This is a test version of Biostars. For the public version, visit https://www.biostars.org.
velveth (fasta does not seem to be in FastA format)

Hey, I am trying to run velveth on my mac but keep getting this error message "F1.fasta does not seem to be in FastA format" which I have no idea why since F1.fasta is a fasta file. Here is my code. Anyone might have an idea what is going on?? both F1.fasta and F2.fasta are fasta files and the terminal directory has these two files.

velveth Assem 31 -fasta -shortPaired F1.fasta F2.fasta
assembly
• 4,461 views • link
updated by John Torcivia • John Torcivia • written by kelvinfrog75 • kelvinfrog75

Show a head of your files to provide further information

• 1 views • link
written by Antonio R. Franco Antonio R. Franco

Actually, I think I pasted something wrong. Here is the sequence head again. F1.fasta

>SRR041654.1 HWI-EAS284_61BKE:5:1:2:1334/1
NGCGAGGCTTCCATCAGTGAAATGTTTCCTTTCTGTTGTTGAAGTTTCATCTCAGCCAGAAGGCGCTCCAACGAAGTTATTTCTTTTTCATAAACAGCCA
>SRR041654.1 HWI-EAS284_61BKE:5:1:2:1334/2
ACAAGGAAATGGCCGGATATCAGTTTCAGGAAATCATGCGCACCTTGCATAGTGAGCTGAACGAACGATTTGTCGAGACTTATTTTCTGACTAGAAATAT
>SRR041654.2 HWI-EAS284_61BKE:5:1:2:1511/1
NGAAGCGTGACAAAATCACGTACAATACTCAGACTACCTCCGCCACCTGAGAAGCTCATATCCGGATAATCCACTTGATATAAATGTCCGAAAATGCGTT
>SRR041654.2 HWI-EAS284_61BKE:5:1:2:1511/2
TCGGGAAATGCTGGAAATCAGAGTGGCTGATACAGGGATCGGAATTAAAAAAGAAGACAGAGAACGCATTTTTGGACATTTTTATCAAGTGGTTTATCCT
>SRR041654.3 HWI-EAS284_61BKE:5:1:2:1671/1
NGGTGTGTCTGTATTGCTGTCTGCCGTAACGGTAATTTTCCTGATTTCGGCAACTATCATTGTTTTTACTCCTTTACGTAATTATTTGCCGGGATATATG

F2.fasta

>SRR041655.1 HWI-EAS284_61BKE:6:1:2:1735/1
NAAATCAGACAAATCTCCGTTATTGGTATATACTTTGGGAGTGTTATGGAATTGCACACCCATTTCGAACATGAAGCCAATTCGTTTCTTAGGAATCGCT
>SRR041655.1 HWI-EAS284_61BKE:6:1:2:1735/2
GAAATCGGAAACTATCGTATACCTGTAGATCAGAACGGAAATATATCTGGTGGTTTGAAGGTTTCTTCATTCCGTCCTTATCTTGGACTAGGCTTCGGAA
>SRR041655.2 HWI-EAS284_61BKE:6:1:2:1264/1
NATGTAGCATTAAAAATTACATCCTAAACTTATCGATAAATGAGTACGCCCATCATAATCATAGTCAGAGGTATTTACACGATCGAATACAACTTTTGCA
>SRR041655.2 HWI-EAS284_61BKE:6:1:2:1264/2
TTACAACAAGGGCTGACTAATTATTATACCTGTGATTACTATCGTATTGGCGGGGCGATAAAGGATTTGCAAAAAAAAAAAGAAAAAAGAAGAAAGAGAA
>SRR041655.3 HWI-EAS284_61BKE:6:1:2:1293/1
NACAAGCTGATTAAGCCTATAAATAAGACCTTTATTTTCCCCATCTGAAATAACTCGAATCCTCCTATCAGTTGCATAACTTAAAGCAATTTCTAAGGAA
• 1 views • link
written by kelvinfrog75 • kelvinfrog75

Do the following 

cat  F1.fasta | grep ">"  | wc -l

And the same with the other file, and give us the numbers. This counts the number of reads, and will see if both files have the same number

• 1 views • link
written by Antonio R. Franco Antonio R. Franco

4 answers

Hey, do you think it has something to do with the type of text file. I have a MAC and my computer indicate the kind of file is "TextEdit Document". I suspect it can be a problem since this code works fine for me before. But between last time I used it and now, I think I downloaded some text file apps on my computer and it changes the kind of text file....

