Missing input file error when file is in directory

[Kylies5]

Hello, I keep getting "MissingInputException" and "Missing input files for rule pair" when I run mgefinder workflow denote however, all files are in the correct directories. I have deleted them and remade the files with no luck. I have run MGEfinder previously without this error.

============================================================ ===== Summary of your script job =====

The script file is: mgefinderworkflow.sh The time limit is 150:00:00 HH:MM:SS. The target directory is: /scratch/aubksw/MGEfinder/MGEfinder/cluster4 The working directory is: /scratch-local/aubksw.mgefinderworkflows.601211 The memory limit is: 8gb The job will start running after: 2021-06-12T13:43:22 Job Name: mgefinderworkflows Virtual queue: medium QOS: --qos=medium Constraints: --constraint=dmc Using 6 cores on master node dmc19 Node list: dmc19 Nodes: dmc19 dmc19 dmc19 dmc19 dmc19 dmc19 Command typed: /apps/scripts/run_script mgefinderworkflow.sh Queue submit command: sbatch --qos=medium -J mgefinderworkflows --begin=2021-06-12T13:43:22 --requeue --mail-user=ksw0029@auburn.edu -o mgefinderworkflows.o601211 -t 150:00:00$

CHECKING DEPENDENCIES

Current version of snakemake: 3.13.3 Expected version of snakemake: 3.13.3 Current version of einverted: EMBOSS:6.6.0.0 Expected version of einverted: EMBOSS:6.6.0.0 Current version of bowtie2: 2.3.5 Expected version of bowtie2: 2.3.5 Current version of samtools: 1.9 Expected version of samtools: 1.9 Current version of cd-hit: 4.8.1 Expected version of cd-hit: 4.8.1 ############################### Get help documentation with --help. Get version with --version.

PARAMETERS

command: workflow workdir: /scratch/aubksw/MGEfinder/MGEfinder/cluster4 cores: 1 memory: 16000 unlock: False rerun_incomplete: False keep_going: False sensitive: False #################### MissingInputException in line 93 of /home/aubksw/anaconda3/envs/mgefinder/lib/python3.6/site-packages/mgefinder/workflow/denovo.original.Snakefile: Missing input files for rule pair: /scratch/aubksw/MGEfinder/MGEfinder/cluster4/00.bam/Xsp60.XretroflexusSp953.bam COMMAND: snakemake -s /home/aubksw/anaconda3/envs/mgefinder/lib/python3.6/site-packages/mgefinder/workflow/denovo.original.Snakefile --config wd=/scratch$ Traceback (most recent call last): File "/home/aubksw/anaconda3/envs/mgefinder/bin/mgefinder", line 8, in sys.exit(cli()) File "/home/aubksw/anaconda3/envs/mgefinder/lib/python3.6/site-packages/click/core.py", line 764, in call return self.main(args, kwargs) File "/home/aubksw/anaconda3/envs/mgefinder/lib/python3.6/site-packages/click/core.py", line 717, in main rv = self.invoke(ctx) File "/home/aubksw/anaconda3/envs/mgefinder/lib/python3.6/site-packages/click/core.py", line 1137, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/home/aubksw/anaconda3/envs/mgefinder/lib/python3.6/site-packages/click/core.py", line 1137, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/home/aubksw/anaconda3/envs/mgefinder/lib/python3.6/site-packages/click/core.py", line 956, in invoke return ctx.invoke(self.callback, ctx.params) File "/home/aubksw/anaconda3/envs/mgefinder/lib/python3.6/site-packages/click/core.py", line 555, in invoke return callback(args, **kwargs) File "/home/aubksw/anaconda3/envs/mgefinder/lib/python3.6/site-packages/mgefinder/main.py", line 78, in denovo _workflow(workdir, snakefile, configfile, cores, memory, unlock, rerun_incomplete, keep_going) File "/home/aubksw/anaconda3/envs/mgefinder/lib/python3.6/site-packages/mgefinder/workflow.py", line 25, in _workflow shell(cmd) File "/home/aubksw/anaconda3/envs/mgefinder/lib/python3.6/site-packages/snakemake/shell.py", line 88, in new raise sp.CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command 'snakemake -s /home/aubksw/anaconda3/envs/mgefinder/lib/python3.6/site-packages/mgefinder/workflow/denovo.original$

[qianxin-kxy]

Hello , I've also encountered this problem. How did you solve it in the end?

[Kylies5]

This error is usually caused by something wrong in the name or formatting of the file. The file names need to match exactly , including matching upper and lowercase. Check that the files names are all correct and that there are no duplicate named files

[qianxin-kxy]

This error is usually caused by something wrong in the name or formatting of the file. The file names need to match exactly , including matching upper and lowercase. Check that the files names are all correct and that there are no duplicate named files

Thank you very much for your prompt reply. I have rechecked the file names in the folder and it was indeed an oversight to mistake a letter!