Comments (1)
lcoombe
commented on June 6, 2024
Hi @ewafula ,
Could you please enclose copy-and-paste blocks in triple back ticks? Using that formatting will make your pasted commands much easier to read.
(https://help.github.com/articles/basic-writing-and-formatting-syntax/#quoting-code)
It looks like the error you are getting in tigmint-cut is very similar to what a user saw in a previous issue reported in the ARCS repo: bcgsc/arcs#48
Try using a newer version of bedtools - I use v2.27.1 and don't get any errors.
Hope that helps!
Lauren
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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
- Understanding tigmint-long outputs HOT 3
- tigmint compilation issue HOT 2
- _sqlite3.cpython-310-x86_64-linux-gnu.so: undefined symbol: sqlite3_trace_v2
- 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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