• 1 views • link
written by kelvinfrog75 • kelvinfrog75

Its possible you've gotten the wrong formatting for the endlines somehow.

If you do:

cat -v F1.fasta

Do you see ^M anywhere (at the end of the lines)?

• 1 views • link
written by John Torcivia • John Torcivia

If you try to run something like 

velveth myOutputdirectory/ 31 -fasta -shortPaired F1.fasta F2.fasta

Do you still get the same problem?

• 0 views • link
written by John Torcivia • John Torcivia

Do you think it is the N messing it up? if so, It is weird since they are the tutorial sequences. 

 > head F1.fasta
    > >SRR041654.1 HWI-EAS284_61BKE:5:1:2:1334/1 NGCGAGGCTTCCATCAGTGAAATGTTTCCTTTCTGTTGTTGAAGTTTCATCTCAGCCAGAAGGCGCTCCAACGAAGTTATTTCTTTTTCATAAACAGCCA
    > >SRR041654.1 HWI-EAS284_61BKE:5:1:2:1334/2 ACAAGGAAATGGCCGGATATCAGTTTCAGGAAATCATGCGCACCTTGCATAGTGAGCTGAACGAACGATTTGTCGAGACTTATTTTCTGACTAGAAATAT
    > >SRR041654.2 HWI-EAS284_61BKE:5:1:2:1511/1 NGAAGCGTGACAAAATCACGTACAATACTCAGACTACCTCCGCCACCTGAGAAGCTCATATCCGGATAATCCACTTGATATAAATGTCCGAAAATGCGTT
    > >SRR041654.2 HWI-EAS284_61BKE:5:1:2:1511/2 TCGGGAAATGCTGGAAATCAGAGTGGCTGATACAGGGATCGGAATTAAAAAAGAAGACAGAGAACGCATTTTTGGACATTTTTATCAAGTGGTTTATCCT
    > >SRR041654.3 HWI-EAS284_61BKE:5:1:2:1671/1 NGGTGTGTCTGTATTGCTGTCTGCCGTAACGGTAATTTTCCTGATTTCGGCAACTATCATTGTTTTTACTCCTTTACGTAATTATTTGCCGGGATATATG
    head F2.fasta
    >SRR041655.1 HWI-EAS284_61BKE:6:1:2:1735/1
    NAAATCAGACAAATCTCCGTTATTGGTATATACTTTGGGAGTGTTATGGAATTGCACACCCATTTCGAACATGAAGCCAATTCGTTTCTTAGGAATCGCT
    >SRR041655.1 HWI-EAS284_61BKE:6:1:2:1735/2
    GAAATCGGAAACTATCGTATACCTGTAGATCAGAACGGAAATATATCTGGTGGTTTGAAGGTTTCTTCATTCCGTCCTTATCTTGGACTAGGCTTCGGAA
    >SRR041655.2 HWI-EAS284_61BKE:6:1:2:1264/1
    NATGTAGCATTAAAAATTACATCCTAAACTTATCGATAAATGAGTACGCCCATCATAATCATAGTCAGAGGTATTTACACGATCGAATACAACTTTTGCA
    >SRR041655.2 HWI-EAS284_61BKE:6:1:2:1264/2
    TTACAACAAGGGCTGACTAATTATTATACCTGTGATTACTATCGTATTGGCGGGGCGATAAAGGATTTGCAAAAAAAAAAAGAAAAAAGAAGAAAGAGAA
    >SRR041655.3 HWI-EAS284_61BKE:6:1:2:1293/1
    NACAAGCTGATTAAGCCTATAAATAAGACCTTTATTTTCCCCATCTGAAATAACTCGAATCCTCCTATCAGTTGCATAACTTAAAGCAATTTCTAAGGAA
• 1 views • link
written by kelvinfrog75 • kelvinfrog75

F1.fasta looks very strange, while F2.fasta looks OK. Is this just formatting from this system or does F1.fasta really have all sequences in one line?

