ERROR 0

[Helen]

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I am currently getting this error when trying to run mifaser:

 ERROR#0 - Translation failed. Error: 'T=0'

My fasta file properties:

head test.fa

NODE_1_length_682069_cov_18.237281_1 # 3 # 101 # 1 # ID=1_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.333
TGGATTGTTAAGAGGTTAGATATAAGATCTTTGTATGAAGTTCTGAAGGTACAGAAAGAAAAGACCGATGAGGTCTTTTTTTTGTGCCATTTAAGTTGA
NODE_1_length_682069_cov_18.237281_2 # 213 # 2462 # 1 # ID=1_2;partial=00;start_type=TTG;rbs_motif=4Base/6BMM;rbs_spacer=13-15bp;gc_cont=0.393
TTGATTCCCCTCTTATTTTGTATATATACAGTACAACGGATAGAAAAAAACGCTTTACGGAATTCGGTGTTTGGATTACTGCTTTCACAGACAGGAATGGTTATGCTGTATGGTATGGCGTTGATGACAGTCGATGAGAAGCTGGCATTGTTTTTTTATGCACTTTTTTATTTTTGTGTAGATTTTATGACGTTGTTGCTGTTTATTTATAGTCGTGTATATGCTGACACCTATCGGCATAAAGTATGGATGCGTCCGGTAACGTATATCCTGTTGCTTACAGATGCGATTGTGTTATTTTCAAATCTTAGAGTGCAGAATGTATTCCATGTGGCTCCGATGACAGACCAGTTCGGTAATGTTTATTATGGTGTAAAAAGCTATGGTATCTTGTATGGGGTTCATACATTGATTTGTTATGCATTTGCTGCGGCATGTCTGATTGTTCTGCTTGTCCGCAGGTCAAAATGCCCAAGAATTTTTCAAGTAAATTATTCTTCGATCATTATTACGCTTATATTGACCGCAATTGCAAATATTATGTTTTTCAAGTTTGAATTCATTTACGATTTTTCATTGATCGGATATACCGCATTATGTTGTGCAATCACTTATTTTACATTCTTTCATATTCCGGCGGGCCTTGTAGAAAAAATGCTGGCCTTGTTTATTAAGACTATCGATGACGGAGTTGTCTGTTATGATGTAAAAGGGAAATGCATTCATGCAAATGAACAGGCAAAGAAGATTCTTCATGTGTCTGAGCTTTCTGCACTTGATAAAAAGTTGCAGGGCTGGCTGAATGGAAAAAATCTTCGGGATATTCATGATATTGCATGGAAAGAACAATTTCGAATAGATGGAAAAGTACATTTCTTTCAGTTTCAATATAAGAAGATGATATATGAGAATCACGAGATTGGAAGCTTTTTTTTGTTACATGACCGAACGGAAGAAGTGGAGCGTGTGAAATCTGAACAGTATAAGGCAAACCATGATGCATTGACAGGTATTTATAATCGGGAATATTTTTATGAGTGCGCAGAACAGATGTTACGGGAGAATTCAGATACGGCGTTTTATATTGTTTGTAGTGATATCCGTGATTTTAAGATTGTGAACGATGTATATGGAAGTAAAAAGGGGGATGATATTTTAATAAAACAGGCAGAAAGTCTGAAACAGAAAACTCCGGCAGGTTGTATTTATGGGCGGTTGGCAGGTGACCGGTTTGCACTGCTTTTGCCAAAGGAATTATTTCAGGAAAACATATTTCGACGGGAGATTTCGCGAATTGAGCATATAGAAGGTAATTCCAGTTTTAGGCTGCGTATGTATATGGGAATCTATGAAGTAGACGATAGGAATACACCGGTTGCAGTTATGTGTGACCGGGCTATTATGGCAATCAAAACCATCAAGGATGATGTTTCAAACCGTATCAGCTATTATGATAAGGAGCTGCGGGAGACTGCACTCAAGGAACAGGGAATTATCAGTCAGTTCCATGATGCGTTAGAGGGCGGACAGTTCTGCTTTTATATTCAGCCACAGATATCTGCGGACGGTGTTGTGCGTGGTGGAGAAGCACTGGTTCGCTGGATTCATCCAGAGCGTGGTATGATTCCGCCGGGAGAGTTTATTGAGCTGTTTGAGCGGACCGGTCTGATCAGTGAGTTGGATCGTTACATATGGGAGAAAGCCTGTATCCAGCTTCGCGACTGGTGCAGACAGGGACATGCAGATTTTTATTTGTCAGTAAACATTTCACCACGTGATTTTTATTATATGGATATCTATAAAGTGTTTACTCAACTGGTACAAAAGCATGGCTTCGAAGCGAAGAATCTTCATCTGGAAATCACGGAAACGGCAGTCATGTCGGATACGAAAAAAGTAATCCGTCTGGTAAACAAACTGCGGCAGTATGGGTTTAAGGTGGAGATGGATGATTTTGGAAGCGGATATTCTTCTTTGAATATGTTGAAGGATATCAAGATGGATACAATCAAACTGGATATGGGATTTTTACGTAAGACCAGAAATAATGAACGAAGTATGTCAATCGTAAGCAATGTTATTCATTTGTCGAAACGACTGGGGATGGAGGTTGTTACCGAGGGAGTAGAAACCAGGGAACAGGTGGATGCATTAACCATGATGGGGTGCGATGTATTTCAAGGATATTATTTTGCAAAACCAATGTCGGTTTGGGATTATGAAGACAAATATATTTCAACCGAAGGATAG

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wc -l test.fa
1236606

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What is the reason for this? Thank you

[Helen]

NB. The method to circumvent this error is to set the split flag to 100 and, it successfully ran.

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[Max Miller]

Hi Helen,

from what I can see in your head output, the headers seem to be incorrect. fasta format requires ant header line to start with “>”, thus a correct output should look like this:

>NODE_1_length_682069_cov_18.237281_1 # 3 # 101 # 1 # ID=1_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.333
TGGATTGTTAAGAGGTTAGATATAAGATCTTTGTATGAAGTTCTGAAGGTACAGAAAGAAAAGACCGATGAGGTCTTTTTTTTGTGCCATTTAAGTTGA
>NODE_1_length_682069_cov_18.237281_2 # 213 # 2462 # 1 # ID=1_2;partial=00;start_type=TTG;rbs_motif=4Base/6BMM;rbs_spacer=13-15bp;gc_cont=0.393
TTGATTCCCCTCTTATTTTGTATATATACAGTACAACGGATAGAAAAAAACGCTTTACGGAATTCGGTGTTTGGATTACTGCTTTCACAGACAGGAATGGTTATGCTGTATG [...]

This is why the translation of mi-faser is aborted with ERROR#0. I assume that if you split that file and headers are correct in other parts of that file, those parts run successfully and only the initial splits containing those malformed headers don’t return any results - and are missing in the final merged output. Can you try to correct those headers?

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[Max Miller]

closed