popscle failing to read scATAC BAM

[daccachejoe]

hi -

I am trying to run demuxlet on Multiome data (the atac seq reads) and have been running into large sorts of problems. The VCF and BAM needed to be filtered, reordered, and reaheadered which I am not sure if that is causing errors in popscle. When I run popscle_pileup.py through singularity, it skips reading every read in the bam file (not due to MQ filter because most reads are good) and then theres an error flag at the end. here is a snippet

NOTICE [2025/09/19 18:21:38] - Reading 1914600 reads at chr1:778900 and skipping 1819864
NOTICE [2025/09/19 18:21:38] - Reading 1914700 reads at chr1:778904 and skipping 1819896
NOTICE [2025/09/19 18:21:38] - Reading 1915000 reads at chr1:778907 and skipping 1819980
NOTICE [2025/09/19 18:21:38] - Reading 1915100 reads at chr1:778915 and skipping 1820010
NOTICE [2025/09/19 18:21:38] - Reading 1915200 reads at chr1:778919 and skipping 1820040
NOTICE [2025/09/19 18:21:38] - Reading 1915300 reads at chr1:778924 and skipping 1820066
NOTICE [2025/09/19 18:21:38] - Reading 1915400 reads at chr1:778947 and skipping 1820111
NOTICE [2025/09/19 18:21:38] - Reading 1915500 reads at chr1:778995 and skipping 1820150
NOTICE [2025/09/19 18:21:38] - Reading 1915600 reads at chr1:779046 and skipping 1820188
NOTICE [2025/09/19 18:21:38] - Reading 1915800 reads at chr1:779087 and skipping 1820249
NOTICE [2025/09/19 18:21:38] - Reading 1916500 reads at chr1:779729 and skipping 1820617
NOTICE [2025/09/19 18:21:38] - Reading 1916800 reads at chr1:780680 and skipping 1820825
[/opt/popscle/sam_filtered_reader.cpp:268 read] Error while reading filtered_bam2_selected.bam
INFO:    Cleaning up image...

Also, anytime I run the code with --tag-UMI "" to keep it empty, it fails with the error

FATAL ERROR - 
[E:/opt/popscle/params.cpp:564 Status] Problems encountered parsing command line:

Cannot correspond command line parameter 1796 (#11) to any of the options

For more context from the bam file. the barcode in the bam file is specified by 'CB' so I included that in the popscle paramaters in --tag-group.

samtools view filtered_bam2_selected.bam | head -n 2
LH00401:450:22WHW2LT4:4:2498:25965:6729 163     chr1    9997    0       49M     =       10178   231     CCCATAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAA   III-IIIIIIIIIIIIIIIIIIIIIIIII9IIIII9IIIII9IIIIIII       NM:i:1  MD:Z:2G46       AS:i:46 XS:i:46     CR:Z:TTATCACAGGAACAAG   CY:Z:IIIIIIIIIIIIIIII   CB:Z:TAGTCAATCGATTATG-1 BC:Z:TACGAGTT   QT:Z:II9IIIII   RG:Z:JOSC01_NYUPsoriasispool2_0:MissingLibrary:1:22WHW2LT4:4
LH00401:450:22WHW2LT4:4:2318:25940:15792        99      chr1    9998    0       50M     =       10179   229     CCATAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACC  II-IIIIIIIIIIIIIIIII-II-IIII-I9I9IIIIIIIIIIIIIII9I      NM:i:1  MD:Z:1G48       AS:i:48     XS:i:48 CR:Z:GCCTGAGCATTCAGGA   CY:Z:IIIIIIIIIIIIIIII   CB:Z:TCGGTAAGTTATAGCG-1 BC:Z:ATGTCCAG   QT:Z:9IIII99I   RG:Z:JOSC01_NYUPsoriasispool2_0:MissingLibrary:1:22WHW2LT4:4

Can confirm the vcf and bam chromosome annotations are the same and in the same order from the log file

BAM file is using chr notation
VCF file is using chr notation
BAM and VCF files are using the same genome notation

If you could please help me sort this out it would be a great help! Thanks