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enormandeau / snplift

Transfer coordinates across genomes
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SNPlift does not run #4

Closed DuttaAnik closed 1 year ago

DuttaAnik commented 1 year ago

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 my old_genome.fasta, new_genome.fasta and old.vcf to folders 03_genomes and 04_input_vcf, respectively. Then, I ran time ./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.

enormandeau commented 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?

DuttaAnik commented 1 year ago

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.

enormandeau commented 1 year ago

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