MissingRuleException error

[hannahgoldswain]

Hi!

I am trying to use the pipeline with the default command: snakemake all --config input_fastq=/path/.fastq reference_fasta=/path/ref.fasta threads=16 --cores 4

(I got told to add the cores on by another error).
However I get this error: MissingRuleException: No rule to produce all (if you use input functions make sure that they don't raise unexpected exceptions).

I'm not too familiar with snakemake but can't seem to find 'all' in the snakefile or scripts? How do I resolve this?

Thanks!

[jpn2021]

I have the same issue

[jimmy200340]

Try to run the command without "all"

snakemake -p -j 4 --configfile $CONF

and it'll run the pipeline with default jobs (calc_depth, call, call_cutesv, filter_vcf, index_lra, index_vcf, map_lra,print_version and sort_vcf).
If you need to run qc, then use

snakemake qc -p -j4 --configfile $CONF

[hannahgoldswain]

Thank you for your comment! However, when I do this I get a further error:

File "pysam/libcutils.pyx", line 115, in pysam.libcutils.encode_filename
TypeError: Argument must be string or unicode.
[W::sam_read1] Parse error at line 1
samtools addreplacerg: [readgroupise] Error reading from input file: Invalid argument
[Sun Apr 11 12:44:14 2021]
Error in rule map_lra:
jobid: 2
output: sv_sample01/alignment/sv_sample01_lra.bam, sv_sample01/alignment/sv_sample01_lra.bam.bai
shell:
catfishq -r ....[with the command following it]
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

I have tried installing the different programmes in the command but still come up with the same error. Please can you help me? Thanks!

[imdanique]

Hi! I have the same problem. Have some of you managed to solve the issue? snakemake all is not working

edit:
I've tried to execute snakemake without 'all' and then it gave me an error:

MissingOutputException in line 111 of /data/ont/286/minread15K/cutesv/pipeline-structural-variation-2.0.2/Snakefile:
Job Missing files after 5 seconds:
/data/ont/hg38/hg38_dna.primary_assembly.fa.gli
This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait.
Job id: 6 completed successfully, but some output files are missing. 6
  File "/home/prom/anaconda3/envs/ont/lib/python3.8/site-packages/snakemake/executors/__init__.py", line 589, in handle_job_success
  File "/home/prom/anaconda3/envs/ont/lib/python3.8/site-packages/snakemake/executors/__init__.py", line 252, in handle_job_success

It means that rule index_lra that should generate reference.fa.gli is not working properly. Do you have any idea how to fix it? Tried to change --latency-wait, nothing changed

[josealvesferrao]

Hi! I have the same problem. Have some of you managed to solve the issue? snakemake all is not working

edit:
I've tried to execute snakemake without 'all' and then it gave me an error:

MissingOutputException in line 111 of /data/ont/286/minread15K/cutesv/pipeline-structural-variation-2.0.2/Snakefile:
Job Missing files after 5 seconds:
/data/ont/hg38/hg38_dna.primary_assembly.fa.gli
This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait.
Job id: 6 completed successfully, but some output files are missing. 6
  File "/home/prom/anaconda3/envs/ont/lib/python3.8/site-packages/snakemake/executors/__init__.py", line 589, in handle_job_success
  File "/home/prom/anaconda3/envs/ont/lib/python3.8/site-packages/snakemake/executors/__init__.py", line 252, in handle_job_success

It means that rule index_lra that should generate reference.fa.gli is not working properly. Do you have any idea how to fix it? Tried to change --latency-wait, nothing changed

Hi imdanique,

I got the same error. To solve it I copied the reference genome fasta file (reference.fa) to another location in the server (a location where I have full access/permisson, such as your home) and then used that new path in the "reference_fasta" parameter. As the pipeline tries to write (output) the reference.fa.gli file in the same location where the reference.fa file is, in my cause would cause this error. Try this to exclude the same issue.