Parallel error when dowloading

[lshilab]

Hi, I tried to download the virus genome indicated in the readme file and the program runs successfully in the home folder. But when trying to download in the /mnt/d/ folder, it shows a parallel error. I need to download to the /mnt/d/ because of space limitations. Can you check if there is something wrong with my settings? Thanks!

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Mode: NEW - DOWNLOAD Working directory: /mnt/d/virus/all_rna_virus/

Downloading assembly summary [2022-04-16_08-25-17]

• Database [refseq]

• 257586 assembly entries available

• Downloading new taxdump and parsing lineages

• 253246 assemblies removed not in taxids [2559587]

• 4340 assembly entries to download

• Downloading 4340 files with 12 threads parallel: This should not happen. You have found a bug. Please follow https://www.gnu.org/software/parallel/man.html#REPORTING-BUGS

Include this in the report:

• The version number: 20220222
• The bugid: Can't dup STDOUT: No such file or directory
• The command line being run
• The files being read (put the files on a webserver if they are big)

If you get the error on smaller/fewer files, please include those instead.

[pirovc]

Looks like it's a parallel issue. In genome_updater, parallel is set to use temporary directory, same as the output directory. You may be able to work around the problem by changing it here. Alternatively you could try using a different parallel version, maybe the one distributed by conda?

[lshilab]

Thank you for pointing out this solution, I think it's quite possible that this will solve the problem. Unfortunately, I am just starting to learn and don't quite understand exactly what to do with the change you are pointing about. I tried to bypass this problem by changing the output folder. I was using the script under wsl, and when I couldn't run it, the output folder was not in wsl, but on another disk. I tried putting the output folder in the home directory and was able to download normally. I guess this is exactly the folder problem you pointed out. Thanks again for the script, it was very useful.