• 1 views • link
written by Philipp Bayer Philipp Bayer

The first sequence is wrong. You have two ">" at the beginning, and you should have only one. In addition, after the >"name" and the comment (the word starting with HWI..) you must have a carriage return to show the fasta sequence in a second lane

In other words. You must get exactly waht you see in F2.fasta

Run this code to fix it

$ cat F1.fasta | awk '{print $2 " " $3 "\n" $4}' > F1_fixed.fasta

Notice the empty spaces. Then, after checking the file, erase the wrong one and rename F1_fixed.fasta as the original, or use that name in velvet directly

You can also run it in this way

$ awk '{print $2 " " $3 "\n" $4}' F1.fasta > F1_fixed.fasta

In both cases, you obtain the correct fasta file

If you notice that the double ">" is not in the original file, take into account that print $2 means print the second word, $3, the third, etc, and then change the code in accordance. "\n" means a carriage return

• 1 views • link
written by Antonio R. Franco Antonio R. Franco

So I think both of them is ok but I will wonder if the error is due to the "N" in the fasta file. I made some mistake in my previous post. F1.fasta is like this 

>SRR041654.1 HWI-EAS284_61BKE:5:1:2:1334/1
NGCGAGGCTTCCATCAGTGAAATGTTTCCTTTCTGTTGTTGAAGTTTCATCTCAGCCAGAAGGCGCTCCAACGAAGTTATTTCTTTTTCATAAACAGCCA
>SRR041654.1 HWI-EAS284_61BKE:5:1:2:1334/2
ACAAGGAAATGGCCGGATATCAGTTTCAGGAAATCATGCGCACCTTGCATAGTGAGCTGAACGAACGATTTGTCGAGACTTATTTTCTGACTAGAAATAT
>SRR041654.2 HWI-EAS284_61BKE:5:1:2:1511/1
NGAAGCGTGACAAAATCACGTACAATACTCAGACTACCTCCGCCACCTGAGAAGCTCATATCCGGATAATCCACTTGATATAAATGTCCGAAAATGCGTT
>SRR041654.2 HWI-EAS284_61BKE:5:1:2:1511/2
TCGGGAAATGCTGGAAATCAGAGTGGCTGATACAGGGATCGGAATTAAAAAAGAAGACAGAGAACGCATTTTTGGACATTTTTATCAAGTGGTTTATCCT
>SRR041654.3 HWI-EAS284_61BKE:5:1:2:1671/1
NGGTGTGTCTGTATTGCTGTCTGCCGTAACGGTAATTTTCCTGATTTCGGCAACTATCATTGTTTTTACTCCTTTACGTAATTATTTGCCGGGATATATG

and F2.fasta is like this 

>SRR041655.1 HWI-EAS284_61BKE:6:1:2:1735/1
NAAATCAGACAAATCTCCGTTATTGGTATATACTTTGGGAGTGTTATGGAATTGCACACCCATTTCGAACATGAAGCCAATTCGTTTCTTAGGAATCGCT
>SRR041655.1 HWI-EAS284_61BKE:6:1:2:1735/2
GAAATCGGAAACTATCGTATACCTGTAGATCAGAACGGAAATATATCTGGTGGTTTGAAGGTTTCTTCATTCCGTCCTTATCTTGGACTAGGCTTCGGAA
>SRR041655.2 HWI-EAS284_61BKE:6:1:2:1264/1
NATGTAGCATTAAAAATTACATCCTAAACTTATCGATAAATGAGTACGCCCATCATAATCATAGTCAGAGGTATTTACACGATCGAATACAACTTTTGCA
>SRR041655.2 HWI-EAS284_61BKE:6:1:2:1264/2
TTACAACAAGGGCTGACTAATTATTATACCTGTGATTACTATCGTATTGGCGGGGCGATAAAGGATTTGCAAAAAAAAAAAGAAAAAAGAAGAAAGAGAA
>SRR041655.3 HWI-EAS284_61BKE:6:1:2:1293/1
NACAAGCTGATTAAGCCTATAAATAAGACCTTTATTTTCCCCATCTGAAATAACTCGAATCCTCCTATCAGTTGCATAACTTAAAGCAATTTCTAAGGAA
• 1 views • link
written by kelvinfrog75 • kelvinfrog75 
velveth Assem 31 -fasta -shortPaired test1.fasta test2.fasta

works perfectly fine for me with those two sequences. Check the end of your files with tail, maybe there's some error hiding there.

• 1 views • link
written by Philipp Bayer Philipp Bayer

Log in to answer this question.

More posts like this