Error processing input file

[johnomics]

Hello,

Thanks for writing minced, it's a very useful tool.

I'm getting an error running minced 0.3.2 installed via conda:

$ minced minced_test.fasta test
Error processing input file 'minced_test.fasta'. Please, check contents.

This test file is one sequence from a larger assembly:
minced_test.fasta.gz

The larger assembly has 78,439 contigs and we see this message 28 times.

I can't see anything obviously wrong with the FASTA file, and we get what looks like sensible output from minced otherwise.

Please could you see what's causing a problem with this contig?

Many thanks
John

[ctSkennerton]

Hi John,

Thanks for reporting this, I can confirm that I get the same bug. Unfortunately I'm super swamped at my day job and don't have time to work on personal projects right now. Sorry I can't provide an immediate fix, I'll get to this as soon as possible.

Cheers,
Connor

[johnomics]

Hi Connor - thanks for confirming. Don't worry, I know how it is. We'll proceed with the existing results for now. Best wishes, John

[ctSkennerton]

Can you try out the latest commit with your full input file. I've fixed it for the example that you sent me.

[johnomics]

Thank you very much for looking into this! The fix resolves some contigs but not others. We previously had 28 contigs causing errors, now we have 8.

I added a line to CRISPRFinder.java so I could see which contigs were causing the problem. Here are the original 28, 20 of which are now fine:
original_contigs.fasta.gz

And here are the remaining contigs that still throw errors:
remaining_contigs.fasta.gz

All of these remaining contigs are in the first set, so the fix hasn't generated new problems. The errors now being output for the contigs that are now resolved were all positive StringIndexOutOfBoundsExceptions:

java.lang.StringIndexOutOfBoundsException: String index out of range: 17435
java.lang.StringIndexOutOfBoundsException: String index out of range: 222542
java.lang.StringIndexOutOfBoundsException: String index out of range: 23163
...

The remaining 8 errors are all:

java.lang.StringIndexOutOfBoundsException: String index out of range: -1

[ctSkennerton]

This time it should be fixed

[johnomics]

Excellent, that fixes the error and gives us another 35 arrays. Thank you very much! Best wishes, John

[johnomics]

(Tiny thing - v0.3.3 looks good except in CHANGES the version number isn't updated, 0.3.2 is there twice.)