While intersecting a bam file and bed to obtain the total number of reads that map to a class of genes, bedtools outputs the following error:

```
bedtools intersect -a some.bam -b LINE.bed -sorted -s -wa -bed -f 1.0 -nonamecheck | wc -l

ERROR: File some.bam has inconsistent naming convention for record:
      -1      -1      HWI-ST558:319:HJHNYADXX:1:1101:10003:66276 1:N:0:GATCAG 0       +
137933
```

I poked [around the internet][1] and this appears to occour when chromosome naming conventions do not match. However, the stated solution, option `-nonamecheck` did not work. The culprit is (at least) this alignment:

```
samtools view some.bam | grep 'HWI-ST558:319:HJHNYADXX:2:2104:11288:74456'
HWI-ST558:319:HJHNYADXX:2:2104:11288:74456      0       chr4    61813677        0       27M     *       0       0       GACAAATCAAGAAAACCATTAAACAGC     FFFFHHDHFHJJJGIGFFFHGIG@GDH      XA:i:0  MD:Z:27 RG:Z:1  NM:i:0  XM:i:2
```

Which to me does not appear to be any different from other alignments in the file:

```
samtools view some.bam | head
HWI-ST558:319:HJHNYADXX:1:1110:11857:4127       0       chr1    5571    255     29M     *       0       0       GCCACATGTGTGGACCAGGTCAACACATA   FFFFHHHHHJJJJJJJJJJIIJJJJJIJJ    XA:i:2  MD:Z:5G12A10    RG:Z:1  NM:i:2
HWI-ST558:319:HJHNYADXX:1:1210:19976:51309      16      chr1    8405    255     27M     *       0       0       GACTCAGTTAGTTTGATCAGTGTGTTT     HCHHGIJJJIJIIIGIIJHGHHHFFDF      XA:i:0  MD:Z:27 RG:Z:1  NM:i:0
HWI-ST558:319:HJHNYADXX:1:2101:16679:94808      0       chr1    13822   255     31M     *       0       0       TTAATTTGCCCTCATAAACTCTGATCAAAGT FFFFHHHHHJJJJJJJJIHJIJJJJJJJJJJ  XA:i:0  MD:Z:31 RG:Z:1  NM:i:0
HWI-ST558:319:HJHNYADXX:1:2209:11460:28507      0       chr1    19815   0       24M     *       0       0       TGACGTTGTGTGGACATTACCACT        DDFFHHHHHJJJJJJJJJJJJJJJXA:i:0   MD:Z:24 RG:Z:1  NM:i:0  XM:i:2
HWI-ST558:319:HJHNYADXX:2:2206:8659:12479       0       chr1    22434   0       27M     *       0       0       TAACCGGCACGGGCTCATTCTGAAAGC     FEFFHDAFHJJDEGBHIIJ>GGCHIJJ      XA:i:3  MD:Z:5A0A3A16   RG:Z:1  NM:i:3  XM:i:2
HWI-ST558:319:HJHNYADXX:2:1116:12702:23989      0       chr1    24671   0       30M     *       0       0       ATAGATATTATCAGACACACTGTGAACATT  FFFFHFHHHJIJIJJJJJJIJJJJIJJFHI   XA:i:1  MD:Z:3A26       RG:Z:1  NM:i:1  XM:i:2
HWI-ST558:319:HJHNYADXX:2:2112:15091:10459      0       chr1    37645   0       29M     *       0       0       CTGTGCAGAGCTGCAGCCCTCAAGGAGTT   FFADDFFDHEGBDD@GIEIGHEGHC8:FG    XA:i:1  MD:Z:21C7       RG:Z:1  NM:i:1  XM:i:2
HWI-ST558:319:HJHNYADXX:1:2101:17286:97920      0       chr1    43096   0       26M     *       0       0       CGGTTTGACTGTACAAGTGAAATACC      FFFDHHHHHJJIJJJJIHIHEIIIJJ       XA:i:0  MD:Z:26 RG:Z:1  NM:i:0  XM:i:2
HWI-ST558:319:HJHNYADXX:2:1108:5430:68222       0       chr1    43273   0       24M     *       0       0       TCGTTGAGAAGAGTAGGGACGGTA        FFFFHHHHHJJJJGHIJJJJIIGIXA:i:0   MD:Z:24 RG:Z:1  NM:i:0  XM:i:2
HWI-ST558:319:HJHNYADXX:2:2207:2908:11814       16      chr1    43750   255     29M     *       0       0       TACGCTTCAGTACGATCACTGATGTTGAT   JIJIJJIJJJJJJJJJJIJJHHHHHFFFF    XA:i:1  MD:Z:9T19       RG:Z:1  NM:i:1
```

This happens for all 12 of my bam files (mapped to Danrer7, bowtie-0.12.8*). I am a bit at a lost of what is happening here. Bedtools Version: v2.23.0

 [1]: https://github.com/arq5x/bedtools2/issues/212
I have spent some more time finding the source of the issue, and it turns to be something simple:

Mapping was done against Zv9 and the bed file contained coordinates from Zv10 - UCSC now has this version as default and I obviously did not pay enough attention (I hang my head in shame). When replacing with the Zv9 bed file the issue is gone.

I would expect that in such a case, the error message would something like '-a and -b coordinates not matching' but the fact that it gives an error is already re-assuring.