Mykrobe-tools/mykrobe

TypeError: argument of type 'NoneType' is not iterable

idolawoye opened this issue · 7 comments

idolawoye commented

Hi @iqbal-lab, I am trying to run Mykrobe on some staph aureus samples and I am encounterig a 'NonType' is not iterable error message:

[mykrobe 2023-03-23T14:26:17 INFO] Running mykrobe predict using species staph, and panel version 20201001
[mykrobe 2023-03-23T14:26:17 INFO] Run command: /usr/local/lib/python3.9/site-packages/mykrobe/cortex/mccortex31 build -q -m 1GB -t 1 -k 15 -s staph-amr-bradley_2015-feb-17-2017-staph-species-160227 -1 /usr/local/lib/python3.9/site-packages/mykrobe/data/staph/staph-amr-bradley_2015-feb-17-2017.fasta.gz -1 /usr/local/lib/python3.9/site-packages/mykrobe/data/staph/staph-species-160227.fasta.gz mykrobe/data/skeletons/staph-amr-bradley_2015-feb-17-2017-staph-species-160227_15.ctx
[mykrobe 2023-03-23T14:26:17 INFO] Run command: /usr/local/lib/python3.9/site-packages/mykrobe/cortex/mccortex31 geno -t 1 -m 1GB -k 15 -o /tmp/tmpegiwu8n5/JGM001-15_staph-amr-bradley_2015-feb-17-2017-staph-species-160227.covgs -I mykrobe/data/skeletons/staph-amr-bradley_2015-feb-17-2017-staph-species-160227_15.ctx -s JGM001-15 -1 JGM001_S1_R1.fastq.gz -1 JGM001_S1_R2.fastq.gz -c /usr/local/lib/python3.9/site-packages/mykrobe/data/staph/staph-amr-bradley_2015-feb-17-2017.fasta.gz -c /usr/local/lib/python3.9/site-packages/mykrobe/data/staph/staph-species-160227.fasta.gz /tmp/tmpegiwu8n5/JGM001-15_staph-amr-bradley_2015-feb-17-2017-staph-species-160227.ctx
Traceback (most recent call last): File "/usr/local/bin/mykrobe", line 33, in <module> sys.exit(load_entry_point('mykrobe==0.12.1', 'console_scripts', 'mykrobe')()) File "/usr/local/lib/python3.9/site-packages/mykrobe/cli.py", line 9, in main args.func(parser, args) File "/usr/local/lib/python3.9/site-packages/mykrobe/parser.py", line 53, in run_subtool run(parser, args) File "/usr/local/lib/python3.9/site-packages/mykrobe/cmds/amr.py", line 338, in run gt.run() File "/usr/local/lib/python3.9/site-packages/mykrobe/typing/typer/genotyper.py", line 321, in run self._type() File "/usr/local/lib/python3.9/site-packages/mykrobe/typing/typer/genotyper.py", line 324, in _type self._type_genes() File "/usr/local/lib/python3.9/site-packages/mykrobe/typing/typer/genotyper.py", line 341, in _type_genes if gene_name in self.lineage_variants: TypeError: argument of type 'NoneType' is not iterable

I ran this on a TB sample and it worked fine, so I'm a bit confused as to what's going wrong here

iqbal-lab commented

Hi there - sorry to hear this. Can you tell me what version you used/how you installed? I must apologise in advance - Friday and Monday are national holidays here, and I have a deadline on thursday. I will try to help if I can, but it is possible I won't get back to you until Tuesday.

idolawoye commented

Thanks @iqbal-lab. I am using version 0.12.1. I didn't install it on our server but I'm guessing it was compiled from source using pip because it is in /usr/local/bin/

davidjstudholme commented

I am having the same issue using the version v0.12.1 installed via conda.
Located at: /home/djs217/miniconda3/envs/mykrobe_env/bin/mykrobe

Everything seems to work fine with the test dataset, but when I try to analyse my fq or fq.gz or .bam files I get the error message. For example:

