Mouse genome is not downloaded

Downloaded the latest version. The mouse config file is there, but the genome is not.

Hello Eliezer,

Could you please try running the setup.sh script which should be able to download the mouse genome and create index. We have not packed the genome and index with the pipeline zip as the size becomes quite large Please let us know if the script is not creating the required files.

-Regards
Swaraj

Thanks Swaraj,
I encountered this issue after running the setup. I then went into the setup script and it turns out the url did not work. So I found the correct url. However, the index files did not get made. So I used Samtools afterwards to create the index files. Now I am getting the following lastal problem bin/last/src/lastal: can't open file: genome/mouse_mt.prj. From looking at various forums it seems like it's either a compiler issue or hyperthreading is not enabled. I checked on my machine and hyperthreading is enabled, not sure how to deal with the compiler issue. Any thoughts?
Thanks and Happy New Year!

Thanks Eliezer. Could you confirm please if this is the URL in the setup.sh script you are using:

ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/635/GCF_000001635.26_GRCm38.p6/GCF_000001635.26_GRCm38.p6_genomic.fna.gz

I am running the setup.sh commands in my system and am able to download the genome (screenshot attached). Hence would like to change the URL in case its causing download issues.

If the genome/mouse_mt.prj is generated and yet lastal is unable to read it, might be a compilation issue in case the GCC compiler is older than v4.7. If the file is not generated then most likely the command from setup.sh bin/last/src/lastdb -uNEAR genome/mouse_mt genome/$MTM_V where MTM_V=mouse_mt.fasta did not run successfully.

Wish you a happy new year too!

Actually now thinking back the url did not work when I ran the setup script in basic mode. However, I was able to get it when I changed the url or if I ran it in advanced mode on a fresh download. My gcc version is 11.1.0, so something else must cause this. The question is what?

Also, regardless of how I run the setup, the index files are not generated. I have to do so manually.

Hi Swaraj,
I just wanted to update you. I was able to get the program to run! It looks to me that the reason it initially failed to download and subsequently failed the proceeding steps may be due to size of the genome downloaded and perhaps my internet speed. The reason I think this is the case is because the server connection to NCBI kept resetting, and the genome file ended up being corrupted causing the program to halt at the mito extraction point. What is odd however is when I increased my download speed and there was no interruption during the download, this still occurred - is there a reason why? Please forgive my ignorance, I am somewhat new to bioinformatics. In any case, my samples are enriched for mito and I have a local copy of the mito fasta, so I imported it into the genome folder, manually created the index with Samtools, and ran the program. For some reason Plotrix and RColorBrewer di not get installed, so I also had to install those manually. Finally, in the script at line 221, I encountered the same error as is mentioned and solved here https://stackoverflow.com/questions/66064793/use-of-uninitialized-value-elements6-in-pattern-match-m
Thanks,
Eliezer