samtools merge will not merge CRAM files aligned to different references. Merge of BAM files works as I expected.
Example data is from an Illumina run. Reads were split by alignment to target organism and phiX.
$ samtools view -b -o 50176_1#4_phix.bam 50176_1#4_phix.sam
$ samtools view -C -o 50176_1#4.cram 50176_1#4.sam
$ samtools view -C -o 50176_1#4_phix.cram 50176_1#4_phix.sam
$ samtools merge -o merged.bam 50176_1#4.bam 50176_1#4_phix.bam
$ samtools view -H merged.bam | grep "^@SQ"
@SQ SN:ENA|CU458896|CU458896.1 LN:5067172 UR:/lustre/scratch120/npg_repository/references/Mycobacterium_abscessus/CU458896.1/all/fasta/CU458896.fasta AS:CU458896 M5:ffb37b1f4cfc02b01cc8f3cafebf1e8e SP:Mycobacterium abscessus ATCC 19977
@SQ SN:phix LN:5386 M5:c3f78539481dde3e7fb732c446d42d93 UR:/lustre/scratch120/npg_repository/references/PhiX/Sanger-SNPs/all/fasta/phix_unsnipped_short_no_N.fa
$ samtools merge -o merged.cram 50176_1#4.cram 50176_1#4_phix.cram
[E::cram_decode_slice] MD5 checksum reference mismatch at phix:1490-1811
[E::cram_decode_slice] CRAM : 61daed23708bef6e28219b8a142433b6
[E::cram_decode_slice] Ref : 2bbaebd6ab6c35f1a740fc83d1c0bf09
[E::cram_decode_slice] @SQ M5: c3f78539481dde3e7fb732c446d42d93
[E::cram_decode_slice] Please check the reference given is correct
[E::cram_next_slice] Failure to decode slice
samtools merge: failed to read first record from "50176_1#4_phix.cram"
$ cat 50176_1#4.sam
@HD VN:1.5 SO:coordinate
@SQ SN:ENA|CU458896|CU458896.1 LN:5067172 UR:/lustre/scratch120/npg_repository/references/Mycobacterium_abscessus/CU458896.1/all/fasta/CU458896.fasta AS:CU458896 M5:ffb37b1f4cfc02b01cc8f3cafebf1e8e SP:Mycobacterium abscessus ATCC 19977
@RG ID:50176_1#4 DT:2025-02-27T00:00:00+0000 PU:250227_A00948_0895_AH3J3WDSXF_1#4 LB:65825089 PG:SCS SM:ERS16371091 CN:SC PL:ILLUMINA DS:ERP149661: My aim is to adapt existing spatial transcriptomic methods
@PG ID:SCS VN:1.8.1 PN:NovaSeq Control Software DS:Controlling software on instrument
@PG ID:basecalling PP:SCS VN:Unknown PN:Unknown DS:Basecalling Package
A00948:895:H3J3WDSXF:1:1551:28492:34867 1187 ENA|CU458896|CU458896.1 5066916 60 151M = 5067101 257 CTGCGAATGCCGTTTCCACCGGGCGCATGCATCGGAACCATACAAACTGGCCTATGCCGATCGCGGTCGGACACCGACTAGCCGGTCCCCCGGAGCAGGTGATCCGACATGATCTCCTGGTATACGCACACTGACAACCATGGGGGTGGTC F,::F,FF,F,FF,,,:FF,F:,F:F:F:FFF:F:FFF,FF,F,,FF:,,,F,F::FF:FFF,F:F:F:,F,FFF,F:F,:,,,:FF,,FF,,F:FF::,,F:FFFFFFF:F:F::FF,FF,:F,FF:FFFF:F:,FF,FF:,,,,F,,FF AS:i:131 XS:i:0 MQ:i:60 ms:i:3857 mc:i:5067251 MC:Z:72M79S MD:Z:41C2C7G82C15 NM:i:4 RG:Z:50176_1#4
