAATAAGTATTTAAAATTTAATATTACGCGCTAGCGTAACATCTGACATCCATTTCTTCCCATGTGATAAGGT
A00129:980:H5TVGDSX2:4:1114:6777:151701:N:0:TGTCGCAT+AAGCTGAC
GTCGGAATGGAATCGTAAATTGGACGGGACTTATACTAAATATTCTAGTCTTACCAGGTATTCTGCATTTTTCCACAGGCACACATGTATCTTTCAAACAATCCGTGAATATAGTGTGAGGCTTTATTCCCTTCTTCCTCATTAACTGAG
A00129:980:H5TVGDSX2:4:1124:1524:98311:N:0:TGTCGCAT+AAGCTGAC
CACCTAACCTAGAGTACCACTTTAATCGTAACTAAAACTACTCTACTACGGAGCTGAGTCTTTAGAGGCAACTCAACCTTCCTCACATATAAGCTAAAAGTGGTGGTCTAATCCACTCTGCTTTTAGACTCTTATATGCAAGTTCACTCC
A00129:980:H5TVGDSX2:4:1126:11279:367461:N:0:TGTCGCAT+AAGCTGAC
ACCCCATCCGAATGCCAACTCTAGCGCTTGTTTAGCATTCTCAATGGTTGCTACTCGACGACCCAATCCTCGAGCATGTGTCCAATTGGTTGTTCCTTCTATAGAAACATTATCCAGATTGGCTAGAAACACGGGTCTTGTTGGATGTTT
A00129:980:H5TVGDSX2:4:1127:7699:341781:N:0:TGTCGCAT+AAGCTGAC
CGGATAAAGGCAAATCAGTAATACCTAACCAAGCTAACCTAATTAACAAACAATTTGAAATTGTATTCAATATGTCCGTTATTGGAGAACCTGATGGAATTCCGCAAGGTACTCGGTACACCAAATCGCGACATAGATGACTAGGCG
A00129:980:H5TVGDSX2:4:1140:5041:243771:N:0:TGTCGCAT+AAGCTGAC
CCACCGTAACAAACTAGCACGACATGTCTAGAAAATTCGGATAAAGGCAAATCAGTAATACCTTGCCAAGCCAATCGAATTAACAAACAATTCGAAATAGTATTCAAAATGTCCGTAATTGGTGATCCAGAAGGAATACCGCATAGTACG
A00129:980:H5TVGDSX2:4:1169:13883:227481:N:0:TGTCGCAT+AAGCTGAC
TATATTTTTCTTTCTTACTCCAATTACTTTCTTCTACGGCAAATACAAGTTATTTCATTTCTTTGCGCTTTATAAGTAACCGTTGTAACTTAGTAACTCTTAGTTCGAGGAATTATTTAGAAAGCTTTTTAAGTAACAATATATTT