I am trying to understand the output of Gemini.

I get the new Bam but comparing the input BAM with the output BAM, it is difficult for me to see/check what Gemini is doing. This program was implemented in a pipeline that has been running in our lab for many years and I am now implementing this in a new pipeline.

I have the feeling that in my development as well as in the production pipeline, this is not doing the realignment. I guess so from the chromosome.log. There are all like the one provided below

 2/16/2024 2:08 AM 1  ************* Starting **************
2/16/2024 2:08 AM 1  Version:  5.2.11.163.
2/16/2024 2:08 AM 1  Command-line arguments: .
2/16/2024 2:08 AM 1  "--samtools D:\samtools.exe --genome D:\human_g1k_v37 --bam F:\Illumina\MiSeqOutput\240214_M01875_1060_000000000-LD5P3\Data\Intensities\Basecalls\\Genotyping_2.22\3563963187_sorted.bam --chromRefId 10 --outFolder F:\Illumina\MiSeqOutput\240214_M01875_1060_000000000-LD5P3\Data\Intensities\Basecalls\\Genotyping_2.22\3563963187\11".
2/16/2024 2:08 AM 1  At 0, prev block is -1, nothing to wait on.
2/16/2024 2:08 AM 1  Borderline pairs left: 0.
2/16/2024 2:08 AM 1  Wrote 0 reads with missing mates to bam.
2/16/2024 2:08 AM 1  Triggering last buffer batch. Read 0 read pairs. Flushed 0 singles.
2/16/2024 2:08 AM 1  Completing buffer.
2/16/2024 2:08 AM 6  Finished processing for region 11:0-10000000. 0 alignments flushed, 0 sent to next block, 0 retrieved from . Realigned 0/0 attempts (0 pairs skipped realignment), silenced 0 messy mates.
2/16/2024 2:08 AM 1  Now waiting on 3 tasks.
2/16/2024 2:08 AM 9  Finished processing for region 11:10000001-20000000. 0 alignments flushed, 0 sent to next block, 0 retrieved from 0-10000000. Realigned 0/0 attempts (0 pairs skipped realignment), silenced 0 messy mates.
2/16/2024 2:08 AM 1  Done waiting on tasks.
2/16/2024 2:08 AM 1  Found 0 total indels, and 0 eligible for realignment.
2/16/2024 2:08 AM 1  Attempts: 0.
2/16/2024 2:08 AM 1  Flushed: 0.
2/16/2024 2:08 AM 1  Realigned: 0.
2/16/2024 2:08 AM 1  Retrieved from Past Block: 0.
2/16/2024 2:08 AM 1  Sent To Next Block: 0.
2/16/2024 2:08 AM 1  Silenced: 0.
2/16/2024 2:08 AM 1  Skipped: 0.
2/16/2024 2:08 AM 1  Calling cat on 1 with output at F:\Illumina\MiSeqOutput\240214_M01875_1060_000000000-LD5P3\Data\Intensities\Basecalls\\Genotyping_2.22\3563963187\11\merged.bam.
2/16/2024 2:08 AM 1  Intermediate bam: F:\Illumina\MiSeqOutput\240214_M01875_1060_000000000-LD5P3\Data\Intensities\Basecalls\\Genotyping_2.22\3563963187\11\out.bam_0_11_All_All_0_11_All_All_0_1_0_9c30c038-cec4-4238-a455-0283f4de280c        1767B.
2/16/2024 2:08 AM 1  Skipping samtools cat due to single input bam, instead moving F:\Illumina\MiSeqOutput\240214_M01875_1060_000000000-LD5P3\Data\Intensities\Basecalls\\Genotyping_2.22\3563963187\11\out.bam_0_11_All_All_0_11_All_All_0_1_0_9c30c038-cec4-4238-a455-0283f4de280c directly to output at F:\Illumina\MiSeqOutput\240214_M01875_1060_000000000-LD5P3\Data\Intensities\Basecalls\\Genotyping_2.22\3563963187\11\merged.bam.
2/16/2024 2:08 AM 1  Calling samtools sort on F:\Illumina\MiSeqOutput\240214_M01875_1060_000000000-LD5P3\Data\Intensities\Basecalls\\Genotyping_2.22\3563963187\11\merged.bam.
2/16/2024 2:08 AM 1  Done finalizing bam.
2/16/2024 2:08 AM 1  Deleting intermediate bams.
2/16/2024 2:08 AM 1  Finished deleting intermediate bams.
2/16/2024 2:08 AM 1  ******************** Ending *********************

My code is this

pisces_all/pisces_all/GeminiMulti \
                                    -bam /p5p7/p5p7_FINAL_mapped.bam   \
                                    --exePath /mainfs/scratch/mdb1c20/pisces_all/pisces_all/Gemini \
                                    -genome v0_masked_new_15092023_4_RACP-PISCES \
                                    -samtools  /local/software/samtools/1.16.1/bin/samtools \
                                    --outFolder Results \
                                    --numProcesses  5 \
                                    --chromosomes chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX,chrY \
                                    --realignonly True \
                                    --logregionsandrealignments True 

Another element that suggests to me that there is no indel realignment done is that files like 3_IndelOutcomes or 3_indels are empty.

Can someone confirm this?? and final question. I cannot see a way to make the app work with single-read. Is this tool not developed for that purpose? I don't find a way to able/disable this option. Is this becaouse the app is not developed for single-read??