Comments (2)
Seems lots of users hit this problem (#35 #44 #52 ). The make
somehow constructs a Makefile
target based on the input filename and if the there directory separators in there, it chokes. Likewise, it chokes when I use shell pipe to feed in a FASTA stream from multiple files:
tigmint-make ... reads=<(cat *.fmlrc2.fa)
make: *** No rule to make target `mygenome-long-scaffs.fa./dev/fd/63.cut500.as0.65.nm500.molecule.size2000.trim0.window1000.spanauto.breaktigs.fa', needed by `tigmint-long'. Stop.
Maybe a sed
call in a proper place could fix that.
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Related Issues (20)
- About samtools invalid option in tigmint-make arcs mode HOT 4
- pre-alignment HOT 2
- Forward+reverse + long reads HOT 4
- yet another "make: *** No rule to make target" issue HOT 5
- Feature has length = 0, Skipping - followed by empty output from tigmint-long HOT 9
- Tigmint not making cuts HOT 3
- tigmint-make tigmint error HOT 2
- Error when attempting tigmint-make arcs HOT 2
- Error : no progress of scaffolding running HOT 5
- tigmint-long error HOT 1
- Respect $TMPDIR as anticipated by sort tool HOT 1
- samtools sort may be replaced by bamsort which scales better HOT 2
- pigz may be better replaced by bgzip HOT 2
- tigmint-make ignores $PATH and is supposed to be run from unpacked source tree instead HOT 3
- README does not list all dependencies HOT 2
- Does bin/tigmint_estimate_dist.py really work with FASTA files as well? HOT 5
- src/long-to-linked-pe v1.0: Using more than 6 threads does not scale, reverting to 6. HOT 5
- tigmint_molecule_paf.py: TypeError: expected string or bytes-like object HOT 11
- Cannot compile the bundled while modified copy of make: make-4.1/glob/glob.c:1342: undefined reference to `__alloca' HOT 6
- tigmint-make: minimap2 is being called with -y argument HOT 3
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