ValueError: not enough values to unpack (expected 2, got 1)

Question

[Neel]

Hi i am using Clinker and it gives following error-

clinker P_aeruginosa_AR_0110.gbk P_aeruginosa_AR_0111.gbk P_aeruginosa_AR_455.gbk P_aeruginosa_ATCC_15692.gbk -r 4_dataforcli.txt -o out_4 -i 70 -p 4_plot.html [15:35:03] INFO - Starting clinker [15:35:03] ERROR - Failed to read range, please check it's in the right format Traceback (most recent call last): File "/home/bvs/anaconda3/envs/clinker/lib/python3.11/site-packages/clinker/main.py", line 46, in parse_range scaffold, coordinates = string.split(":") ^^^^^^^^^^^^^^^^^^^^^ ValueError: not enough values to unpack (expected 2, got 1)

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "/home/bvs/anaconda3/envs/clinker/lib/python3.11/site-packages/clinker/main.py", line 59, in parse_ranges
scaffold, start, end = parse_range(string)
^^^^^^^^^^^^^^^^^^^
File "/home/bvs/anaconda3/envs/clinker/lib/python3.11/site-packages/clinker/main.py", line 49, in parse_range
raise ValueError("Expected format scaffold:start-stop (e.g. scaf_1:100-3000)") from e
ValueError: Expected format scaffold:start-stop (e.g. scaf_1:100-3000)
Traceback (most recent call last):
File "/home/bvs/anaconda3/envs/clinker/lib/python3.11/site-packages/clinker/main.py", line 46, in parse_range
scaffold, coordinates = string.split(":")
^^^^^^^^^^^^^^^^^^^^^
ValueError: not enough values to unpack (expected 2, got 1)

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "/home/bvs/anaconda3/envs/clinker/bin/clinker", line 10, in
sys.exit(main())
^^^^^^
File "/home/bvs/anaconda3/envs/clinker/lib/python3.11/site-packages/clinker/main.py", line 330, in main
clinker(
File "/home/bvs/anaconda3/envs/clinker/lib/python3.11/site-packages/clinker/main.py", line 120, in clinker
ranges = parse_ranges(ranges)
^^^^^^^^^^^^^^^^^^^^
File "/home/bvs/anaconda3/envs/clinker/lib/python3.11/site-packages/clinker/main.py", line 59, in parse_ranges
scaffold, start, end = parse_range(string)
^^^^^^^^^^^^^^^^^^^
File "/home/bvs/anaconda3/envs/clinker/lib/python3.11/site-packages/clinker/main.py", line 49, in parse_range
raise ValueError("Expected format scaffold:start-stop (e.g. scaf_1:100-3000)") from e
ValueError: Expected format scaffold:start-stop (e.g. scaf_1:100-3000)

And data 4_dataforcli.txt look like-

Chr1:215234-216385
Chr1:3817094-3818245
chr1:1837109-1838260
Chr1:471545-472696

If anyone know anything please let me know.

Thank you!

[lacb]

Have you checked if there is an empty line at the end of your 4_dataforcli.txt that would make the command to fail?

Also if the file was imported from a Windows computer you can try toi fix line endings with the dos2unix command.