ctx63 clean can't read "magic word"

[er432]

I am trying to clean a joined graph containing three colors as follows:

ctx63 clean ${GRAPH_DIR} -o /refAndSamples.basalAndropogonae.clean.ctx ${GRAPH_DIR}/refAndSamples.basalAndropogonae.ctx

I get the following output:

[05 Jun 2014 23:46:12-Wij][cmd] /programs/mccortex/bin/ctx63 clean /workdir/er432/andropogonae/mccortex_out -o /refAndSamples.basalAndropogonae.clean.ctx /workdir/er432/andropogonae/mccortex_out/refAndSamples.basalAndropogonae.ctx
[05 Jun 2014 23:46:12-Wij][cwd] /local/workdir/er432/andropogonae/mccortex_out
[05 Jun 2014 23:46:12-Wij][version] ctx=470b4ca zlib=1.2.3 htslib=0.2.0-rc8-6-gd49dfa6 ASSERTS=ON CHECKS=ON k=33..63
[src/kmer/graph_reader.c:101] Error graph_file_read_header(): Couldn't read 'Magic word': expected 6; recieved: 0; [file: /workdir/er432/andropogonae/mccortex_out]
[05 Jun 2014 23:46:12-Wij] Fatal Error

[noporpoise]

McCortex is picky about command argument order. Arguments must come before the end:

ctx63 clean -o output [.. more options ...] <in.ctx>

The error message indicates it is trying to read your output (rather than write to it).

Also, I've just made a new release - you can update to the latest version with:

git pull
cd libs && make && cd ..
make MAXK=63

I'm closing the issue - please reopen if the problem persists.