AmbiguousRuleException: Rules calculate_proportion and compute_coverage are ambiguous for the file results/bed/28 /test/reads/28_1.fastq.gz.proportion.bed. about rdscan HOT 12 CLOSED

Can you provide your samples sheet?

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from rdscan.

I do not see any attached files. Can you add it via Attach files directly in this GitHub issue thread?

from rdscan.

please find the attached, I missed

Run_accession R1 R2
28 /test/reads/28_1.fastq.gz /test/reads/28_2.fastq.gz

samples.txt

from rdscan.

In the provided file, in the second line, you have two spaces instead of a tab character between 28 and /test/reads/28_1.fastq.gz. Also make sure that the provided path for files exist, in the current state it leads to the root directory, maybe you want to add . before / if files located in the RDscan/test/reads directory. I have attached the
samples.txt file which works on my computer; in my case, files are located in the RDscan/test/reads.

from rdscan.

Thanks for the suggestion went further, but again ended up in another error with my files
The error doesnt happen with test fastq files
localrule compute_coverage:
input: results/mapped/28.proportion.bam, resources/IS6110.bed
output: results/bed/28.proportion.bed
log: logs/bedtools/28.proportion.coverage.log
jobid: 1
reason: Missing output files: results/bed/28.proportion.bed
wildcards: sample=28.proportion
resources: tmpdir=/tmp

Waiting at most 5 seconds for missing files.
regards

from rdscan.

If you send me your FASTQ files, I can look further into it.
Also, please attach all log files from logs/

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from rdscan.

I ran RDscan using your reads and couldn't reproduce your error, everything worked correctly on Linux and macOS. I did make minor changes to the pipeline to fix SyntaxWarning, so you can try to use the latest version.
I also attached the result files for your reads:
RD_known.xlsx
RD_known.bin.txt
RD_known.txt
RD_putative.txt

If the new version still throws an error, send me all log files

from rdscan.

Hi, still a different kind of issue,
Same results also in dry run

tried also with also an new to RDscan2 in enviroment.yml file

Log file attatched
2024-02-10T130809.240069.snakemake.log

Building DAG of jobs...
WorkflowError:
InputFunctionException (rule bwa_mem, line 2, /mnt/f/RD/RDscan-1.0.4/workflow/rules/mapping.smk):
Error:
KeyError: '28.proportion'
Wildcards:
sample=28.proportion
Traceback:
File "/mnt/f/RD/RDscan-1.0.4/workflow/rules/common.smk", line 19, in get_fastq
File "/mnt/e/Miniconda3/envs/RDscan2/lib/python3.12/site-packages/pandas/core/indexing.py", line 1192, in getitem
File "/mnt/e/Miniconda3/envs/RDscan2/lib/python3.12/site-packages/pandas/core/indexing.py", line 1432, in _getitem_axis
File "/mnt/e/Miniconda3/envs/RDscan2/lib/python3.12/site-packages/pandas/core/indexing.py", line 1382, in _get_label
File "/mnt/e/Miniconda3/envs/RDscan2/lib/python3.12/site-packages/pandas/core/generic.py", line 4295, in xs
File "/mnt/e/Miniconda3/envs/RDscan2/lib/python3.12/site-packages/pandas/core/indexes/base.py", line 3809, in get_loc (rule bwa_mem, line 2, /mnt/f/RD/RDscan-1.0.4/workflow/rules/mapping.smk)
MissingInputException: Missing input files for rule bwa_mem:
output: results/mapped/28.bam, results/mapped/28.bam.bai
wildcards: sample=28
affected files:
/test/reads/28_1.fastq.gz
/test/reads/28_2.fastq.gz

from rdscan.

The error indicates that the files are not accessible at the specified file path, try using the absolute path (in terminal go to the location of 28_*.fastq.gz, type pwd and use that path). Also try ls /test/reads/ does it print 28_1.fastq.gz and 28_2.fastq.gz?

from rdscan.

Resolved,
As suggested was not having access to files with faulty path

Thanking again for prompt respone and help

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