Different filetype error with bismark2summary

[yaaminiv]

I've gone through all steps of the bismark pipeline except for bismark2summary. I ran into this error:

It looks like there is a mix of samples, e.g. RRBS as well as WGBS, in this folder. Please consider running bismark2summary only on samples of the same data type,
or specify the input files manually (--help for more information). Extiting...

My two files were processed identically (YRVA processed with this script and YRVL processed with this script). Did I miss something? Is there a reason why bismark thinks I have different sample types?

[yaaminiv]

Also tried running bismark2summary specifying files and got the same error (script here).

[sr320]

Try running separately on each file thanks Steven Steven B. Roberts, Associate Professor Associate Director - Graduate Program Coordinator School of Aquatic and Fishery Sciences University of Washington Fisheries Teaching and Research (FTR) Building - Office 232 1140 NE Boat Street - Seattle, WA 98105 robertslab.info - sr320@uw.edu - @sr320 vm:206.866.5141 - cell:360.362.3626

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On Sep 12, 2019, 9:17 AM -0700, Yaamini Venkataraman ***@***.***>, wrote: Also tried running bismark2summary specifying files and got the same error (script here). — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

[yaaminiv]

@sr320 I already have HTML reports for each file; bismark2summary should concatenate those 2 HTML reports so I don't have to look at multiple files. bismark2summary does not run with only 1 file

[sr320]

not sure of larger reason for the need for the summary

... but my guess is one you deduped.

Note you can force to work by specifying manually -see error message

[yaaminiv]

I mainly want to confirm that my samples were processed identically...bismark saying one sample is RRBS and another is WGBS is a bit concerning. I tried doing it manually (see my second comment) but I got the same error.

[sr320]

I would spend the time re-running in same job script

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On Sep 12, 2019, 9:57 AM -0700, Yaamini Venkataraman ***@***.***>, wrote: I mainly want to confirm that my samples were processed identically...bismark saying one sample is RRBS and another is WGBS is a bit concerning. I tried doing it manually (see my second comment) but I got the same error. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.