No such file or directory: 'data_files/<>_haplotype_timecourse.txt'

[rraadd88]

Hi, I was trying to make the timecourse figure using following command:

$ python plot_timecourse.py argR.settings.txt

But seems like some file named 'haplotype_timecourse.txt' is missing in data_files folder.

Processing Ara-5...
Traceback (most recent call last):
  File "plot_timecourse.py", line 84, in <module>
    dummy_times,fmajors,fminors,haplotype_trajectories = parse_file.parse_haplotype_timecourse(population)
  File "/path/to/LTEE-metagenomic/parse_file.py", line 1005, in parse_haplotype_timecourse
    file = open(haplotype_filename,"r")
IOError: [Errno 2] No such file or directory: 'data_files/m5_haplotype_timecourse.txt'

Please let me know if I need to generate it using some other script or something. Thanks.

[benjaminhgood]

Yes, sorry for the poor documentation. These files should be generated by running the script

$ python process_cluster_output.py

(I've also added these instructions to the README.md file.)

[rraadd88]

It kinda worked. There was a silent error at the start: IOError: [Errno 2] No such file or directory: 'cluster_output_files/m5_likelihood_timecourse.txt'. Thereon it seemed to run fine.

$ python process_cluster_output.py

Trajectory post-processing output for LTEE metagenomic sequencing project
Date: 2017-11-16

Performing final filtering and annotation step...
Filtering trajectories with FDR=0.05
Traceback (most recent call last):
  File "combined_annotate_timecourse.py", line 28, in <module>
    file = open(input_filename_template % population,"r") 
IOError: [Errno 2] No such file or directory: 'cluster_output_files/m5_likelihood_timecourse.txt'
Error!
Inferring trajectory states in well-mixed HMM...
Processing m5
Processing p2
Processing p4
Processing p1
Processing m6
Processing p5
Processing m1
Processing m2
Processing m3
Processing m4
Processing p3
Processing p6
Done!
..
..

Thanks for the prompt response.

[Yixiangzhang1996]

really mess scripts......