MissingInputException

[Siupek]

Hi,

When I try to run binny I constantly get MissingInputException:

Config file /home/piotrs/miniforge3/envs/binny/lib/python3.10/site-packages/binny/config/config.default.yaml is extended by additional config specified via the command line. Building DAG of jobs... MissingInputException in rule prepare_input_data in file /home/piotrs/miniforge3/envs/binny/lib/python3.10/site-packages/binny/Snakefile, line 136: Missing input files for rule prepare_input_data: output: /mnt/Dane/piotrs/arsenic/metagenome/mags/binny/binny/intermediary/assembly.fa, /mnt/Dane/piotrs/arsenic/metagenome/mags/binny/binny/intermediary/reads_sample_000001_sorted.bam, /mnt/Dane/piotrs/arsenic/metagenome/mags/binny/binny/intermediary/reads_sample_000002_sorted.bam affected files: /mnt/Dane/piotrs/arsenic/metagenome/mags/binny/bam_binny/zs1_2.bam /mnt/Dane/piotrs/arsenic/metagenome/mags/binny/bam_binny/zs1_1.bam /mnt/Dane/piotrs/arsenic/metagenome/mags/binny/bam_binny/zs1.fa

All files with contigs as well as bam files are present.
Any idea how to solve that?

[Siupek]

Some update and clarification:

1. I am using binny v2.2.18 installed via conda from bioconda channel. Cloning repository and installing it as in documentation didn't work, there was problem with mantis and it could not pass installation check.

2. In this version Snakefile seems to expect that the input files will be in directory named 'binny'. I ran software from the project directory and above error appeared. After checking it carefully I noticed that in the path reported by the error there is additional /binny/ that was not present in path to the input files. So in my project directory after making 'binny' directory and copying files there (into subdirectory 'input') the above error didn't appear anymore...

3. ... but another error appeared:

Config file /home/piotrs/miniforge3/envs/binny/lib/python3.10/site-packages/binny/config/config.default.yaml is extended by additional config specified via the command line.
Building DAG of jobs...
MissingInputException in rule merge_contig_depths in file /home/piotrs/miniforge3/envs/binny/lib/python3.10/site-packages/binny/Snakefile, line 211:
Missing input files for rule merge_contig_depths:
output: /mnt/Dane/piotrs/arsenic/metagenome/mags/binny/binny/intermediary/assembly.contig_depth.txt
affected files:
/mnt/Dane/piotrs/arsenic/metagenome/mags/binny/binny/intermediary/assembly_contig_depth_.txt

This seems to be more tricky and might be some bug within Snakefile but I am not sure. At the same time it appear to me that even though I have passed bam files as an arguments (flag -b) it still was looking for depth.txt file. To overcome this problem instead of bam files I provided depth.txt (calculated for metabat2) and it went pass the error...

4. ...just to crash at singularity image (I am working on remote server at the University):

Activating singularity image /home/piotrs/miniforge3/envs/binny/lib/python3.10/site-packages/binny/32440e0ace399ac6f985ecb10b7501fa.simg
INFO: Converting SIF file to temporary sandbox...
FATAL: while extracting /home/piotrs/miniforge3/envs/binny/lib/python3.10/site-packages/binny/32440e0ace399ac6f985ecb10b7501fa.simg: root filesystem extraction failed: extract command failed: ERROR : Failed to create container process: Operation not permitted
: exit status 1
[Tue Jan 27 14:38:57 2026]
Error in rule annotate:
jobid: 3
input: /mnt/Dane/piotrs/arsenic/metagenome/mags/binny/binny/intermediary/assembly.formatted.fa
output: /mnt/Dane/piotrs/arsenic/metagenome/mags/binny/binny/intermediary/prokka.gff, /mnt/Dane/piotrs/arsenic/metagenome/mags/binny/binny/intermediary/annotation.filt.gff, /mnt/Dane/piotrs/arsenic/metagenome/mags/binny/binny/intermediary/prokka.faa
log: /mnt/Dane/piotrs/arsenic/metagenome/mags/binny/binny/logs/analysis_annotate.log (check log file(s) for error details)
shell:

    export TMPDIR=/mnt/Dane/piotrs/tmp/
        /home/piotrs/miniforge3/envs/binny/lib/python3.10/site-packages/binny/bin/prokkaP --force --outdir /mnt/Dane/piotrs/arsenic/metagenome/mags/binny/binny/intermediary --tmpdir /mnt/Dane/piotrs/tmp/ --prefix prokka                       --noanno --cpus 24 --metagenome /mnt/Dane/piotrs/arsenic/metagenome/mags/binny/binny/intermediary/assembly.formatted.fa >> /mnt/Dane/piotrs/arsenic/metagenome/mags/binny/binny/logs/analysis_annotate.log 2>&1

        # Prokka gives a gff file with a long header and with all the contigs at the bottom.  The command below keeps
        # only the gff table.

    LN=`grep -Hn "^>" /mnt/Dane/piotrs/arsenic/metagenome/mags/binny/binny/intermediary/prokka.gff | head -n1 | cut -f2 -d ":" || if [[ $? -eq 141 ]]; then true; else exit $?; fi`
    LN1=1
    LN=$(($LN-$LN1))
    head -n $LN /mnt/Dane/piotrs/arsenic/metagenome/mags/binny/binny/intermediary/prokka.gff | grep -v "^#" | sort | uniq | grep -v "^==" > /mnt/Dane/piotrs/arsenic/metagenome/mags/binny/binny/intermediary/annotation.filt.gff

    (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: .snakemake/log/2026-01-27T143536.309306.snakemake.log

This one I do not how to tackle and would appreciate any help or suggestions.

Cheers,
Piotr

[ohickl]

Hi Piotr,

FATAL: while extracting /home/piotrs/miniforge3/envs/binny/lib/python3.10/site-packages/binny/32440e0ace399ac6f985ecb10b7501fa.simg: root filesystem extraction failed: extract command failed: ERROR : Failed to create container process: Operation not permitted

seems like there is a permission (or space?) issue. Do your home and working dirs have enough quota?
In the binny out log dir, what does analysis_annotate.log say?

[Siupek]

Hi,

Thanks for reply.

The analysis_annotate.log file is empty.

The directory where all the data are and from where I run binny is on disk with approx. 2T free space, but if the extraction is into home directory it indeed can have not enough space (approx. 68G left). It is shared machine, so convincing other users to release some of the space can be tricky. Will give an update when I try this or I will try to check it on another machine.