error when running calctruequality

[coyk]

I'm trying to recalibrate Q scores of a NextSeq run using MiSeq contigs assembled with Tadpole
#mapping reads to reference

bbmap.sh in=concatABC.fastq.gz outm=mapped.sam ref=./Lpe09_06TdpAssemblies/contigs09_06.fa ignorequality maxindel=100 minratio=0.4 ambig=toss qahist=qahist_raw.txt qhist=qhist_raw.txt mhist=mhist_raw.txt
#generating calibration matrices
calctruequality.sh in=mapped.sam

I get the following output
java -ea -Xmx57992m -Xms57992m -cp /home/me/bbmap/current/ jgi.CalcTrueQuality in=mapped.sam
Executing jgi.CalcTrueQuality [in=mapped.sam]

Exception in thread "Thread-2" Exception in thread "Thread-1" java.lang.AssertionError: TODO: Encountered a read with 'M' in cigar string but no MD tag and no ScafMap loaded.
at stream.SamLine.toShortMatch(SamLine.java:1212)
at stream.SamLine.toRead (SamLine.java:2015)
at stream.SamLine.toRead (SamLine.java:1875)
at stream.SamReadStreamer$ProcessThread.makeReads (SamReadStreamer.java:206)
at stream.SamReadStreamer$ProcessThread.run (SamReadStreamer.java:135)
java.lang.AssertionError: TODO: Encountered a read with 'M' in cigar string but no MD tag and no ScafMap loaded.
at stream.SamLine.toShortMatch(SamLine.java:1212)
at stream.SamLine.toRead (SamLine.java:2015)
at stream.SamLine.toRead (SamLine.java:1875)
at stream.SamReadStreamer$ProcessThread.makeReads (SamReadStreamer.java:206)
at stream.SamReadStreamer$ProcessThread.run (SamReadStreamer.java:135)
Exception in thread "Thread-3" java.lang.AssertionError: TODO: Encountered a read with 'M' in cigar string but no MD tag and no ScafMap loaded.
at stream.SamLine.toShortMatch(SamLine.java:1212)
at stream.SamLine.toRead (SamLine.java:2015)
at stream.SamLine.toRead (SamLine.java:1875)
at stream.SamReadStreamer$ProcessThread.makeReads (SamReadStreamer.java:206)
at stream.SamReadStreamer$ProcessThread.run (SamReadStreamer.java:135)

The program didn't quit so I don't know if it's still doing something or not. I don't see /ref/qual/ files being generated. It's been hanging for over an hour. I'm not sure how to proceed. Since the mapped sam file was generated with bbmap using contigs from Tadpole, I'm not sure why there are Ms in the cigar strings. The infile I used for bbmap was made by first concatenating all Read1 from 3 libraries then all Read2 from 3 libraries then those two files concatenated.