Warning: cannot detect conda environment

[med-ss20]

Hi
The following problem I got with V-pipe master (HIV-1 analysis): when I try to initialise the project I have the following Warning:
Warning: cannot detect conda environment V-pipe project initialized!

Conda V-pipe environment is activated.

And after trying --dryrun, the following error came up:
$ ./vpipe --dryrun
VPIPE_BASEDIR = /Users/sviat/V-pipe
Migrating .snakemake folder to new format...
Migration complete
Building DAG of jobs...
WorkflowError:
WorkflowError:
MissingInputException: Missing input files for rule gunzip:
samples/ADA1038B/20210521/extracted_data/R1.fastq.gz
CyclicGraphException: Cyclic dependency on rule convert_to_ref.
MissingInputException: Missing input files for rule sam2bam:
samples/ADA1038B/20210521/alignments/REF_aln.sam

ADA1038B is the first sample in my sample list.
Samples prepared according to the manual:
v-pipe_workdir/samples/ADA1038B/20210521/raw_data/ADA1038B_R1.fastq
v-pipe_workdir/samples/ADA1038B/20210521/raw_data/ADA1038B_R2.fastq
...

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

Can you please help me with this issue?
Thank you!
P.S. SARS-CoV-2 V-pipe branch works perfect!

[DrYak]

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

[jiaqili-fl]

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.

[aitorgarzia]

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,

[DrYak]

@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 file

  samples/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