zero counts: wrong options or ESAT not working?

[ferreirafm]

I'm running ESAT with options below:
esat -task score3p -alignments sample_sheet.tsv -geneMapping EquCab3_GenGenPred_NCBIRefSeq_All_mod.tsv -multimap normal -scPr -wExt 2500 -all -out all_samples

The reads were aligned with Cellranger so I inserted the barcodes in the read names as follows:
VH00972:3:AAAL2FTHV:1:2304:71932:48820:GGTGGCTTCGGAAACG::TAGCTCCCGCGG

I also tested other combinations of ESAT options. In all of them I got an empty counts table.

In the script.log I have been getting a series of warnings as follows:
WARN main umms.esat.NewESAT - location 9082 in NC_001640.1 (+) has >65535 counts.
WARN main umms.esat.NewESAT - location 9092 in NC_001640.1 (+) has >65535 counts.
WARN main umms.esat.NewESAT - location 9138 in NC_001640.1 (+) has >65535 counts.
WARN main umms.esat.NewESAT - location 9164 in NC_001640.1 (+) has >65535 counts.
INFO main umms.esat.NewESAT - Experiment IGFD BAM file /home/ferreirafm/work/colab/falko7/esat/refseq/IGFD_possorted_ge
name_newreadname.bam processed in 206.412144227 sec
INFO main umms.esat.NewESAT - 123412491 valid reads
INFO main umms.esat.NewESAT - 2828461 invalid reads
INFO main umms.esat.NewESAT - 4 BAM files processed in 835.893653349 sec
INFO main umms.esat.NewESAT - 493649964 total valid reads
INFO main umms.esat.NewESAT - 11313844 total invalid reads
INFO main umms.esat.NewESAT - Total window count: 0

I can´t see what I'm doing wrong nor how to know if ESAT is working appropriately. Is there any way to check it.
Any help is appreciated.

[AlexStewartAPHA]

Similar issue:
INFO [2025-01-10 14:34:52,719] [InDropPreprocess.java:105] [main] temporary file created: /tmp/sc_umiFiltered_10083657534316891029.bam
1056939 [main] INFO umms.core.utils.InDropPreprocess - temporary file created: /tmp/sc_umiFiltered_10083657534316891029.bam
INFO [2025-01-10 14:50:42,309] [InDropPreprocess.java:174] [main] Reads: 516839924 writes: 0
2006529 [main] INFO umms.core.utils.InDropPreprocess - Reads: 516839924 writes: 0
INFO [2025-01-10 14:50:42,310] [InDropPreprocess.java:175] [main] Preprocessing file: /home/alex/Desktop/cellranger-8.0.1/U1_Nettie/outs/BAM/possorted_genome_bam.bam took 949.626699289 sec

2006530 [main] INFO umms.core.utils.InDropPreprocess - Preprocessing file: /home/alex/Desktop/cellranger-8.0.1/U1_Nettie/outs/BAM/possorted_genome_bam.bam took 949.626699289 sec

INFO [2025-01-10 14:50:42,310] [InDropPreprocess.java:180] [main] Preprocessing complete: Total reads in: 516839924 Total reads out: 0
2006530 [main] INFO umms.core.utils.InDropPreprocess - Preprocessing complete: Total reads in: 516839924 Total reads out: 0
INFO [2025-01-10 14:50:42,310] [InDropPreprocess.java:181] [main] Total aligned UMIs: 0 Total de-duped UMIs: 0
2006530 [main] INFO umms.core.utils.InDropPreprocess - Total aligned UMIs: 0 Total de-duped UMIs: 0
INFO [2025-01-10 14:50:42,600] [NewESAT.java:1120] [main] Total window count: 0
2006820 [main] INFO umms.esat.NewESAT - Total window count: 0
INFO [2025-01-10 14:50:42,614] [NewESAT.java:1157] [main] Processing file: /tmp/sc_umiFiltered_10083657534316891029.bam...
2006834 [main] INFO umms.esat.NewESAT - Processing file: /tmp/sc_umiFiltered_10083657534316891029.bam...
INFO [2025-01-10 14:50:42,615] [NewESAT.java:233] [main] Total processing time: 2009.884648442 sec

2006835 [main] INFO umms.esat.NewESAT - Total processing time: 2009.884648442 sec