MALT exception: Collapsed file skipped from the analysis

MALT: Megan Alignment Tool
1

Hello,
I am new to MALT and I am getting an error in the analysis of one sample previously filtered and collapsed using AdapterRemoval.
Running malt-run I get the following message:
Malt Exception for file: 'R628.out.collapsed.gz', skipped (java.io.IOException: File format not (or no longer) supported)
On the manual i red that it should support .gz file so I am not understanding why it is not working, does anyone can help understanding that?
Thanks a lot

2

Likely you need to specify in the name that it’s FASTQ (e.g. fastq.gz or fq.gz), not just that it is gzipped.

3

Yes I thought that could be the problem, but I have changed it adding the extension “.fq” but I get exactly the same error.

4

I had the same issue, it has NOTHING to do with files or anything…
Malt wants to store data into -o [path/to/output]… however it doesn’t make this folder itself.
If this folder isn’t made by you beforehand, it considers this a file for some reason instead of a folder? And then gives the error that it cannot handle that file because it’s not longer supported… I’m unsure why they chose this error message for this problem, as it clearly a folder management issue.
Just add mkdir -p [path/to/output] before running Malt with option -o and you shouldn’t get those weird “file format not supported” issues anymore.

Cheers!

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5

Thanks a lot for your help!

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6

Thank you all for the bug report and discussion. I have looked into this and have modified the program accordingly.

Now, before running the search, MaltRun first checks whether it will be able to write to the specified output files, and if not, it will provide a (hopefully) more helpful error message like this:

Directory doesn’t exist: /Users/huson/data/malt/output

or

Can’t create file: /out.rma6

This improvement is available in the latest release, 0.5.2, which I will upload now.

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