"ChIP-seq analysis" workflow generates many warnings in the log

Scenario to reproduce:

1. Open "ChIP-seq analysis with Cistrome tools" workflow sample.
2. Run the sample with the next parameters:
   Analysis type: only treatment tags;
   MACS input: "_common_data/NIAID_pipelines/Chip-seq/input_data/chr4.bed".
   Other parameters should be default.
   Current state: log contains many warnings like

   [ERROR][19:00] BED parsing error: incorrect strand value '0' at line 1039!

Next should be done:

• Warnings should be shown on the workflow dashboard.
• It looks like the file that is read with warnings is produced by some tool. Find the reason of warnings and fix it. I suppose that the tool generates a correct file, but UGENE can't read it.
• Conservation plot doesn't produce a result:

  [ERROR][19:08] conservation plot: Error: unexpected symbol in "plot(x,y0,type="l",col=rainbow(1)[1],main=Average Phastcons"
  [DETAILS][19:08] Tool conservation_plot finished successfully
  [ERROR][19:08] Conservation Plot error: Can not find a required output file /var/folders/c1/vql5jmsj3rd03xlwyd_gzxzw0000gn/T/ugene_tmp/p82504/ConservationPlot_tmp/1445605217_0/tmp.bmp.

• Conduct GO produces a very suspicious result: the result file contains only several links. The file is attached to the issue.