Remaining adapter sequence

[cdermita]

Describe the bug
hts_AdapterTrimmer and hts_PolyATTrim did not remove adapters in some reads that have incomplete, degeneracy or extra sequence in the adapter sequence of the 3' end of the reads

To Reproduce
Example sequence reads that will help reproduce the bug:
@A01488:145:HHFCKDSX5:4:1101:19895:1000_TATA_NTGGCT 1:N:0:TAACCAGCACTT+NATGTCGTTGGA
GAGTTTGTGATTTAAACATTTTGTTGTTAATAATATTGATATTGTATTTTCTTGAATGTGGAACTTTCTTTTTTATGCTTACGTACCAAAAAAAAAAAAAAAAAAAACGGAATAGCAAACGTCTTAAAACCAGTCAAAAA

@A01488:145:HHFCKDSX5:4:1101:25247:1000_TATA_NTGGGG 1:N:0:TAACCAGCACTT+NATGTCGTTGGA
TTGAGATGGGTGTTCCAAGAGTCGAATAGCTTGGGAATGCTGTTCTAAATGGGTGGTAAATTTCATCTAAAGCTAAATATCGACGAGAGACCGATAGCGAACAAGTACCGTGAGGGAAAAAAAAAAAAAAAAAAAGATCG

@A01488:145:HHFCKDSX5:4:1101:7139:1016_TATA_TGAGTT 1:N:0:TAACCAGCACTT+AATGTCGTTGGA
TTGCTTTCATCATCCCTTTTACAGGGTGAAATTAATTGTTACTTTCAACAGATGCTTCTGATTAAAAAAAAAAAAAAAAAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTAACCAGCACTTATCTCGTTTGCCGGG

Commands to reproduce the behavior:
module load miniconda
source activate process_reads

for x in ${umi_folder[@]}; do
y=${x##/}
echo Working on $y
hts_Stats -F -L ${log_folder}${y}.log -U ${x} | #read stats
hts_SeqScreener -AL ${log_folder}${y}.log | #remove contaminants
hts_AdapterTrimmer -AL ${log_folder}${y}.log | #trim adaptors
hts_PolyATTrim -AL ${log_folder}${y}.log |
hts_QWindowTrim -AL ${log_folder}${y}.log | #remove low-quality
hts_NTrimmer -AL ${log_folder}${y}.log | #remove Ns
hts_Stats -AL ${log_folder}${y}.log -f ${clean_folder}${y} #read stats and save cleaned
done

conda deactivate
module unload miniconda

Expected behavior
Since the Lexogen 3' end which consists of 5' – A{18}AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC – 3' (adepter sequence same as default TruSeq), we expect that the sequence of PolyA tail and adapetr sequence will be trimmed.

Screenshots

Desktop (please complete the following information):

• OS: macOS Catalina 10.15.7 but terminal is connected to HPC

Additional context
Add any other context about the problem here.