Error with make_common_bf: one of commands exited with non-zero exit code

[Dragonweaver223]

Hello! I am trying to use ntsynt installed through conda on MacOS. I have run into two bugs thus far: when running snakemake, the program throws an error that it cannot find the fasta files even for the demo when I am in the tests folder. Same as issue #68, with the stated fix (putting double quotations around the references list instead of single quotations) working, although I am unable to figure out how to fix this in the script itself.

Following that, after I run the snakemake code on its own with my own files, I get an issue that one of the commands exited with a non-zero exit code. Also, I have noticed that I get an Error that says "NtHash: sequence length (18) is smaller than k (19)", with the sequence length always being smaller than whatever I set k to (in this case I set k to 19 after being told that the sequence length was 20 when k was set to 24).

I have copied and pasted the log below:

Building DAG of jobs...
Using shell: /bin/bash
Provided cores: 12
Rules claiming more threads will be scaled down.
Provided resources: load=2
Job counts:
count jobs
1 all
2 faidx
2 indexlr
1 make_common_bf
1 ntsynt_synteny
7

Building DAG of jobs...
Using shell: /bin/bash
Provided cores: 12
Rules claiming more threads will be scaled down.
Provided resources: load=2
Job counts:
count jobs
1 all
2 faidx
2 indexlr
1 make_common_bf
1 ntsynt_synteny
7

[Sat Aug 15 20:31:01 2026]
rule make_common_bf:
input: NMRcdna.fa.gz, Mousecdna.fa.gz
output: ntSynt.k24.w1000.common.bf
jobid: 4
threads: 12

/opt/anaconda3/envs/GenomicViewer/bin/ntsynt_make_common_bf --genome NMRcdna.fa.gz Mousecdna.fa.gz -p ntSynt.k24.w1000.common --fpr 0.025 -k 19 -t 12
[Sat Aug 15 20:31:09 2026]
Error in rule make_common_bf:
jobid: 4
output: ntSynt.k24.w1000.common.bf
shell:
/opt/anaconda3/envs/GenomicViewer/bin/ntsynt_make_common_bf --genome NMRcdna.fa.gz Mousecdna.fa.gz -p ntSynt.k24.w1000.common --fpr 0.025 -k 19 -t 12
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /Users/Dragonweaver/Documents/.snakemake/log/2026-08-15T203101.092915.snakemake.log

Thanks in advance! Happy to answer any questions that can help to figure out this problem!

[lcoombe]

Hi @Dragonweaver223,

Thanks for the report!

For your first issue - the fix would be in the ntSynt runner file where the snakemake command is called from (You could find where it is by running which ntSynt). I will make that fix upstream, and make a new release as well since it seems to be that a few people are encountering that issue.

For your second issue - Could you let me know what the smallest sequence length in your input assembly is? You could run something like abyss-fac or an awk command. You will get that error if you have any sequences in the input assembly that are shorter than k.

Based on the naming of your files, it looks like you are running ntSynt using cDNA sequences? That’s a really interesting use case, but also one that the default ntSynt parameters might not work well with - so feel free to give me more info and I can try to make some other recommendations.

Thank you for your interest in ntSynt!
Lauren

[Dragonweaver223]

Hi @lcoombe, thank you so much for the quick response, especially on a weekend!

It looks like the smallest sequence length in my input assembly is 9. Thank you for the heads up about using the cDNA sequences -- I am fairly new to genomics and bioinformatics work and so have been playing around loosely with different tools and files! I will try running ntSynt again with the full genomes.

[lcoombe]

Hi @Dragonweaver223,

No worries - happy to help!
Ah yes, those short sequences would be the issue. I'll make an update to make that error a bit more descriptive in the next release.
I hope that things go well with the full genomes test - let me know if you have any further questions!