Cross post from HOPS

[valery-shap]

rhuebler/HOPS#9
There is no heatmaps and pdf candidates files and error:

During startup - Warning message:
Setting LC_CTYPE failed, using "C" 
Read 356 items
Error in image.default(x = 1:ncol(red.res), y = 1:nrow(red.res), z = t(red.res),  : 
  increasing 'x' and 'y' values expected
Calls: image -> image.default
Execution halted

What could be the reason of this? There is no ancient candidates in my database and data?

Best regards,
Valery

[MeriamOs]

Hey @valery-shap,

Did you ever figure this out? Having something similar with some of my samples.

Cheers,
Meriam

[MeriamOs]

Also getting the following error for some other samples:

Error in pdf(paste(path, "pdf_candidate_profiles/", tax, "/stp", red.res[tax, :
invalid 'file' argument '/path/to/HOPS/sample-1/maltExtract/pdf_candidate_profiles/Mycobacterium_avium/stp3_6949-01_90%-reads.rma6_Mycobacterium_avium_summary.pdf'
Execution halted
Process Exited with status: 1

[ilight1542]

This is due to the requirement of minimum 10 reads assigned at a node for calculating edit distance (see postprocessingAMPS in #5 (pull request changes) lines 30, then the actual source of error in line 258.

If no files exceed the threshold and/or have a declining edit distance, no output will be made and the error is produced when trying to output the heatmap. I added a check to avoid this and a print statement to indicate that no candidate is found with declining edit distance.

this should not happen going forward and will be updated and shipped with new distribution of HOPS on conda soon (ish) :)