[mykrobe 2023-05-08T09:42:06 INFO] Start runnning mykrobe predict. Command line: /home/djs217/miniconda3/envs/mykrobe_env/bin/mykrobe predict --sample ERR1212589 --species staph --output ERR1212589.json --format json --seq ERR1212589.fq.gz
[mykrobe 2023-05-08T09:42:06 INFO] Running mykrobe predict using species staph, and panel version 20201001
[mykrobe 2023-05-08T09:42:06 INFO] Run command: /home/djs217/miniconda3/envs/mykrobe_env/lib/python3.10/site-packages/mykrobe/cortex/mccortex31 geno -t 1 -m 1GB -k 15 -o /tmp/tmpdit5nxrw/ERR1212589-15_staph-amr-bradley_2015-feb-17-2017-staph-species-160227.covgs -I mykrobe/data/skeletons/staph-amr-bradley_2015-feb-17-2017-staph-species-160227_15.ctx -s ERR1212589-15 -1 ERR1212589.fq.gz -c /home/djs217/miniconda3/envs/mykrobe_env/lib/python3.10/site-packages/mykrobe/data/staph/staph-amr-bradley_2015-feb-17-2017.fasta.gz -c /home/djs217/miniconda3/envs/mykrobe_env/lib/python3.10/site-packages/mykrobe/data/staph/staph-species-160227.fasta.gz /tmp/tmpdit5nxrw/ERR1212589-15_staph-amr-bradley_2015-feb-17-2017-staph-species-160227.ctx
Traceback (most recent call last):
  File "/home/djs217/miniconda3/envs/mykrobe_env/bin/mykrobe", line 11, in <module>
    sys.exit(main())
  File "/home/djs217/miniconda3/envs/mykrobe_env/lib/python3.10/site-packages/mykrobe/cli.py", line 9, in main
    args.func(parser, args)
  File "/home/djs217/miniconda3/envs/mykrobe_env/lib/python3.10/site-packages/mykrobe/parser.py", line 53, in run_subtool
    run(parser, args)
  File "/home/djs217/miniconda3/envs/mykrobe_env/lib/python3.10/site-packages/mykrobe/cmds/amr.py", line 338, in run
    gt.run()
  File "/home/djs217/miniconda3/envs/mykrobe_env/lib/python3.10/site-packages/mykrobe/typing/typer/genotyper.py", line 321, in run
    self._type()
  File "/home/djs217/miniconda3/envs/mykrobe_env/lib/python3.10/site-packages/mykrobe/typing/typer/genotyper.py", line 324, in _type
    self._type_genes()
  File "/home/djs217/miniconda3/envs/mykrobe_env/lib/python3.10/site-packages/mykrobe/typing/typer/genotyper.py", line 341, in _type_genes
    if gene_name in self.lineage_variants:
TypeError: argument of type 'NoneType' is not iterable```
iqbal-lab commented

Jen Guthrie says the same thing

"This is the error that we’re getting when we try to run Mykrobe for S. aureus but it works fine for Mtb

mykrobe predict -S staph -s sa50 -i sa50_S29_R1_001.fastq.gz sa50_S29_R2_001.fastq.gz -o ./myk_out/sa50_out.csv
[mykrobe 2023-03-22T18:01:06 INFO] Start runnning mykrobe predict. Command line: /usr/local/bin/mykrobe predict -S staph -s sa50 -i sa50_S29_R1_001.fastq.gz sa50_S29_R2_001.fastq.gz -o ./myk_out/sa50_out.csv
[mykrobe 2023-03-22T18:01:06 INFO] Running mykrobe predict using species staph, and panel version 20201001
[mykrobe 2023-03-22T18:01:06 INFO] Run command: /usr/local/lib/python3.9/site-packages/mykrobe/cortex/mccortex31 geno -t 1 -m 1GB -k 15 -o /tmp/tmpui7f3yeo/sa50-15_staph-amr-bradley_2015-feb-17-2017-staph-species-160227.covgs -I mykrobe/data/skeletons/staph-amr-bradley_2015-feb-17-2017-staph-species-160227_15.ctx -s 50-15 -1 sa50_S29_R1_001.fastq.gz -1 sa50_S29_R2_001.fastq.gz -c /usr/local/lib/python3.9/site-packages/mykrobe/data/staph/staph-amr-bradley_2015-feb-17-2017.fasta.gz -c /usr/local/lib/python3.9/site-packages/mykrobe/data/staph/staph-species-160227.fasta.gz /tmp/tmpui7f3yeo/50-15_staph-amr-bradley_2015-feb-17-2017-staph-species-160227.ctx
Traceback (most recent call last):
  File "/usr/local/bin/mykrobe", line 33, in <module>
    sys.exit(load_entry_point('mykrobe==0.12.1', 'console_scripts', 'mykrobe')())
  File "/usr/local/lib/python3.9/site-packages/mykrobe/cli.py", line 9, in main
    args.func(parser, args)
  File "/usr/local/lib/python3.9/site-packages/mykrobe/parser.py", line 53, in run_subtool
    run(parser, args)
  File "/usr/local/lib/python3.9/site-packages/mykrobe/cmds/amr.py", line 338, in run
    gt.run()
  File "/usr/local/lib/python3.9/site-packages/mykrobe/typing/typer/genotyper.py", line 321, in run
    self._type()
  File "/usr/local/lib/python3.9/site-packages/mykrobe/typing/typer/genotyper.py", line 324, in _type
    self._type_genes()
  File "/usr/local/lib/python3.9/site-packages/mykrobe/typing/typer/genotyper.py", line 341, in _type_genes
    if gene_name in self.lineage_variants:
TypeError: argument of type 'NoneType' is not iterable
iqbal-lab commented

Apologies everyone, @martinghunt and I were at ABPHM at the end of last week. We will take a look

idolawoye commented
martinghunt commented

This is now fixed, and there's a new release v0.12.2.

https://github.com/Mykrobe-tools/mykrobe/releases/tag/v0.12.2

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