Closed DuttaAnik closed 1 year ago
Hi. Would it be possible for you to share the full snplift
folder, including all your data, exactly as you ran in, including the exact command and output you get on the terminal so I can look at this?
Hello, Thank you for the reply. I have uploaded the entire folder to Google Drive. Please download it from here [https://drive.google.com/file/d/11Spsa3M8mbhgsiyrv-55-47Nnspieerf/view?usp=sharing] to check. I used the following commands and got the time printed on the terminal:
time ./02_infos/snplift_config.sh
./02_infos/snplift_config.sh 0.00s user 0.00s system 69% cpu 0.005 total
There was no output except that above line.
From your command above, you didn't launch SNPLift.
Try:
time ./snplift ./02_infos/snplift_config.sh
Also, consider deleting your info from Google Drive since the link you shared will be working for everyone.
Take care
Hello, Thank you very much for developing this tool. I am very much looking forward to using it since I have lots of old VCF files. I cloned to the repository and installed all the dependencies. Then, I ran the
run_test.sh
as you recommended. It ran perfectly and produced all the output files. Then, I removed all these downloaded files of the test data and copied myold_genome.fasta
,new_genome.fasta
andold.vcf
to folders03_genomes
and04_input_vcf
, respectively. Then, I rantime ./02_infos/snplift_config.sh
.I did not get any output, the command just printed the time and nothing else. No error message or anything.
I did not change anything in the config file as I just renamed my files according to the pattern mentioned in the config file. I also changed the chromosome names in the VCF file to match with the
old_genome.fasta
file.Could you please suggest what might have gone wrong? Because everything ran smoothly with the
run_test.sh
file.