MeHelmy/princess

Can't run this line...

Opened this issue · 10 comments

Gedofs commented

Hi! Hope you can help me. I can't run this readme line:

princess all -d ./princess_all -r ont -s reads.split00.fastq.gz reads.split01.fastq.gz -f hs37d5_mainchr.fa

I also tried to run samtools unsuccessfully...

Screen Shot 2022-11-14 at 15 50 22

MeHelmy commented

You need to install samtools first. E.g., conda install samtools if you have Conda installed. For more details regarding samtools installation; please, visit http://www.htslib.org/download/

Gedofs commented

thanks @MeHelmy! I installed samtools successfully but now there is a new error besides that, I still can´t this line (princess all -d ./princess_all -r ont -s reads.split00.fastq.gz reads.split01.fastq.gz -f hs37d5_mainchr.fa)

Screen Shot 2022-11-15 at 16 47 52

Screen Shot 2022-11-15 at 16 53 34

Gedofs commented

Is this step necessary before running a sample or even the test case? where can i download the splitoo fasta?

MeHelmy commented

thanks @MeHelmy! I installed samtools successfully but now there is a new error besides that, I still can´t this line (princess all -d ./princess_all -r ont -s reads.split00.fastq.gz reads.split01.fastq.gz -f hs37d5_mainchr.fa)

Screen Shot 2022-11-15 at 16 47 52 Screen Shot 2022-11-15 at 16 53 34

As the error explains, it can not find your reference.
"Failed to open ....."

Gedofs commented

ok! I fixed that but now im not sure if I need to install this packages as I supposed they were installed during princess Screenshot 2022-11-16 at 14 54 18

Gedofs commented

Sorry, once again! Still have the same problem. Is it related to conda environment? Hope u can help me

MeHelmy commented

Sorry for the late answer, Which conda version you are using?

Gedofs commented
MeHelmy commented

Hi, we just made an update to reduce Conda dependency. I hope that you can give it a try.

Gedofs commented