According to the STAR docs, soft-clipping using the --clip[3p,5p]Nbases option automatically clips the corresponding end of the read during alignment, so that we don't try to map adapters.

In the following example, I clipped the 5-prime 10X adapter,bc,umi by setting STAR ... --clip5pNbases 41 0....

Just looking at the R1 FWD reads shows many reads whose CIGAR has a clip (S) value is less than 41, which seems to ignore the directive above to clip (at least) 41 bases:

(/nfs/turbo/[...]/shared3012) [user@gl1527 FCA_gut8015057_S1_L001_bigwig]$ samtools view -f 99 /tmpssd/user/test_chr1_min40.bam|head -n 4
A00708:13:HTC7MDSXX:4:1364:26720:35462  99      chr1    14467   255     39S62M  =       14642   240     ACGCAGCGTCGAATCTTCTGTGCTGGTTTCTTATATGGGGGCGCAGGCTGGGTGGAGCCGTCCCCCCATGGAGCACAGGCAGACAGAAGTCCCCGCCCCAG   FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF   NH:i:1  HI:i:1  nM:i:0  AS:i:125        CR:Z:ACGCAGCGTCGAATCT       UR:Z:TCTGTGCTGG GX:Z:ENSG00000310526.1  GN:Z:WASH7P     sS:Z:ACGCAGCGTCGAATCTTCTGTGCTGGTTTCTTATATGGGGGCGCAGGCTGGGTGGAGCCGTCCCCCCATGGAGCACAGGCAGACAGAAGTCCCCGCCCCAG      sQ:Z:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF      sM:i:0  CB:Z:ACGCAGCGTCGAATCT   UB:Z:TCTGTGCTGG
A00708:13:HTC7MDSXX:4:2668:2311:21997   99      chr1    17470   255     39S62M  =       17703   477     CCCTCCTCATCAGGGGCACAGCGTGCACTGGGGGGTCCCAGGCCTCCCGAGCCGAGCCACCCGTCACCCCCTGGCTCCTGGCCTATGTGCTGTACCTGTGT   ,FFFFF,FFFFFFFFFFFFFFFFFFF,,,F:,,,,F,,,FFFFFFFFFFF:FFFFFFFFFFF:,FFFFFFFFFFFFFF:FFFFFFFF:FFFFFFFFFFFF:   NH:i:1  HI:i:1  nM:i:4  AS:i:126        CR:Z:CCCTCCTCATCAGGGG       UR:Z:CACAGCGTGC GX:Z:ENSG00000310526.1  GN:Z:WASH7P     sS:Z:CCCTCCTCATCAGGGGCACAGCGTGCACTGGGGGGTCCCAGGCCTCCCGAGCCGAGCCACCCGTCACCCCCTGGCTCCTGGCCTATGTGCTGTACCTGTGT      sQ:Z:,FFFFF,FFFFFFFFFFFFFFFFFFF,,,F:,,,,F,,,FFFFFFFFFFF:FFFFFFFFFFF:,FFFFFFFFFFFFFF:FFFFFFFF:FFFFFFFFFFFF:      sM:i:-1 CB:Z:-  UB:Z:-
A00708:13:HTC7MDSXX:4:2668:1750:23469   99      chr1    17470   255     39S62M  =       17703   477     CCCTCCTCATCAGGGGCACAGCGTGCACTGTGGGGTCCCAGGCCTCCCGAGCCGAGCCACCCGTCACCCCCTGGCTCCTGGCCTATGTGCTGTACCTGTGT   FFFFFFFFFFFFFFFFFFFFFFFFFF,,,::,,,,F,,,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF   NH:i:1  HI:i:1  nM:i:3  AS:i:128        CR:Z:CCCTCCTCATCAGGGG       UR:Z:CACAGCGTGC GX:Z:ENSG00000310526.1  GN:Z:WASH7P     sS:Z:CCCTCCTCATCAGGGGCACAGCGTGCACTGTGGGGTCCCAGGCCTCCCGAGCCGAGCCACCCGTCACCCCCTGGCTCCTGGCCTATGTGCTGTACCTGTGT      sQ:Z:FFFFFFFFFFFFFFFFFFFFFFFFFF,,,::,,,,F,,,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF      sM:i:-1 CB:Z:-  UB:Z:-
A00708:13:HTC7MDSXX:4:2253:19913:14904  99      chr1    17470   255     39S62M  =       17656   459     CCCTCCTCATCAGGGGCACAGCGTGCACTGTGGGGTCCCAGGCCTCCCGAGCCGAGCCACCCGTCACCCCCTGGCTCCTGGCCTATGTGCTGTACCTGTGT   FFFFFFFFFFFFFFFFFFFFFFFFFF,,FF,,,,,:,,,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF   NH:i:1  HI:i:1  nM:i:0  AS:i:163        CR:Z:CCCTCCTCATCAGGGG       UR:Z:CACAGCGTGC GX:Z:ENSG00000310526.1  GN:Z:WASH7P     sS:Z:CCCTCCTCATCAGGGGCACAGCGTGCACTGTGGGGTCCCAGGCCTCCCGAGCCGAGCCACCCGTCACCCCCTGGCTCCTGGCCTATGTGCTGTACCTGTGT      sQ:Z:FFFFFFFFFFFFFFFFFFFFFFFFFF,,FF,,,,,:,,,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF      sM:i:-1 CB:Z:-  UB:Z:-