# ShortBRED run failed due to \<Signals.SIGBUS: 7\>

**URL:** <https://forum.biobakery.org/t/shortbred-run-failed-due-to-signals-sigbus-7/6664>\
**Category:** ShortBRED\
**Created:** [February 20, 2024, 9:47pm UTC](https://forum.biobakery.org/t/shortbred-run-failed-due-to-signals-sigbus-7/6664 "2024-02-20T21:47:56Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![Carlos\_Gomez](https://avatars.discourse-cdn.com/v4/letter/c/3ab097/32.png) [@Carlos\_Gomez](https://forum.biobakery.org/u/Carlos_Gomez)\
**Post date:** [February 20, 2024, 9:47pm UTC](https://forum.biobakery.org/t/shortbred-run-failed-due-to-signals-sigbus-7/6664/1 "2024-02-20T21:47:56Z")

</div>

Hi everyone,  
I’m interested in using ShortBRED to identify the most most abundant genes in my metagenomic dataset using a reference protein database. Here’s a breakdown of what I’ve done so far:

1. Installed ShortBRED by downloading the file from GitHub: [ShortBRED GitHub Repository](https://github.com/biobakery/shortbred/archive/0.9.4.zip)
2. Loaded dependencies including CD-HIT, BLAST+, USEARCH, MUSCLE, and NumPy with the following module loads:

- module load CBI miniconda3/23.5.2-0-py311
- module load Sali blast+
- module load Sali usearch
- module load Sali muscle
- module load python3/numpy/1.19.5

Currently, I’m following the ShortBRED tutorial on GitHub, specifically using method 1 to generate new markers from a set of proteins of interest and a reference set of proteins. However, I’ve hit a couple of roadblocks along the way and could use some assistance in resolving them.

# Error 1

```auto
python /wynton/group/lynch/c-gomez/software/shortbred/shortbred_identify.py --goi example/input_prots.faa --ref example/ref_prots.faa --markers mytestmarkers.faa --tmp example_identify --cdhit /wynton/group/lynch/c-gomez/software/cd-hit-v4.8.1-2019-0228/cd-hit

```

```auto
Traceback (most recent call last):
  File "/wynton/group/lynch/c-gomez/software/shortbred/shortbred_identify.py", line 56, in <module>
    from Bio.Alphabet import IUPAC
  File "/wynton/home/lynchlab/c-gomez/.local/lib/python3.11/site-packages/Bio/Alphabet/ __init__.py", line 20, in <module>
    raise ImportError(
ImportError: Bio.Alphabet has been removed from Biopython. In many cases, the alphabet can simply be ignored and removed from scripts. In a few cases, you may need to specify the ``molecule_type`` as an annotation on a SeqRecord for your script to work correctly. Please see https://biop

```

# I managed to resolve it by commenting out the import of Bio.Alphabet in the shortbred\_identity.py script.

# Error 2: After that, I encountered another issue, which seems to be related to the deprecation of the dumb\_consensus method in Biopython. However, I’m unsure how to address this problem effectively.

Here’s the error message I’m currently dealing with:

```auto
Making BLAST database for the family consensus sequences...
Traceback (most recent call last):
  File "/wynton/group/lynch/c-gomez/software/shortbred/shortbred_identify.py", line 279, in <module>
    subprocess.check_call([
  File "/wynton/home/cbi/shared/software/CBI/miniconda3-23.5.2-0-py311/lib/python3.11/subprocess.py", line 413, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['makeblastdb', '-in', 'example_identify/clust/clust.faa', '-out', 'example_identify/clustdb/goidb', '-dbtype', 'prot', '-logfile', 'example_identify/goidb.log']' died with <Signals.SIGBUS: 7>.

```

Has anyone run into this issue?

Thank you in advance for the assistance!

Best,  
Carlos