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Old 11-10-2009, 09:35 AM   #1
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Location: Canada

Join Date: Oct 2009
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Default Mosaik Merge Error


I've been trying to merge all of the sorted alignment files in a directory. According to the documentation this is possible. Each time I try do it I get the following error: ERROR: It seems that the input file (directory) is not in the MOSAIK alignment format..

I am supply the command as follows:

./MosaikMerge -in directory -out co-assembly file

The files in the directory are all individually sorted. To test that there wasn't a problem with the files, I also tried to just merge two files in that directory as follows:

./MosaikMerge -in directory/file1 -in directory/file2 -out co-assembly file

And that worked just fine. I didn't note any timeouts or failures while running MosaikSort which could have cause something to become corrupted.

Has this ever been encountered previously? I am trying to merge 67 alignments in the directory. I am using illumina data.

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Old 11-11-2009, 01:05 PM   #2
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Default I think it's a bug

The same thing happened to me when I updated to version 1.0. I think it's a bug. You can get around it by moving into the directory that contains the sorted alignments and entering each filename into the command separately with the -in flag. Since it would be a pain to do that for 60+ files, if you're working on a linux system and let's say your sorted files all end with .Aln, you could do something like:
ls | sed -r 's/Aln/Aln -in/g' | tr "\n" " "
Then copy and paste the results into your MosaikMerge command after erasing the final -in flag and adding -in before the first filename.

I made it past that bug but was stopped in my tracks by a MosaikAssembler bug that's already been listed on the project website: ""ERROR: An attempt
was made to get reads from an alignment archive that hasn't been opened yet".

Everything was working fine for 0.9, guess I should have waited to update to 1.0...
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