(partition_bam_reads) Error: line number 29869383 of file - has 3 fields, but 6 were expected.

Hitting an error in partition_bam_reads:

rule partition_bam_reads:
    input: inputs/star_2_7_gencode40_sjdb/chrNameLength.txt, output/bams/dedup/genome/IP.genome.Aligned.sort.dedup.bam, annotations/gencode.v38.annotation.tiled_partition.bed.gz
    output: output/counts/genome/vectors/IP.counts
    jobid: 0
    benchmark: benchmarks/counts/unassigned_experiment.IP.partition_bam_reads.txt
    reason: Forced execution
    wildcards: replicate_label=IP
    resources: mem_mb=6599, disk_mb=6599, tmpdir=/scratch/bay001/30691944.tscc-mgr7.local

bedtools bamtobed -i output/bams/dedup/genome/IP.genome.Aligned.sort.dedup.bam | awk '($1 != "chrEBV") && ($4 !~ "/2$")' | bedtools flank -s -l 1 -r 0 -g inputs/star_2_7_gencode40_sjdb/chrNameLength.txt -i - | bedtools shift -p 1 -m -1 -g inputs/star_2_7_gencode40_sjdb/chrNameLength.txt -i - | bedtools sort -i - | bedtools coverage -counts -s -a annotations/gencode.v38.annotation.tiled_partition.bed.gz -b - | cut -f 7 | awk 'BEGIN {print "IP"} {print}' > output/counts/genome/vectors/IP.counts;
Error: line number 29869383 of file - has 3 fields, but 6 were expected.
[Fri Feb  3 17:24:31 2023]

Start by reproducing the partition_bam_reads rule with the shown command and inspect the pipeline around line 29869383, including the BAM-to-BED and annotation streams. Determine which stage emits three fields instead of six; done means the rule completes and produces output/counts/genome/IP.counts without the field-count error.