Unable to run lathe due to error raised while building DAG of jobs

[jainv45]

The below-mentioned command was used to run lathe on nanopore and Illumina reads I had. snakemake --use-singularity --singularity-args '--bind /home/veeral/,/media/wangikarlab/Veeral/Seq_data/lathe_runs/' -s /home/veeral/lathe/Snakefile \ --configfile /media/wangikarlab/Veeral/Seq_data/lathe_runs/config.yaml --restart-times 0 --keep-going --latency-wait 30 --cores all

The delimited text file required for data input was written in the following style V1 /path to nanopore data.fastq /path to illumina read1.fastq,/path to illumina read2.fastq

The following error messaged is been put: {'V1': ['/media/wangikarlab/Veeral/Seq_data/illuminaclean/V1_clean1.fastq', '/media/wangikarlab/Veeral/Seq_data/illuminaclean/V1_clean2.fastq']} Building DAG of jobs... MissingRuleException: No rule to produce (if you use input functions make sure that they don't raise unexpected exceptions).

[bsiranosian]

Hi, to clarify, it's saying No rule to produce (blank space)?

Usually there would be an output file listed there, which is why I'm confused. If you attach your config file and the input file I can help you debug further.

[jainv45]

Hi, thank you for replying. I'm not getting any output file, it falls empty with the previously mentioned error. Can you share an example config file and text file indicating the sample information for nanopore and illumina reads? Since our input data is confidential, dropping them on a public platform would be a tricky job.

PFA config file and sample information file used for the run. config.txt V1.txt

I hope this would be helpful to some extent.

[bsiranosian]

Your V1.txt file should be delimited with tabs. Right now it's delimited by spaces. That should fix things. (I hope!)

[jainv45]

Hi, I tried tab delimiter as well. Still, it could not parse through the 1st (sample_name) and 3rd (short_reads) column entry in the text file. However, it is not showing any error with the 2nd (nanopore_reads) column entry. I suspect the problem is something else and not about delimiter.

As same error pops in every time. The logfile of the run also has the same error logged. The error messaged is been put and logged: {'V1': ['/media/wangikarlab/Veeral/Seq_data/illuminaclean/V1_clean1.fastq', '/media/wangikarlab/Veeral/Seq_data/illuminaclean/V1_clean2.fastq']} Building DAG of jobs... MissingRuleException: No rule to produce (if you use input functions make sure that they don't raise unexpected exceptions).

[dgmaghini]

Hi! Thank you for sharing your config.txt and V1.txt files. I went ahead and tried running them, setting the paths to empty placeholder files and changing the min_contig_cutoff to 0. Here is my setup: config.txt V1.txt

Using Snakemake 5.10.0, if I run snakemake -s /path/to/lathe/Snakefile --configfile config.txt -np, it successfully builds the DAG and prints out the job schedule. Are you able to replicate that with the same input files and command?

[jainv45]

Hi, Thank you for sharing the revised setup files. I tried replicating your suggestion with the path to actual input files. I got a dry-run message. Kindly find the attached log file for the same. Logfile.txt