Starting /dee2/code/volunteer_pipeline.sh SRR30542860
    current disk space = 1230655164
    free memory = 196222276 
SRR30542860 SRAfilesize
70591bdf6f54d9876652cbd928e73ba4  SRR30542860.sra
SRR30542860.sra file validated
SRR30542860 is single end
SRR30542860 is conventional basespace
SRR30542860 read1 length is 36 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR30542860_1.fastq
File type	Conventional base calls
Encoding	Sanger / Illumina 1.9
Total Sequences	4000
Sequences flagged as poor quality	0
Sequence length	36
%GC	51
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	33.223	32.0	32.0	37.0	32.0	37.0
2	34.58775	37.0	32.0	37.0	32.0	37.0
3	36.036	37.0	37.0	37.0	32.0	37.0
4	36.30725	37.0	37.0	37.0	32.0	37.0
5	36.50775	37.0	37.0	37.0	37.0	37.0
6	36.52025	37.0	37.0	37.0	37.0	37.0
7	36.5025	37.0	37.0	37.0	37.0	37.0
8	36.61175	37.0	37.0	37.0	37.0	37.0
9	36.6035	37.0	37.0	37.0	37.0	37.0
10	36.553	37.0	37.0	37.0	37.0	37.0
11	36.6335	37.0	37.0	37.0	37.0	37.0
12	36.534	37.0	37.0	37.0	37.0	37.0
13	36.505	37.0	37.0	37.0	37.0	37.0
14	36.55925	37.0	37.0	37.0	37.0	37.0
15	36.63475	37.0	37.0	37.0	37.0	37.0
16	36.607	37.0	37.0	37.0	37.0	37.0
17	36.55	37.0	37.0	37.0	37.0	37.0
18	36.6215	37.0	37.0	37.0	37.0	37.0
19	36.681	37.0	37.0	37.0	37.0	37.0
20	36.50425	37.0	37.0	37.0	37.0	37.0
21	36.594	37.0	37.0	37.0	37.0	37.0
22	36.614	37.0	37.0	37.0	37.0	37.0
23	36.534	37.0	37.0	37.0	37.0	37.0
24	36.5365	37.0	37.0	37.0	37.0	37.0
25	36.5385	37.0	37.0	37.0	37.0	37.0
26	36.547	37.0	37.0	37.0	37.0	37.0
27	36.5945	37.0	37.0	37.0	37.0	37.0
28	36.57325	37.0	37.0	37.0	37.0	37.0
29	36.527	37.0	37.0	37.0	37.0	37.0
30	36.57475	37.0	37.0	37.0	37.0	37.0
31	36.498	37.0	37.0	37.0	37.0	37.0
32	36.527	37.0	37.0	37.0	37.0	37.0
33	36.51875	37.0	37.0	37.0	37.0	37.0
34	36.44875	37.0	37.0	37.0	37.0	37.0
35	36.482	37.0	37.0	37.0	37.0	37.0
36	36.383	37.0	37.0	37.0	37.0	37.0
>>END_MODULE
>>Per tile sequence quality	pass
#Tile	Base	Mean
11101	1	0.0
11101	2	0.0
11101	3	0.0
11101	4	0.0
11101	5	0.0
11101	6	0.0
11101	7	0.0
11101	8	0.0
11101	9	0.0
11101	10	0.0
11101	11	0.0
11101	12	0.0
11101	13	0.0
11101	14	0.0
11101	15	0.0
11101	16	0.0
11101	17	0.0
11101	18	0.0
11101	19	0.0
11101	20	0.0
11101	21	0.0
11101	22	0.0
11101	23	0.0
11101	24	0.0
11101	25	0.0
11101	26	0.0
11101	27	0.0
11101	28	0.0
11101	29	0.0
11101	30	0.0
11101	31	0.0
11101	32	0.0
11101	33	0.0
11101	34	0.0
11101	35	0.0
11101	36	0.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
20	1.0
21	0.0
22	1.0
23	5.0
24	3.0
25	8.0
26	11.0
27	6.0
28	11.0
29	14.0
30	27.0
31	26.0
32	35.0
33	48.0
34	65.0
35	155.0
36	2844.0
37	740.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	24.075	20.7	26.450000000000003	28.775000000000002
2	57.325	14.649999999999999	14.899999999999999	13.125
3	16.45	31.825	12.625	39.1
4	42.35	12.775	28.175	16.7
5	31.474999999999998	30.4	16.475	21.65
6	31.05	10.525	25.7	32.725
7	31.974999999999998	22.325	21.025	24.675
8	25.3	21.25	39.375	14.075
9	19.075	25.825	22.6	32.5
