Automatic adapter detection detects ~1000x fewer adapter trimmed reads compared to specifying TruSeq adapters manually

[pmoris]

I encountered a few oddly behaving samples where automatic adapter detection seems to miss the majority of adapters.

Automatic detection finds ~173,660 adapter trimmed reads and retains 41M reads after filtering, whereas providing the TruSeq adapters via --adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter_sequence_r2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT results in ~66M adapter trimmed reads and only 701,128 reads remain after filtering.

	"command": "fastp --in1 bb_sample_1.hostremoval.fq.gz --in2 bb_sample_2.hostremoval.fq.gz --out1 ./out_bb_sample_1.auto.fq.gz --out2 ./out_bb_sample_2.auto.fq.gz --trim_poly_x --trim_poly_g --thread 2 --json out_bb_sample.auto.json --verbose "

	"summary": {
		"fastp_version": "0.24.0",
		"sequencing": "paired end (150 cycles + 150 cycles)",
		"before_filtering": {
			"total_reads":133570850,
			"total_bases":20035627500,
			"q20_bases":19432311088,
			"q30_bases":18848090065,
			"q20_rate":0.969888,
			"q30_rate":0.940729,
			"read1_mean_length":150,
			"read2_mean_length":150,
			"gc_content":0.869149
		},
		"after_filtering": {
			"total_reads":41267932,
			"total_bases":2978659410,
			"q20_bases":2655644424,
			"q30_bases":2457715637,
			"q20_rate":0.891557,
			"q30_rate":0.825108,
			"read1_mean_length":64,
			"read2_mean_length":79,
			"gc_content":0.67889
		}
	},
	"filtering_result": {
		"passed_filter_reads": 41267932,
		"low_quality_reads": 363662,
		"too_many_N_reads": 388,
		"too_short_reads": 91938868,
		"too_long_reads": 0
	},
	"duplication": {
		"rate": 0.783437
	},
	"insert_size": {
		"peak": 0,
		"unknown": 10500167,
		"histogram": [22827736,69,69,3,11,0,0,0,0,0,41,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,16,9,2,0,0,5,8,5,2,2,8,6,11,1,5,3,41,82,5,45,7,7,1,15,14,19,34,60,32,60,85,1149,262,242,1028,39190,803,22,10,8,21,73,6,12,12,15,15,11,17,22,15,9,24,12,15,16,28,21,14,14,20,23,36,26,48,22,21,56,26,49,49,110,35,39,73,68,1077,38,27,43,41,106,266,1491,183,44,21,38,30,35,45,269,39,69,125,53,196,276,1450,113,205,116,1410,313,108,798,1073,1982,1707,1009,115,44,34,28,38,33,40,39,43,455,29,41,46,42,29,40,45,36,30,43,54,45,29,53,37,39,41,45,31,42,48,35,28,51,36,34,43,33,70,53,34,31,47,32,31,35,51,47,36,25,45,47,34,46,38,48,33,24,46,51,27,40,35,42,43,50,40,34,51,24,41,40,44,37,63,45,45,54,31,25,38,34,42,41,27,38,42,50,47,35,41,24,31,36,22,35,49,31,39,28,44,42,33,29,37,40,37,38,37,33,36,42,38,36,40,31,36,54,49,40,47,33,44,38,26,49,27,36,25,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]
	},
	"adapter_cutting": {
		"adapter_trimmed_reads": 173660,
		"adapter_trimmed_bases": 7099869,
		"read1_adapter_sequence": "unspecified",
		"read2_adapter_sequence": "unspecified",
		"read1_adapter_counts": {"AGATCGGAAGAGCACACGTCTGAACTCCAGTCACTTGGAATGGTATCT":948, "others":85564},
		"read2_adapter_counts": {"C":2675, "CGATC":1737, "CGCTC":1525, "CGGTC":2003, "CGGTCT":1019, "CGATCGGAA":2310, "CGCTCGGAA":1392, "CGGTCGGAA":1278, "others":72891}
	},
	"polyx_trimming": 	{
		"total_polyx_trimmed_reads": 1131079,
		"polyx_trimmed_reads":{"A": 234071, "T": 83902, "C": 129582, "G": 683524},
		"total_polyx_trimmed_bases": 31474811,
		"polyx_trimmed_bases":{"A": 2042823, "T": 1077599, "C": 1666300, "G": 26688089}
	},

vs

	"command": "fastp --in1 bb_sample_1.hostremoval.fq.gz --in2 bb_sample_2.hostremoval.fq.gz --out1 ./out_bb_sample_1.adapter.fq.gz --out2 ./out_bb_sample_2.adapter.fq.gz --trim_poly_x --trim_poly_g --adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter_sequence_r2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --thread 2 --json out_bb_sample.adapter.json --verbose "

