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bcgsc / tigmint

⛓ Correct misassemblies using linked AND long reads
https://bcgsc.github.io/tigmint/
GNU General Public License v3.0
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yet another "make: *** No rule to make target" issue #116

Closed salvatierra8 closed 1 year ago

salvatierra8 commented 1 year ago

Greetings,

First of all, sorry for opening another thread about previously posted issues, but after trying several times, i can't use tigmint. So, to be precise i actually installed longstitch through conda command and created a sole enviroment for this tool, i haven't been able use it, that's why i decided to use tigmint alone with no luck either. This is the comand i used (taking longmap=pb out makes no difference) tigmint-make tigmint longmap=pb draft=assembly1 reads=H1_1

And get this message back

make: *** No rule to make target 'assembly1.H1_1.sortbx.bam', needed by 'assembly1.H1_1.as0.65.nm5.molecule.size2000.dist50000.bed'. Stop.

From what i understand after reading similar issues, the problem was that the command was not being run in the working directory, which my Windows derived n00b bioinformatic brain understand as the directory where the files are, however the problem still persist.

And this directory looks like this: (longstitch) salvatierra@salvatierra-FXZR:~/Documents/Secuencias/PacBio$

I would appreciate your help. Thanks in advance.

lcoombe commented 1 year ago

Hello @salvatierra8,

It looks like you are trying to use tigmint-long (Ie. inputting long reads to correct assembly1.fa)? In that case you need to specify the tigmint-long target. Ie:

tigmint-make tigmint-long longmap=pb draft=assembly1 reads=H1_1

There is more information about tigmint-long and how to use it here: https://github.com/bcgsc/tigmint#usage

I hope that helps - thanks for your interest in Tigmint! Lauren

salvatierra8 commented 1 year ago

No, I still get the error with a few changes to the error message:

make: *** No rule to make target 'assembly1.fa', needed by 'assembly1.H1_1.cut500.molecule.size2000.dist50000.bed'. Stop.

lcoombe commented 1 year ago

Could you provide the full log, as well as the command? Do you have a file called assembly1.fa in your current working directory? Seeing a ls in your current working directory (where you run the command) would also help.

salvatierra8 commented 1 year ago

It's running! ... It never crossed my mind that the extension would need to be as described in the code tag, until you empathized in the previous comment, as i understood that fasta=fa=fna, and in a similar way the gzip versions. I had my files named like assemble1.fasta and H1.fasta.gz . Thanks for your help!

lcoombe commented 1 year ago

Excellent - very glad to hear that it's working now!