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wjian8 / psvcp_v1.01

Pan-genome Construction and Population Structure Variation Calling pipeline
GNU General Public License v3.0
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bash script "1Genome_construct_Pangenome.sh" not found #16

Open bioinfoanalyst opened 3 months ago

bioinfoanalyst commented 3 months ago

I tried to run following given command:

bash $path_of_the_pipeline/1Genome_construct_Pangenome.sh ref.fa query.fa > job.sh && bash job.sh But 1Genome_construct_Pangenome.sh script is not provided in the pipeline kindly update

wjian8 commented 3 months ago

please use "Refgenome_update_by_quest.sh" I have updated README.

bash $path_of_the_pipeline/Refgenome_update_by_quest.sh ref.fa query.fa > job.sh && bash job.sh

bioinfoanalyst commented 3 months ago

Okay thanks wjian8.

bioinfoanalyst commented 3 months ago

By running suggested command I got following error @wjian8 : 

Error in file(file, "rt") : cannot open the connection
Calls: read.table -> file
In addition: Warning message:
In file(file, "rt") :
  cannot open file 'genome_gff_dir_example/MSU_0-2M.pav.gff': No such file or directory
Execution halted
bioinfoanalyst commented 3 months ago

Also by running Construct_pan_and_Call_sv.py on example data as given in readme, I got following console:

No gene and PAV has overlap, next round

Why it is so? Even though it is an example data.

wjian8 commented 3 months ago

bash $path_of_the_pipeline/Refgenome_update_by_quest.sh ref.fa query.fa > job.sh

Did you get the job.sh script? You can use cat job.sh to view its contents. The job.sh script executes commands sequentially. Ensure that the input and output files are specified correctly, as this will help identify where the issue begins.

Have you confirmed that all dependencies are installed?

MUMMER v4.0.0 (https://github.com/mummer4/mummer)

Assemblytics v1.2.1 (https://github.com/marianattestad/assemblytics)

BWA-MEM v0.7.17-r1198-dirty (http://bio-bwa.sourceforge.net/)

Picard (https://github.com/broadinstitute/picard)

Samtools v.1.9-49-gb321ed1 (https://github.com/samtools/samtools)

bedtools v2.29.2 (https://github.com/arq5x/bedtools2)

seqkit v1.2 (https://bioinf.shenwei.me/seqkit/)

blastn v2.2.3 (https://blast.ncbi.nlm.nih.gov/Blast.cgi)

R v3.5.0 or later (https://www.r-project.org/) and packages: -hash -parallel -snowfall

python3 (https://www.python.org/) and packages: -pandas -gzip -argparse -threading -re

bioinfoanalyst commented 3 months ago

Yes dependencies are already satisfied. And working on example data as it is.

94yangll commented 2 months ago

Also by running Construct_pan_and_Call_sv.py on example data as given in readme, I got following console:

No gene and PAV has overlap, next round

Why it is so? Even though it is an example data.

I had the same problem. @wjian8