Stuck at the last step of makedb

[AlexSongh]

Hi I have a question about the step of Creating the reference database and index

Here is my output log file I used 5 cores, RAM of 800G and a walltime of 30 hours and it still didn't finish and stuck at this step.

Do you have any recommendations to solve this? Thanks!

[pmenzel]

Is it automatically terminated by the cluster when the requested wall clock time runs out?

I had this the last time I made the nr index: Elapsed (wall clock) time (h:mm:ss or m:ss): 61:01:03

Your mileage will vary depending on download speed and CPU speed. Maybe set it to 70 hours or more and try again. When you already have downloaded the nr.gz file, you can add option --no-download to makedb to reuse the existing file and also use --index-only, when you already have kaiju_db_nr_euk.faa

[AlexSongh]

Yes it is automatically terminated by the cluster when it reaches the wall time.

Yes, I will try that! Thanks a lot!

[ipetrushin]

I totally agree with this issue. The process wget -c -nv --show-progress -P nr_euk... hanging several hours, while file was finished (I even checked the md5 sum, it was correct). Re-runnig with --no-download says Missing file prot.accession2taxid.gz. After getting prot.accession2taxid.gz by hand re-runnig was successful.