	"summary": {
		"fastp_version": "0.24.0",
		"sequencing": "paired end (150 cycles + 150 cycles)",
		"before_filtering": {
			"total_reads":133570850,
			"total_bases":20035627500,
			"q20_bases":19432311088,
			"q30_bases":18848090065,
			"q20_rate":0.969888,
			"q30_rate":0.940729,
			"read1_mean_length":150,
			"read2_mean_length":150,
			"gc_content":0.869149
		},
		"after_filtering": {
			"total_reads":701128,
			"total_bases":54433681,
			"q20_bases":47954426,
			"q30_bases":41785382,
			"q20_rate":0.88097,
			"q30_rate":0.767638,
			"read1_mean_length":69,
			"read2_mean_length":85,
			"gc_content":0.63706
		}
	},
	"filtering_result": {
		"passed_filter_reads": 701128,
		"low_quality_reads": 329342,
		"too_many_N_reads": 8,
		"too_short_reads": 132540372,
		"too_long_reads": 0
	},
	"duplication": {
		"rate": 0.783437
	},
	"insert_size": {
		"peak": 0,
		"unknown": 10500167,
		"histogram": [22827736,69,69,3,11,0,0,0,0,0,41,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,16,9,2,0,0,5,8,5,2,2,8,6,11,1,5,3,41,82,5,45,7,7,1,15,14,19,34,60,32,60,85,1149,262,242,1028,39190,803,22,10,8,21,73,6,12,12,15,15,11,17,22,15,9,24,12,15,16,28,21,14,14,20,23,36,26,48,22,21,56,26,49,49,110,35,39,73,68,1077,38,27,43,41,106,266,1491,183,44,21,38,30,35,45,269,39,69,125,53,196,276,1450,113,205,116,1410,313,108,798,1073,1982,1707,1009,115,44,34,28,38,33,40,39,43,455,29,41,46,42,29,40,45,36,30,43,54,45,29,53,37,39,41,45,31,42,48,35,28,51,36,34,43,33,70,53,34,31,47,32,31,35,51,47,36,25,45,47,34,46,38,48,33,24,46,51,27,40,35,42,43,50,40,34,51,24,41,40,44,37,63,45,45,54,31,25,38,34,42,41,27,38,42,50,47,35,41,24,31,36,22,35,49,31,39,28,44,42,33,29,37,40,37,38,37,33,36,42,38,36,40,31,36,54,49,40,47,33,44,38,26,49,27,36,25,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]
	},
	"adapter_cutting": {
		"adapter_trimmed_reads": 66049042,
		"adapter_trimmed_bases": 2115760613,
		"read1_adapter_sequence": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCA",
		"read2_adapter_sequence": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT",
		"read1_adapter_counts": {"AGATCGGAAGAGCACACGTCTGAACTCCAGTC":65820410, "others":136992},
		"read2_adapter_counts": {"C":2675, "CGATC":1737, "CGCTC":1525, "CGGTC":2003, "CGGTCT":1019, "CGATCGGAA":2581, "CGCTCGGAA":1392, "CGGTCGGAA":1278, "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTG":1120, "others":75992}
	},
	"polyx_trimming": 	{
		"total_polyx_trimmed_reads": 776022,
		"polyx_trimmed_reads":{"A": 233968, "T": 71893, "C": 129568, "G": 340593},
		"total_polyx_trimmed_bases": 26910713,
		"polyx_trimmed_bases":{"A": 2041943, "T": 962832, "C": 1666061, "G": 22239877}
	},

I have no idea what to make of this, so any help would be much appreciated!