makeblastdb undocumented exit code

Question

[mpaco]

Hello,

I am relatively new to blast (version 2.10.0+) on Windows 10, so please bare with me. I tried to make a blast database with the following command in command prompt:

makeblastdb -in "\"C:\Users\SomeName\Dropbox\all combinations.fasta\"" -dbtype nucl -parse_seqids -out all_sequence_combinations

The all combinations.fasta file contains 810000 sequences. Now this is the output that I got from that command:

Building a new DB, current time: 06/15/2020 14:13:22
New DB name:   C:\Users\MarceloPaco\Desktop\InnovativeTargetingSolutions\all_sequence_combinations
New DB title:  "C:\Users\MarceloPaco\Dropbox (ITS)\Raw Data Current\Marcelo Paco 2020\all combinations.fasta"
Sequence type: Nucleotide
Deleted existing Nucleotide BLAST database named C:\Users\MarceloPaco\Desktop\InnovativeTargetingSolutions\all_sequence_combinations
Keep MBits: T
Maximum file size: 1000000000B
Adding sequences from FASTA; added 810000 sequences in 32.2474 seconds.

It seems as if the program ran fine and there were no issues, but when I check the exit code for the makeblastdb command I get the following:

echo %ERRORLEVEL%
-1073740791

The exit code suggest to me that there was some sort of error with the command since the exit code is non zero. I wanted to verify that I was getting a non zero exit code, so I tried to run the same makeblastdb command on python3 using the subprocess.checkoutput() function. To my surprise I got a different exit code, but it was still non zero. Here is that output:

subprocess.CalledProcessError: Command 'makeblastdb -in "\"C:\Users\SomeName\Dropbox\all combinations.fasta\"" -dbtype nucl -parse_seqids -out all_sequence_combinations' returned non-zero exit status 3221226505.

Now here the exit code is 3221226505! Is there an explanation as of why the exit code is non-zero and why makeblastdb didn't seem to fail? Any support would be appreciated

~ Cheers

[GenoMax]

Also remove all spaces in directory and file names (replace with underscores). See if that helps.

[mpaco]

Yeah, spaces are kind of a pain. I stumbled upon this piece of information though: Makeblastdb With Whitespace In -Out Filename Helps with managing spaces.

[JC]

You are doing this in Windows, error codes will be incorrect

[mpaco]

If I were to do this in another operating system - like linux - would I get the correct error codes?

[Mensur Dlakic]

Did you try running blastn on this database, and if so, did it work? If all worked as expected, everything we are typing here is just an exercise in understanding the idiosyncrasy of Windows error codes.

By the way, you didn't give use a true output of your command, as the input command has a different directory from the rest.

[mpaco]

I have not tried running blastn on this database. That's a good idea though. Also, I know I didn't give the true output of the command. The directories happened to have my full name on them (company standard naming convention). I didn't think that would make too much of a difference, but good eye! :)

[timothy.kirkwood]

Hi! I am getting the same issue, did you manage to confirm that the database was getting made correctly and that the non-0 exit code can be ignored? Thanks :)