E.g. on a file with 100,000 lines, QCTOOL ends with
!! Error (genfile::MalformedInputError): Source "/tmp/z.vcf" is malformed on line 99997..
heading and tailing the file to make a smaller version does not display the error. Moreover, this file was itself shrunk from one with around 190,000 lines which also failed on what was apparently the 3rd last line.
(It may be that the error message has the wrong line.)