LOGGER variable is not inherited to child processes

[Ulises-Rosas]

When I ran a line like this:

./atram_preprocessor.py --mixed-ends XXXX.fastq 

I got the following error:

multiprocessing.pool.RemoteTraceback: 
"""
Traceback (most recent call last):
  File "/Users/admin/anaconda3/envs/aTRAM/lib/python3.8/multiprocessing/pool.py", line 125, in worker
    result = (True, func(*args, **kwds))
  File "/Users/admin/Desktop/aTRAM/lib/core_preprocessor.py", line 135, in create_one_blast_shard
    blast.create_db(args['temp_dir'], fasta_path, shard)
  File "/Users/admin/Desktop/aTRAM/lib/blast.py", line 18, in create_db
    log.subcommand(cmd, temp_dir)
  File "/Users/admin/Desktop/aTRAM/lib/log.py", line 78, in subcommand
    LOGGER.debug(cmd)
AttributeError: 'NoneType' object has no attribute 'debug'
"""

Upon looking the code, I noticed that the variable LOGGER is used as a global to generate log files. However,multiprocessing creates complete new instances without inheriting changes in this global variable. Then, I think the way this variable is sent it into a parallel run needs further review.

One solution is basically block log file updates when atram_preprocessor.py is running in parallel. But I do not think this is a good solution.

[rafelafrance]

Yes, the global logging variable is one per process by design. That in itself is unlikely to be the issue. It is almost certainly a bug I introduced recently when cutting down on the log chatter. I'll look into it asap.

---

FYI: Logging across processes is a mess because Python streams can be blocking which causes hangs. So, subprocesses log into a temp file which is then appended to the main log file upon completion.

https://github.com/juliema/aTRAM/blob/master/lib/log.py#L71-L93

[rafelafrance]

I am unable to replicate the error. Would you please send me the exact command you ran to get this error. I don't need the data just the command.

[Ulises-Rosas]

Pretty much something like this:

atram_preprocessor.py --mixed-ends [fastq file]

where [fastq file] is the input for the --mixed-ends argument. I am also using a conda environment and a makeblastdb version 2.9.0+

I also had to add __spec__ = None at the __main__ conditional of atram_preprocessor.py in order avoid other issue. Without it the LOGGER issues persist

[rafelafrance]

I'm still unable to replicate the issue. I've tried various scenarios:

• Blast versions 2.8 & 2.10
• conda & pip environments
• I hard coded the log.subcommand() to always throw an error.
• I added the __spec__ = None to the __main__ of atram_preprocessor.py

The sequence always looks similar too...

(base) ~/work/aTRAM$ conda activate aTRAM
(aTRAM) ~/work/aTRAM$ ./atram_preprocessor.py --mixed-ends input/ptgor_small_1.fasta.gz --gzip --path ~/bin/ncbi-blast-2.10.0+/bin/
2020-04-10 11:46:58 INFO: ################################################################################
2020-04-10 11:46:58 INFO: aTRAM version: v2.3.0
2020-04-10 11:46:58 INFO: Python version: 3.8.2 (default, Mar 26 2020, 15:53:00) [GCC 7.3.0]
2020-04-10 11:46:58 INFO: ./atram_preprocessor.py --mixed-ends input/ptgor_small_1.fasta.gz --gzip --path ~/bin/ncbi-blast-2.10.0+/bin/
2020-04-10 11:46:58 INFO: Loading "input/ptgor_small_1.fasta.gz" into sqlite database
2020-04-10 11:47:55 INFO: Creating an index for the sequence table
2020-04-10 11:48:00 INFO: Assigning sequences to shards
2020-04-10 11:48:01 INFO: Making blast DBs
2020-04-10 11:48:50 INFO: Finished making blast all 9 DBs

• What python version are you running? (3.8.2?)
• Did you make other modifications to atram to avoid the other issue?
• Would it be possible for you to try a git pull?
• Do you have any other ideas for scenarios that might reveal the issue?

[Ulises-Rosas]

Then, this issue is coming from my local configuration rather than aTRAM code itself. I'm not sure how to replicate this issue outside my local configuration. I really appreciate you could review the code anyways.

• I'm using python 3.8.1

I could fix my issue by basically checking the existence of LOGGER (i.e. not None) variable at the subcommand function from log.py file

Thank you!

[rafelafrance]

Yes, I can review your code. I'm guessing it's in your repo's master branch?

[Ulises-Rosas]

Yes, it is, but it's fine if you don't review it! You already did a lot by demonstrating that this issue is basically an issue of my local configuration