divide by 0 error during read cleaning step

[tuataratuatarae]

Hi there, I have been trying to use Captus to clean some read files on a HPC and have been getting this divide by 0 error during the adaptor trimming step:

Traceback (most recent call last):
File "/users/5/chan2624/.conda/envs/captus/bin/captus", line 10, in
sys.exit(main())
~~~~^^
File "/users/5/chan2624/.conda/envs/captus/lib/python3.14/site-packages/captus/captus_assembly.py", line 1620, in main
CaptusAssembly()
~~~~~~~~~~~~~~^^
File "/users/5/chan2624/.conda/envs/captus/lib/python3.14/site-packages/captus/captus_assembly.py", line 86, in init
getattr(self, args.command)()
~~~~~~~~~~~~~~~~~~~~~~~~~~~^^
File "/users/5/chan2624/.conda/envs/captus/lib/python3.14/site-packages/captus/captus_assembly.py", line 297, in clean
clean(full_command, args)
~~~~~^^^^^^^^^^^^^^^^^^^^
File "/users/5/chan2624/.conda/envs/captus/lib/python3.14/site-packages/captus/clean.py", line 220, in clean
tqdm_serial_run(
~~~~~~~~~~~~~~~^
bbduk_trim_adaptors,
^^^^^^^^^^^^^^^^^^^^
...<4 lines>...
args.show_less,
^^^^^^^^^^^^^^^
)
^
File "/users/5/chan2624/.conda/envs/captus/lib/python3.14/site-packages/captus/misc.py", line 106, in tqdm_serial_run
function_message = function(*params)
File "/users/5/chan2624/.conda/envs/captus/lib/python3.14/site-packages/captus/clean.py", line 569, in bbduk_trim_adaptors
ftr = trim_AT_GC_bias(in_dir, in_fastq)
File "/users/5/chan2624/.conda/envs/captus/lib/python3.14/site-packages/captus/clean.py", line 517, in trim_AT_GC_bias
delta_AT = abs((nt["A"] / reads_processed) - (nt["T"] / reads_processed)) * 100
~~~~~~~~^~~~~~~~~~~~~~~~~
ZeroDivisionError: division by zero

slurm_captus.sh
slurm_out.txt

[edgardomortiz]

Hi @tuataratuatarae ,

My first guess is that BBTools has an issue and it is not actually running or producing empty FASTQs. The problem happens with certain versions (all the 39.7X versions) of BBTools provided by bioconda.

The solution is to reinstall BBTools, with the captus environment activated run the following to go back to v39.52 or forward to v39.80:

conda activate captus
conda install -c bioconda bbmap=39.80

If 39.80 is still not available for your system try 39.52, let me know if this helps.

Edgardo

[tuataratuatarae]

Hi Edgardo,

The original version of bbmap that I used was 39.81. Regardless, I tried it at both 39.80 and 39.52, and neither worked for me

[edgardomortiz]

Hmm, ok. Have you verified you FASTQs are not corrupted? Run gzip -t on your files, if anyone is corrupted it will show some output, if the file is OK the command doesn't show any output.

[tuataratuatarae]

None of the files were corrupted, but one pair of read files was empty. The cleaning step worked fine when I removed those files from the directory. Thanks!

[edgardomortiz]

Excellent, I will add an empty/corrupted file check for next version 1.6.6

glad to help