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I installed Longstitch and ran the test script with no issues. The output files matched the expected output files. But when I am now trying to run Longstitch on my own data I am getting this error.

(medaka) operations@LabPC1:~/medaka/longstitch-1.0.5$ ./longstitch run draft=~/medaka/~medaka/medaka_results/consensus.fa reads=~/medaka/combined.fastq G=4.5e8
make: command: Command not found
make: command: Command not found
make: *** No rule to make target'/home/operations/medaka/~medaka/medaka_results/consensus.fa.fa', needed by'/home/operations/medaka/~medaka/medaka_results/consensus.fa.cut250.tigmint.fa'.  Stop.

I changed the file name from .fasta to .fa for my draft assembly because it requires a .fa file, but now I am getting ".fa.fa" What is wrong here?

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  • $\begingroup$ Please provide a link and/or additional information about what Longstitch is. It would also be useful if you could provide a few lines of input and output (e.g. from both the example data and your own data). $\endgroup$
    – gringer
    Dec 21, 2023 at 9:10

2 Answers 2

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Could you download it from conda and try again? Its here, https://docs.conda.io/en/main/miniconda.html

Then,

conda create --name myenv
conda activate myenv
conda install -c bioconda longstitch
longstitch ...

Conda avoids all the build stuff.


Notes

If you find that "conda" is slow and doesn't ever load.

There is an alternative to conda called mamba, this is fast and designed to address this exact issue. I have never needed to use it so the following is a rough guide only.

Download and install via

conda create --name myenv
conda activate myenv
conda install -c conda-forge mamba

The documentation is here, https://mamba.readthedocs.io/en/latest/user_guide/mamba.html

I've never used it but the idea is ...

mamba create -n mambaenv <list of packages>
mamba activate mambaenv

The list of packages could be left blank for now, then,

mamba install "Python>=3.10.0" numpy pandas pathlib
mamba install longstitch 

Can also do

mamba install -n mambaenv longstitch

NOTE longstitch exists strictly in -c bioconda. You do not seem to search and install via channels in mamba

You search for a package and its dependencies via

mamba repoquery search longstitch
mamba repoquery depends -a longstitch

It is important to place a virtual environment between the system Python and package Python (don't want a system corruption).


Finally ... For fa.fa ... hmmmm, try ls *.fa and check for .fa.fa files.

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The main issue I can see is the filenames, and should be easily solvable.

Simply put, LongStitch is very particular about filenames. It expects the input draft to have the extension .fa, and the input reads to have any from a range of extensions (your .fastq is perfectly fine, though).

The main issue is that LongStitch expects the extensions to be missing from the command. So if your draft is draft is called consensus.fa and your reads are combined.fastq, then the command would include something like draft=consensus reads=combined, not draft=consensus.fa reads=combined.fastq.

(unsure if it accepts input from different directories, or whether you'll need to move your input to the same directory as well)

More generally, when having issues with a particular tool which is available via github, I would encourage you to have a look at the 'Issues' or 'Help' section. What I normally do is to delete the 'is:issue is:open' terms in the search bar, which allows me to search for my bug among older, potentially solved issues (e.g. https://github.com/bcgsc/LongStitch/issues/54), and also generally to check that the software is still supported.

Good luck!

(*that said, M_'s suggestion of using mamba is generally a good one, and has helped me with another LongStitch bug)

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