A00948:895:H3J3WDSXF:1:1551:28492:34867 1107 ENA|CU458896|CU458896.1 5067101 60 72M79S = 5066916 -257 GAAACCCACGACCGATCGTTCAAAAGGGGCTAGTGTCGACGTGTCCCCACCAGCTGAGAGAGATGCTCGCCGTTGACTTACGAACTGAATTCCCAGTTCACGGCGGTATGTAATACCTTCGTCTCAGAGCTCAACGGTGACGACAATCAAT ,:FFFFF,FFFF,F::,,FF,:F,,:FFFFF:FFFF:,FF,FFF:F:,,,FFF:FF,F:FFF,:F,F,::,,FFF,:F,F,:FF:FFFFFF,F,,:::FFF:F,:,FFFF,FFFFF:,F,FF,,FF:FF,FF,F:,FF,FF,F,:FF:FFF AS:i:72 XS:i:0 SA:Z:ENA|CU458896|CU458896.1,1,-,72S79M,60,4; BC:Z:CGTCGTCG-TTTCTGAG QT:Z:F:FFF:FF :::,::,F MQ:i:60 ms:i:3649 mc:i:5066916 MC:Z:151M MD:Z:72 NM:i:0 RG:Z:50176_1#4
$ cat 50176_1#4_phix.sam
@HD VN:1.5 SO:coordinate
@SQ SN:phix LN:5386 M5:c3f78539481dde3e7fb732c446d42d93 UR:/lustre/scratch120/npg_repository/references/PhiX/Sanger-SNPs/all/fasta/phix_unsnipped_short_no_N.fa
@RG ID:50176_1#4 DT:2025-02-27T00:00:00+0000 PU:250227_A00948_0895_AH3J3WDSXF_1#4 LB:65825089 PG:SCS SM:ERS16371091 CN:SC PL:ILLUMINA DS:ERP149661: My aim is to adapt existing spatial transcriptomic methods
@PG ID:SCS VN:1.8.1 PN:NovaSeq Control Software DS:Controlling software on instrument
@PG ID:basecalling PP:SCS VN:Unknown PN:Unknown DS:Basecalling Package
A00948:895:H3J3WDSXF:1:2315:25319:10551 99 phix 1490 60 151M = 1661 322 TGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCACAGCTCGTGACATTATGGGTCTGCACGCTGCTTATGCTCATTTGCATACTGCCCAAGAAGGTGATTGCTTCATGC FFFF:FFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFF,F:,,FF,,F,FFFFFF::FFFF,:FFFFFF,FFF:,:::FF:,:,FFF,F,F,FF:,F,F,FF,FFFF,F:F AS:i:222 nn:i:0 tp:A:P cm:i:10 s1:i:156 s2:i:0BC:Z:CGTCGTCG-TTTCTGAG QT:Z::F,,FF,F FFF:FFF, MQ:i:60 MC:Z:151M ms:i:3856 MD:Z:78T2A0T18A12A12A7C6A8 NM:i:8 RG:Z:50176_1#4
A00948:895:H3J3WDSXF:1:2315:25319:10551 147 phix 1661 60 151M = 1490 -322 ACTTCCTTTGGCGGTAAAACCTCTTATGACGCTGACAACCGTCCTTTACATGTCATGCTCTCTTATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACTGACCTATAAAA ,,,,F,:,,F,,,:F::FF,F:F,,FFF,FFFFFF,,,FFFF::F,F,,,,F,FFFFF,::,F,,F,FFFF:F:FFFFF,:F,FFFF,F:FFFFFFF,FFF:FFF,,:FF:FFFFFFF:F:FF:F:FFF:F:FFFF:FF,FFF,FFF,:,, AS:i:238 nn:i:0 tp:A:P cm:i:9 s1:i:156 s2:i:0MQ:i:60 MC:Z:151M ms:i:4704 MD:Z:0T4A5A37T8G4A75A10C0 NM:i:8 RG:Z:50176_1#4```
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