Structure_Threader not reading the mainparams file

[Omar Zayas]

Hello all:

I am trying to run Structure_Threader for a file with SNPs data. However, when running the command, it seems like the software can not find the mainparams file but reads the extraparams file. However, when running just ./structure, the command runs without any problem. 

Any thoughts on this? I attached the error message, the input file example, and the params file data I am using here.

Command: I have tried several commands using --params and using -m and -e.

structure_threader run -K 4 -R 10 --log 1 -i /home/rosalind/.local/bin/new_29samples_R0.60 -o /home/rosalind/.local/bin/results -t 8 -st ~/.local/bin/structure --params /home/rosalind/.local/bin/mainparams --params /home/rosalind/.local/bin/extraparams

structure_threader run -K 4 -R 10 --log 1 -i /home/rosalind/.local/bin/new_29samples_R0.60 -o /home/rosalind/.local/bin/results -t 8 -st /home/rosalind/.local/bin/structure --params /home/rosalind/.local/bin/

structure_threader run -K 4 -R 10 --log 1 -i /home/rosalind/.local/bin/new_29samples_R0.60 -o /home/rosalind/.local/bin/results -t 8 -st ~/.local/bin/structure -m /home/rosalind/.local/bin/mainparams -e /home/rosalind/.local/bin/extraparams

This is the Structure command that works well:

./structure -K 4 -R 10 --log 1 -i /home/rosalind/.local/bin/new_29samples_R0.60 -o /home/rosalind/.local/bin/results_normal -t 8 -st ~/.local/bin/structure --params /home/rosalind/.local/bin/

Error message in command-line:

:~$ structure_threader run -K 4 -R 10 --log 1 -i /home/rosalind/.local/bin/new_29samples_R0.60 -o /home/rosalind/.local/bin/results -t 8 - st /home/rosalind/.local/bin/structure --params /home/rosalind/.local/bin/
INFO: Running: /home/rosalind/.local/bin/structure -K 4 -i /home/rosalind/.local/bin/new_29samples_R0.60 -o /home/rosalind/.local/bin/results/str_K4_rep10 

-D 2153978 -m /home/rosalind/.local/bin -e /home/rosalind/.local/extraparams

CRITICAL: 40 structure runs exited with errors. Check the log files of the following output files:
ERROR: /home/rosalind/.local/bin/results/str_K4_rep10

Traceback (most recent call last):
  File "/home/rosalind/.local/bin/structure_threader", line 8, in <module>
    sys.exit(main())
  File "/home/rosalind/.local/lib/python3.6/site-packages/structure_threader/structure_threader.py", line 353, in main
    full_run(arg)
  File "/home/rosalind/.local/lib/python3.6/site-packages/structure_threader/structure_threader.py", line 311, in full_run
    bestk = structure_harvester(arg.outpath, wrapped_prog)
  File "/home/rosalind/.local/lib/python3.6/site-packages/structure_threader/structure_threader.py", line 192, in structure_harvester
    bestk = sh.main(resultsdir, outdir)
  File "/home/rosalind/.local/lib/python3.6/site-packages/structure_threader/evanno/structureHarvester.py", line 169, in main
    harvestFiles(data, resultsdir)
  File "/home/rosalind/.local/lib/python3.6/site-packages/structure_threader/evanno/structureHarvester.py", line 87, in harvestFiles
    'the results directory %s' % resultsdir)
structure_threader.evanno.structureHarvester.Exception: Error, unable to locateany _f files in the results directory /home/rosalind/.local/bin/results

Error message in the results file: 

Reading file "/home/rosalind/.local/bin".
Reading file "/home/rosalind/.local/extraparams".
Need to set NUMINDS>0 in the file mainparams
Need to set NUMLOCI>0 in the file mainparams
Need to set LABEL=0 or 1 in the file mainparams
Need to set POPDATA=0 or 1 in the file mainparams
Need to set POPFLAG=0 or 1 in the file mainparams
Need to set PHENOTYPE=0 or 1 in the file mainparamsNeed to set EXTRACOLS>=0 in the file mainparams

Exiting the program due to error(s) listed above.

The first column the sample ID and in the second column the Locdata, then the markers ID.

Mainparams file

Ps. In other matters, Structure accepts the missing information identified as 0, or it has to be -9? The output file of Stacks identified the missing information with a 0. I changed it to -9 but would like to know if it works with the 0.

Thank you in advance,

-Omar

[Francisco Pina Martins]

Dear Omar,

You need only specify the path to yourmainparams file.
When you pass the --params switch twice, only the last one is read (which pointed to extraparams).

Just run your command like this:

structure_threader run -K 4 -R 10 --log 1 -i /home/rosalind/.local/bin/new_29samples_R0.60 -o /home/rosalind/.local/bin/results -t 8 -st ~/.local/bin/structure --params /home/rosalind/.local/bin/mainparams

This is stated in the manual, but maybe I should clarify it…

Regarding the 0 and -9, as far as I know you can set missing information to 0 and it should work just fine. But the -9 value is the “recommended” default due to being hard to confuse for anything else.

Hope this helps,

Francisco

​

[Omar Zayas]

Hello Francisco, thank you for your response!

That solved my problem! Certainly, I read it in the manual and tried it in the first command that I wrote, but it didn't work (it had another error). For some reason, I started changing things in the command and forgot to use the first command, since Structure read it that way, I thought it was a problem with Structure_threader. I see that the program is generating .Stlog and _f  files hope everything goes well.

Thanks again,

Omar

--
You received this message because you are subscribed to the Google Groups "structure-software" group.
To unsubscribe from this group and stop receiving emails from it, send an email to structure-softw...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/structure-software/fe596464-ec4a-4bde-b50d-05160c74e59cn%40googlegroups.com.

--

Omar Zayas Cruz

Email: ozaya...@gmail.com

[Francisco Pina Martins]

Hi Omar,

Glad to hear it’s sorted. I have, nevertheless clarified the documentation on the --params switch.

https://structure-threader.readthedocs.io/en/latest/usage/

Thank you for your feedback.

Best,

Francisco

You received this message because you are subscribed to a topic in the Google Groups "structure-software" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/structure-software/Bp6bF_x6pq4/unsubscribe.
To unsubscribe from this group and all its topics, send an email to structure-softw...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/structure-software/CAE0Jn_b0S82ZcZLUnqq6BMEf67UeruyiecBgXXMZmXKjkZDUVA%40mail.gmail.com.

​