10	36.85921480370092	39.509877469367346	11.552888222055515	12.07801950487622
11	45.800000000000004	23.0	15.9	15.299999999999999
12	32.25	35.449999999999996	16.175	16.125
13	20.925	14.05	43.025000000000006	22.0
14	22.2	26.025	25.4	26.375
15	38.224999999999994	28.7	16.275000000000002	16.8
16	30.349999999999998	28.875	30.2	10.575
17	31.275	35.6	16.925	16.2
18	29.4	14.725	27.700000000000003	28.175
19	38.65	19.375	28.825	13.15
20	28.199999999999996	20.525	33.85	17.424999999999997
21	37.1	20.5	31.225	11.175
22	35.45886471617904	23.355838959739934	28.182045511377847	13.003250812703177
23	18.625	39.375	16.650000000000002	25.35
24	38.85	36.95	12.4	11.799999999999999
25	23.925	38.75	18.8	18.525
26	18.475	20.025000000000002	28.875	32.625
27	20.175	16.6	20.424999999999997	42.8
28	32.175	19.650000000000002	8.475000000000001	39.7
29	47.075	32.725	6.175	14.025000000000002
30	33.625	37.55	8.9	19.925
31	21.146146146146148	38.93893893893894	26.05105105105105	13.863863863863864
32	40.5	32.525	9.175	17.8
33	26.424999999999997	48.9	7.6499999999999995	17.025000000000002
34	29.65	37.45	8.225	24.675
35	19.900000000000002	24.325	27.950000000000003	27.825
36	17.37934483620905	39.38484621155289	16.27906976744186	26.9567391847962
>>END_MODULE
>>Per sequence GC content	fail
#GC Content	Count
0	0.0
1	0.0
2	0.0
3	0.0
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.0
10	0.0
11	0.0
12	0.0
13	0.5
14	1.0
15	1.5
16	2.0
17	2.0
18	4.0
19	6.0
20	6.0
21	6.0
22	6.0
23	6.0
24	4.0
25	2.0
26	5.0
27	8.0
28	8.0
29	6.5
30	5.0
31	5.0
32	8.5
33	12.0
34	12.0
35	15.0
36	18.0
37	18.0
38	55.0
39	92.0
40	120.5
41	149.0
42	149.0
43	346.0
44	543.0
45	543.0
46	547.0
47	551.0
48	551.0
49	624.5
50	698.0
51	530.0
52	362.0
53	362.0
54	412.0
55	462.0
56	462.0
57	419.0
58	376.0
59	376.0
60	414.0
61	452.0
62	452.0
63	315.5
64	179.0
65	111.0
66	43.0
67	43.0
68	31.5
69	20.0
70	20.0
71	15.0
72	10.0
73	10.0
74	6.0
75	2.0
76	1.5
77	1.0
78	1.0
79	0.5
80	0.0
81	0.0
82	0.0
83	0.0
84	0.0
85	0.0
86	0.0
87	0.0
88	0.0
89	0.0
90	0.0
91	0.0
92	0.0
93	0.0
94	0.0
95	0.0
96	0.0
97	0.0
98	0.0
99	0.0
100	0.0
>>END_MODULE
>>Per base N content	pass
#Base	N-Count
1	0.0
2	0.0
3	0.0
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.0
10	0.025
11	0.0
12	0.0
13	0.0
14	0.0
15	0.0
16	0.0
17	0.0
18	0.0
19	0.0
20	0.0
21	0.0
22	0.025
23	0.0
24	0.0
25	0.0
26	0.0
27	0.0
28	0.0
29	0.0
30	0.0
31	0.1
32	0.0
33	0.0
34	0.0
35	0.0
36	0.025
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
36	4000.0
>>END_MODULE
>>Sequence Duplication Levels	fail
#Total Deduplicated Percentage	48.875
#Duplication Level	Percentage of deduplicated	Percentage of total
1	85.9846547314578	42.025
2	6.240409207161125	6.1
3	2.3017902813299234	3.375
4	1.329923273657289	2.6
5	0.5115089514066496	1.25
6	0.40920716112531963	1.2
7	0.40920716112531963	1.4000000000000001
8	0.35805626598465473	1.4000000000000001
9	0.2557544757033248	1.125
>10	1.8414322250639386	16.925
>50	0.2557544757033248	9.55
>100	0.10230179028132991	13.05
>500	0.0	0.0
