2.0 years ago by

Seattle, WA USA

(Assuming single-line FASTA, as input.)

You could verify your sequences are of different length, as a way to troubleshoot:

```
$ awk '($0 !~ /^>/) { print length($0); }' in.fa | sort -n | uniq
```

If you get multiple values back, then you might investigate your input and cut them to the shortest length.

The following cuts the prefix of any input sequence string down to the shortest length:

```
$ SHORTEST_LENGTH=`awk '($0 !~ /^>/) { print length($0); }' in.fa | sort -n | uniq | head -1`
$ awk -vSL=${SHORTEST_LENGTH} '($0 !~ /^>/) { print($0, 1, SL); } ($0 ~ /^>/) { print $0 }' in.fa > out.fa
```

You could write different logic, if you wanted to trim flanking regions. It's a little more work to deal with an odd-numbered shortest length, however.

No, this seems to be a more basic problem with loading libraries required to run the tool itself. How did you install it? Try to get it via conda and see if this solves the problem.

42kThanks, I installed it using conda. Could there be another issue to do with installation?

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