list index out of range: using stacks on galaxy

Question: list index out of range: using stacks on galaxy

17 months ago by

I did process radtags with the new barcode file and I got the result without error and then I moved forward to next step creating population map. Afterward I did the de novo map but when I waned to run the population, I received an error:

list index out of range

So I checked the previous steps and I found out that population map.txt on galaxy is not correct and it contain 95 lines instead of 96 lines. I don't know how I can change the population map text file to do the rest of analysis. Can you help me solving the problem. I am using UGA galaxy to run my job.

Traceback (most recent call last): File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 630, in finish_job job_state.job_wrapper.finish( stdout, stderr, exit_code ) File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/jobs/__init__.py", line 1301, in finish dataset.set_peek() File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/model/__init__.py", line 2031, in set_peek return self.datatype.set_peek( self, is_multi_byte=is_multi_byte ) File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/datatypes/data.py", line 782, in set_peek dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte, WIDTH=WIDTH, skipchars=skipchars, line_wrap=line_wrap ) File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/datatypes/data.py", line 1007, in get_file_peek temp = compression_utils.get_fileobj( file_name, "U" ) File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/util/compression_utils.py", line 34, in get_fileobj return zh.open(zh.namelist()[0], cmode) IndexError: list index out of range

software error galaxy • 426 views

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modified 17 months ago • written 17 months ago by haniehhadizadeh63 • 0

17 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The administrators of this Galaxy server should be contacted to determine the root cause of the problem and to perform any server-side corrections (as needed).

Thanks! Jen, Galaxy team

ADD COMMENT • link written 17 months ago by Jennifer Hillman Jackson ♦ 25k

17 months ago by

haniehhadizadeh63 • 0

haniehhadizadeh63 • 0 wrote:

So you have no idea what has caused this problem ?

ADD COMMENT • link written 17 months ago by haniehhadizadeh63 • 0

This error is a general one and indicates that the input given is in an unexpected format for the python script executing the process, but beyond that, the root issue cannot be determined from the shared information. You also mention that one of the inputs from a prior tool/index is incorrect, which complicates the problem space. Because you are working on a different server than I can go in as an administrator to review the analysis (inputs, tool version, Galaxy version - meaning enough to exactly reproduce the problem), help to resolve the root issue is limited.

Double checking the inputs and usage is one way to try to resolve the problem on your own. The general troubleshooting help here resolves many tool issues and may be worth reviewing. In particular, check the inputs and usage. If you believe that the tool wrapper itself has a problem, an issue describing the problem can be opened against the tool repository. From the tool form, click on "Options > View in Tool Shed" to find where the repository is located.

Others may still reply if they have seen this particular tool/data issue and know the specific solution (I have not). Changing the title of the post to be more specific for the tool plus version and including more details about the server configuration or URL (if public) will attract more community help. And if you do discover the problem, and it is likely to impact other Galaxy users, posting back here (even if just a link to an issue opened against the tool), that would be helpful!

Thanks! Jen

ADD REPLY • link written 17 months ago by Jennifer Hillman Jackson ♦ 25k

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