Run error

[bigsuicideparty]

Dear Sir or Madam,

I followed your installation recommondations but I am unable to run DiTing on the example read data.

with:

diting.py -r /ext/DiTing/example -o Clean-reads_interleaved.diting.out

I get the following error message:

Traceback (most recent call last): File "/ext/DiTing/diting.py", line 255, in main() File "/ext/DiTing/diting.py", line 62, in main BASENAMES, READS_SUF, READS_INTER = check_reads(READS_DIR) File "/ext/DiTing/scripts/check.py", line 66, in check_reads reads_suf = ''.join(match_res.groups('')[1:]) AttributeError: 'NoneType' object has no attribute 'groups'

Could you help me solve this problem?

Kind regards

[xuechunxu]

Hi,

Could you please show the contents of your directory /ext/DiTing/example?

Best Chunxu

[bigsuicideparty]

Hey,

I used the recommended example data. So it is:

Sample1.fq sample2.fq sample3.fq

Best

[xuechunxu]

Hey,

In my opinion, the /ext/DiTing/example is a absolute path. Are you sure the example data are in there?

You can enter the previous directory of the example directory, and run diting.py -r example -o Clean-reads_interleaved.diting.out.

Best

[bigsuicideparty]

Running the from the folder /ext/DiTing both

diting.py -r /ext/DiTing/example -o Clean-reads_interleaved.diting.out

and

diting.py -r example -o Clean-reads_interleaved.diting.out

will give me the same error message:

2021-09-15 08:42:52 [INFO ] [1/12] Check database* 2021-09-15 08:42:52 [INFO ] The KEGG database is set 2021-09-15 08:42:52 [INFO ] The DMSP database is set Traceback (most recent call last): File "/ext/anaconda3/envs/diting-env/bin/diting.py", line 255, in main() File "/ext/anaconda3/envs/diting-env/bin/diting.py", line 62, in main BASENAMES, READS_SUF, READS_INTER = check_reads(READS_DIR) File "/ext/anaconda3/envs/diting-env/bin/scripts/check.py", line 66, in check_reads reads_suf = ''.join(match_res.groups('')[1:]) AttributeError: 'NoneType' object has no attribute 'groups'

[bigsuicideparty]

The output of ls example is

Sample1.fq sample2.fq sample3.fq

[xuechunxu]

Hey,

I have run it like you. It has no problem. Here is example folder:

Enter the previous directory of the example directory, and run diting.py -r example -o Clean-reads_interleaved.diting.out:

It works well.

Could please show your screenshots?

Best

[bigsuicideparty]

Alright, I figured it out. I created an additional folder inside the example folder before the run which did conflict with your script. Now I am able to run the script like you, except that it crashes at step 7/12:

[xuechunxu]

Hey,

It had a bug in script/func.py. I have revised it. You can download the file script/func.py and replace that in the folder ~/miniconda2/envs/diting-env/bin/scripts in your conda environment. I will update the DiTing through conda later. Thus you can reinstall DiTing after my update.

Best

[bigsuicideparty]

Thank you for your fast help. I managed to get it to run with the sample files, however when trying to run diting with my own assembly and read files I get an error at step [9/12]:

[SilentGene]

Hi @bigsuicideparty ,

Sorry for the inconvenience. Could you please attach the full log.txt file generated from this failure? That would help us investigate where the problem is.

Thanks, Heyu

[bigsuicideparty]

log.txt is attached Please ignore the early timestamps as I had to restart the pipeline due to naming issues

log.txt

Let me know if you need further information. I really would like to find a way to integrate diting into our metagenome analysis pipeline but first I have to figure out how I should organize the data to make it work