I am getting below warning when trying to crawl Sharepoint Site collection :-

The FAST Search backend reported warnings when processing the item. (Customer-supplied command failed: Output- and errorfile were both empty )

As checked, the documents which are throwing warning are not empty and does contain text.

However, when the documents are re-crawled , they get crawled successfully.

Any suggestions on what is wrong here ?

Do you get the error for certain types of documents? The error can be thrown if  the encoding is not recognized. You may want to gather infotool output when reproducing the error to review FAST backend logs. You can as well enable doctrace when feeding sample document when it fails to see if it fails in one of the stages in the document processing pipeline.

Error is for any type of document pdf/doc/ppt/xls/aspx and it is random. The document may or may not get processed successfully.

I was able to reproduce the warning for one of the document by recrawl after enabling doctrace (psctrl doctrace on) and debug (psctrl debug on). However, doclog did not retrieve any logs for that document using below commands :-

doclog.exe documentID

doclog.exe -w

Does this comand take time or i am missing something?

One of the previously generated log shows warning after CustomerExtensibility stage :-

INFO   Processor ECMTaxonomy:
INFO   Processor FieldsToCPsMapper:
INFO   Processor CustomerExtensibility:
INFO   Running customer-supplied command in a child process: CallPipelineExtensibilityWebService.exe %(input)s %(output)s http://localhost:8001/PipelineExtensibilityWebService.svc -logging disable -timeout 1
WARNING Customer-supplied command failed: Output- and errorfile were both empty (warning code 0)
INFO   Processor DefaultCrawledProperties: