Assertion `mapping_output_file_ != __null' failed

[lunky-zao]

When I run the chromap software, I keep getting the following error
chromap: src/mapping_writer.h:62: void chromap::MappingWriter::InitializeMappingOutput(uint32_t, const string&, chromap::MappingOutputFormat&) [with MappingRecord = chromap::SAMMapping; uint32_t = unsigned int; std::string = std::_cxx11::basic_string]: Assertion `mapping_output_file != __null' failed.
00.chromap_alignment.sh: line 4: 675118 Aborted (core dumped) chromap --preset hic -r $contigsFasta -x contigs.index --remove-pcr-duplicates -1 $r1Reads -2 $r2Reads --SAM -o aligned.sam -t 4

[mourisl]

Which version of Chromap are you using? I think this is regarding the number of temporary files, which might be fixed in the github version. Could you please git clone to get the newest version and give it a try?