Issue with Incomplete Chromosome Loading in SoloTE for a Human-Virus Fusion Genome

[liuweihahaha]

Dear author,

I apologize for bothering you. While using SoloTE to quantify transposable elements (TEs), I noticed that during the final step of splitting the BAM file, only a few chromosomes were loaded, rather than all of them. Is this because SoloTE only quantifies the first few chromosomes, or is it just displaying those few? I am using a reference genome that is a fusion of the human genome and a viral genome, and I’m concerned that this might lead to missing information from the viral genome after fusion.

Running command: python SoloTE_pipeline.py --threads 50 --bam /home/lw/newdisk/project/bamdata/A5_345Aligned.sortedByCoord.out.bam --teannotation hg38_rmsk.bed --outputprefix A5_345 --outputdir /home/lw/newdisk/project/result_soloTE --dual SoloTE started at 15:07:42 [OK] samtools found! [OK] bedtools found! SoloTE v1.10 started! SoloTE Home directory /home/lw/newdisk/project/soloTE SoloTE executed from /home/lw/newdisk/project/soloTE Results will be stored in /home/lw/newdisk/project/result_soloTE Input BAM file: /home/lw/newdisk/project/bamdata/A5_345Aligned.sortedByCoord.out.bam Input TE BED file: /home/lw/newdisk/project/soloTE/hg38_rmsk.bed Dual mode enabled. SoloTE will calculate TE expression also considering reads annotated to genes. Currently working in temporary directory: /home/lw/newdisk/project/result_soloTE/A5_345_SoloTE_temp samtools view -@ 50 -O BAM -o A5_345_nogenes_overlappingtes.bam -L /home/lw/newdisk/project/soloTE/hg38_rmsk.bed -e '(exists([CB]) && exists([UB]) && [CB]!="-" && [UB]!="-")' /home/lw/newdisk/project/bamdata/A5_345Aligned.sortedByCoord.out.bam samtools index A5_345_nogenes_overlappingtes.bam bedtools bamtobed -i A5_345_nogenes_overlappingtes.bam -split > A5_345_nogenes_overlappingtes.bed bedtools intersect -a /home/lw/newdisk/project/soloTE/hg38_rmsk.bed -b A5_345_nogenes_overlappingtes.bed -u > A5_345_selectedtes.bed python /home/lw/newdisk/project/soloTE/annotateBAM.py A5_345_nogenes_overlappingtes.bam A5_345_selectedtes.bed temp_annotated_te.bam 1 samtools sort -@ 50 -O BAM -o A5_345_teannotated.bam temp_annotated_te.bam [bam_sort_core] merging from 0 files and 50 in-memory blocks... samtools merge --threads 50 -o - /home/lw/newdisk/project/bamdata/A5_345Aligned.sortedByCoord.out.bam A5_345_teannotated.bam|samtools view -@ 50 -O BAM -o A5_345_final.bam -e 'exists([CB]) && exists([UB]) && exists([GN]) && [CB]!="-" && [UB]!="-" && [GN]!="-"' --keep-tag GN,CB,UB samtools index A5_345_final.bam Counts for chromosome chr1 are being generated in process: 35704 Counts for chromosome chr2 are being generated in process: 35705 Counts for chromosome chr3 are being generated in process: 35706 Counts for chromosome chr5 are being generated in process: 35708 Counts for chromosome chr4 are being generated in process: 35707 Counts for chromosome chr6 are being generated in process: 35709 Counts for chromosome chr7 are being generated in process: 35710 Counts for chromosome chr8 are being generated in process: 35711 Counts for chromosome chr9 are being generated in process: 35712 Counts for chromosome chr10 are being generated in process: 35713 Counts for chromosome chr11 are being generated in process: 35714 Counts for chromosome chr12 are being generated in process: 35715 Counts for chromosome chr13 are being generated in process: 35716 Counts for chromosome chr14 are being generated in process: 35717 Counts for chromosome chr15 are being generated in process: 35718 Counts for chromosome chr16 are being generated in process: 35719 Counts for chromosome chr17 are being generated in process: 35720 Counts for chromosome chr18 are being generated in process: 35721 Counts for chromosome chr19 are being generated in process: 35722 Counts for chromosome chr20 are being generated in process: 35723 Counts for chromosome chr21 are being generated in process: 35724 Counts for chromosome chr22 are being generated in process: 35725 Counts for chromosome chrX are being generated in process: 35726 Counts for chromosome chrY are being generated in process: 35727 Counts for chromosome chrM are being generated in process: 35728 Counts for chromosome GL000194.1 are being generated in process: 35729 Counts for chromosome GL000195.1 are being generated in process: 35730 Counts for chromosome GL000218.1 are being generated in process: 35731 Counts for chromosome GL000219.1 are being generated in process: 35732 Counts for chromosome KI270711.1 are being generated in process: 35733 Counts for chromosome KI270721.1 are being generated in process: 35734 Counts for chromosome KI270726.1 are being generated in process: 35735 Counts for chromosome KI270727.1 are being generated in process: 35736 Counts for chromosome KI270734.1 are being generated in process: 35737 Creating final results directory /home/lw/newdisk/project/result_soloTE/A5_345_SoloTE_output was created Rscript /home/lw/newdisk/project/soloTE/generate_mtx.R A5_345_legacytes.txt A5_345_legacytes_MATRIX Rscript /home/lw/newdisk/project/soloTE/generate_mtx.R A5_345_locustes.txt A5_345_locustes_MATRIX Rscript /home/lw/newdisk/project/soloTE/generate_mtx.R A5_345_classtes.txt A5_345_classtes_MATRIX Rscript /home/lw/newdisk/project/soloTE/generate_mtx.R A5_345_familytes.txt A5_345_familytes_MATRIX Rscript /home/lw/newdisk/project/soloTE/generate_mtx.R A5_345_subfamilytes.txt A5_345_subfamilytes_MATRIX A total of 32182705 UMIs are in the final matrix. Of these, 25047426 (77.829%) correspond to genes. and 7135279 (22.171%) correspond to TEs. TE detected UMIs are distributed as follows: Locus-specific TEs: 6798252 UMIs (95.277%). Subfamily TEs: 337027 (4.723%). Creating A5_345_SoloTE.stats TE statistics file Finished creating A5_345_SoloTE.stats SoloTE finished with /home/lw/newdisk/project/bamdata/A5_345Aligned.sortedByCoord.out.bam SoloTE finished at 18:46:18 SoloTE total running time: 3:38:35.398095

[liuweihahaha]

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