Handling highly fragmented assemblies#37
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fka21 wants to merge 1 commit intoMaggi-Chen:masterfrom
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…agmented assemblies, also added a line which cleans assembly headers from bash incompatible characters
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Following up on issue: #16 I had a closer look at what could be causing this. As I wrote in my latest comment of the issue, it seems that the
catcommand cannot handle a lot of contigs simultaneously. My assemblies also had 38.000 contigs and I had the same error. I replaced allcatcommands with afindapproach, which can handle multiple arguments. In my system this resolved the issue.Also, I got errors because I had bash incompatible characters in some of my assemblies, f.ex. "|". These are stripped now with a regex approach.