Comments (4)
Hi!
We have recently extensively updated the master branch.
could you please give it another try?
Note:
With this new branch you should be able to have V-pipe automatically set some base configuration for your HIV virus if you give it a vpipe.config that looks like:
[general]
virus_base_config=hiv
[output]
snv=true
local=true
global=false
visualization=true
QA=true
Note: it also works with YAML/JSON files (called config.yaml or specified on command line option --configfile
)
general:
virus_base_config: hiv
output:
snv: true
local: true
global: false
visualization: true
QA: true
from v-pipe.
If the files are in *fastq.gz format, the error message looks a bit different:
Building DAG of jobs...
MissingInputException in line 10 of /Users/sviat/V-pipe/rules/quality_assurance.smk:
Missing input files for rule gunzip:
samples/ADA1038B/20210521/extracted_data/R1.fastq.gz
This is because of the name of your .fastq file. The name of the fastq file should be *R1.fastq after unzip from .gz file.
from v-pipe.
Hi,
I am sorry for coming back to this type of problem, but i am trying to run the SARS-CoV-2 first test (datasets SRR10903401 and SRR10903402) but I am always getting the same error and I do not really know what I am doing wrong.
MissingInputException in rule gunzip in file /V-pipe/workflow/rules/quality_assurance.smk, line 11:
Missing input files for rule gunzip:
output: results/SRR10903401/20200102/extracted_data/R1.fastq
wildcards: file=results/SRR10903401/20200102/extracted_data/R1, ext=fastq
affected files:
results/SRR10903401/20200102/extracted_data/R1.fastq.gz
Even when I try to run the ./vpipe --dryrun I get the same error.
VPIPE_BASEDIR = /V-pipe/workflow
No virus base configuration, using defaults
WARNING: protocols YAML look-up file </V-pipe/workflow/../resources/sars-cov-2/primers.yaml> specified, but no sample ever uses it: fourth column absent from samples TSV file.
Building DAG of jobs...
MissingInputException in rule gunzip in file /V-pipe/workflow/rules/quality_assurance.smk, line 11:
Missing input files for rule gunzip:
output: results/SRR10903401/20200102/extracted_data/R1.fastq
wildcards: file=results/SRR10903401/20200102/extracted_data/R1, ext=fastq
affected files:
results/SRR10903401/20200102/extracted_data/R1.fastq.gz
Could please someone help me?
Thanks,
from v-pipe.
@aitorgarzia : This message happens when Snakemake has trouble finding the input files.
To create this file:
…
Missing input files for rule gunzip:
output: results/SRR10903401/20200102/extracted_data/R1.fastq
…
...it should in theory search for a file called:
- either
samples/SRR10903401/20200102/raw_data/SRR10903401_R1.fastq
- or
samples/SRR10903401/20200102/raw_data/SRR10903401_R1.fastq.gz
(see Preparing a small dataset section)
Please check that it corresponds.
Common troubles:
-
typos: the name of directories should match the columns of the
samples.tsv
filesamples/SRR10903401/20200102/raw_data/ vs
SRR10903401 20200102 250
check that there hasn't been any mistake while copy-pasting names when naming the directories or writing the TSV.
-
subdirectory: the files must be inside a
raw_data/
subdirectory:samples/SRR10903401/20200102/raw_data/SRR10903401_R1.fastq
-
filename: When in paired-end mod, the file must follow the format {sample}
_R
{n}.fastq
, i.e.: the base name must have_R1
and_R2
attached at the end for each member of the read pairs:samples/SRR10903401/20200102/raw_data/SRR10903401_R1.fastq
from v-pipe.
Related Issues (20)
- Haplotype percentage or frequency estimation
- The order of jobs does not reflect the order of execution. Any help? HOT 1
- wrong url for release download in quick install HOT 2
- Running with tutorial dataset giving all empty file HOT 6
- Getting snake error HOT 23
- please document haploclique.extra_parameters HOT 3
- SARS-CoV-2 workflow comparison - kindly check if your work is represented correctly HOT 1
- Warning: All reads at position 4045 in the same reverse orientation ? HOT 1
- Conflict in quality_assurance.smk with custom datadir-path
- frameshift_deletion_checks, simBench & Haplotype callers HOT 6
- [UX issue] unknown keywords in config file HOT 1
- [UX issue] multiple GFF HOT 1
- predicthaplo does not work on sars-cov-2 tutorial HOT 1
- hiv-tutorial works with haploclique, but fails with predicthaplo
- hiv-tutorial fails with haplotype_reconstruction: savage, and SAVAGE command output is dumped into terminal instead of log
- Error in rule hmm_align: HIV in Vpipe HOT 2
- Missing input files for rule generate_web_visualization
- vpipe broken? ModuleNotFoundError: No module named 'pandas' HOT 2
- Activating snv in sars tutorial leads to error HOT 2
- Snakemake dry run 404 HOT 9
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from v-pipe.