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Unable to run lathe due to error raised while building DAG of jobs #16
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Hi, to clarify, it's saying 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. |
Hi, thank you for replying. PFA config file and sample information file used for the run. I hope this would be helpful to some extent. |
Your V1.txt file should be delimited with tabs. Right now it's delimited by spaces. That should fix things. (I hope!) |
Hi, As same error pops in every time. The logfile of the run also has the same error logged. |
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: Using Snakemake 5.10.0, if I run |
Hi, |
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).
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