download_all_data.sh failed

[kttn8769]

Hi,

I executed download_all_data.sh as follows,
scripts/download_all_data.sh ../data > download.log 2> download_all.log &

but the script failed on the mgnify database preparation.

I have attached the log files.

gzip complained that gzip: ../data/mgnify/mgy_clusters_2022_05.fa.gz: No such file or directory, but that file do exist in the path.

> ls -l ../data/mgnify/mgy_clusters_2022_05.fa.gz
-rw-r--r-- 1 kttn emstf 72741135623 Mar 16 00:30 ../data/mgnify/mgy_clusters_2022_05.fa.gz

[paulasanematsu]

I ran into the same issue. I think the problem in the script download_mgnify.sh is created due to the command pushd "${ROOT_DIR}", which sets the working directory to ../data, but then tries to gunzip including the $ROOT_DIR. Then, it can't find the file.

After the mgnify file is downloaded, you can:

cd ../data/mgnify/
gunzip mgy_clusters_2022_05.fa.gz

Or you can delete lines 41 (pushd "${ROOT_DIR}") and 43 (popd) from scripts/download_mgnify.sh

I ran into this issue with other scripts too, such as download_uniprot.sh and download_uniref90.sh.

[Vincy1230]

This issue is not caused by the use of pushd/popd itself, but by the lack of normalization of user-provided paths. I’ve addressed it in pull request #1115. Please take a look.