Exomedepth missing chromosome number in the output

Hello everyone,

i’m running exomedepth and i got the following warning message:

Warning message:
In scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
number of items read is not a multiple of the number of columns

and in the output table i don’t have the chromosome number but NA (see the first row as an example):

NA 16718 17479 deletion X037.V.1.recal 0.991013585083835 3 39.4 0.148

What can i do?

Hi @mttfnc

The coordinates do not specify a genome region if the chromosome is missing. The problem is likely with the input, and the tool’s algorithm was confused.

This is an error produced by R and it usually means there is an input problem to fix. The message can be reported whether using tools in Galaxy or otherwise, which means that an internet search will usually discover what it means.

In general, that message indicates that a “data frame” – your input, likely a tabular file – has missing values. Maybe start checking there? All rows should contain the same number of columns, and the values in each column need to be populated (not empty).

Keep in mind that since you are submitting a job through a form, any values that you input on the form are part of the “input”. Missing labels will generally prohibit the job submitting at all – but format problems in those labels are tricky to catch. Instructions for formatting are usually on the form directly but in general, tool prefer labels values that are all oneWord, with no whitespace, and no special characters (easier for a computer to parse).

This tutorial covers a bunch of tools that can be used to explore data if interested. Or, browse the Text Manipulation sections of the tool panel. Data Manipulation Olympics

Most of this advice is generalized as best guesses about what the root problem is! So, if you cannot spot the problem, please share more details and we can try to help more. This FAQ explains where to review inputs, parameters, and job logs directly in the application (the best place to start your own review, too) – plus how to share those same details so others can help. Troubleshooting errors