>1k	0.0	0.0
>5k	0.0	0.0
>10k+	0.0	0.0
>>END_MODULE
>>Overrepresented sequences	fail
#Sequence	Count	Percentage	Possible Source
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATT	265	6.625	No Hit
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACTA	257	6.425	TruSeq Adapter, Index 7 (97% over 35bp)
GTTTCCGTAGTGTAGTGGTTATCAGATCGGAAGAGC	97	2.4250000000000003	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTAGAT	81	2.025	No Hit
TGAGGTAGTAGGTTGTATGGTTAGATCGGAAGAGCA	74	1.8499999999999999	No Hit
CGCGACCTCAGATCAGACGTAGATCGGAAGAGCACA	65	1.625	No Hit
TGAGGTAGTAGTTTGTGCTGTTAGATCGGAAGAGCA	65	1.625	No Hit
GGAAGAGCACACGTCTGAACTCCAGTCACTAGCTTA	46	1.15	TruSeq Adapter, Index 10 (100% over 36bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATAGATC	41	1.0250000000000001	No Hit
TGAGGTAGTAGATTGTATAGTTAGATCGGAAGAGCA	37	0.9249999999999999	No Hit
GGGGATGTAGCTCAGTGGTAGATCGGAAGAGCACAC	29	0.7250000000000001	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATA	29	0.7250000000000001	No Hit
CGCGACCTCAGATCAGATCGGAAGAGCACACGTCTG	28	0.7000000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
TAGCTTATCAGACTGATGTTGACAGATCGGAAGAGC	27	0.675	No Hit
GTCTACGGCCATACCACCCTGAACGCGCCCGATCTC	27	0.675	No Hit
CGCGACCTCAGATCGGAAGAGCACACGTCTGAACTC	26	0.65	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
GTTTCCGTAGTGTAGTGGTTATTAGATCGGAAGAGC	23	0.575	No Hit
TTCAAGTAATCCAGGATAGGCTAGATCGGAAGAGCA	21	0.525	No Hit
AACCCGTAGATCCGATCTTGTAGATCGGAAGAGCAC	19	0.475	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAAAG	19	0.475	No Hit
TGAGGTAGTAGGTTGTATAGTTAGATCGGAAGAGCA	18	0.44999999999999996	No Hit
TGAGGTAGTAGGTTGTGTGGTTAGATCGGAAGAGCA	18	0.44999999999999996	No Hit
CGCGACCTCAGATCAGACGTGGCAGATCGGAAGAGC	17	0.42500000000000004	No Hit
TGAGGTAGTAGGTTGTATGGTCAGATCGGAAGAGCA	17	0.42500000000000004	No Hit
CGCGACCTCAGATCAGACGTGGTAGATCGGAAGAGC	16	0.4	No Hit
GTTTCCGTAGTGTAGTGGTTATAAGATCGGAAGAGC	16	0.4	No Hit
TAGCTTATCAGACTGATGTTGATAGATCGGAAGAGC	15	0.375	No Hit
CGACTCTTAGCGGTGGATCACTCGGCTCGTGAGATC	15	0.375	No Hit
TGAGGTAGTAGATTGTATAGTCAGATCGGAAGAGCA	14	0.35000000000000003	No Hit
CGCGACCTCAGATCAGACGCAGATCGGAAGAGCACA	14	0.35000000000000003	No Hit
CGCGACCTTAGATCGGAAGAGCACACGTCTGAACTC	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
CCGCGACCTCAGATCAGACGTGGCGACCCGCTGAAT	13	0.325	No Hit
TAGCTTATCAGACTGATGTTGACTAGATCGGAAGAG	13	0.325	No Hit
GACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGA	12	0.3	No Hit
TCGATGTGGTGCTGCCGCGTTCTCTTCGGGCCGGGG	11	0.27499999999999997	No Hit
TGAGGTAGTAGTTTGTGCTGTCAGATCGGAAGAGCA	11	0.27499999999999997	No Hit
TACCTGGTTGATCCTGCCAGATCGGAAGAGCACACG	11	0.27499999999999997	No Hit
TGGAATGTAAGGAAGTGTGTGGAGATCGGAAGAGCA	11	0.27499999999999997	No Hit
CGCGACCTCAGATTAGATCGGAAGAGCACACGTCTG	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAAGATCGG	10	0.25	No Hit
TGAGATGAAGCACTGTAGCTCAGATCGGAAGAGCAC	10	0.25	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAACA	10	0.25	No Hit
ACAGTAGTCTGCACATTGGTTAGATCGGAAGAGCAC	10	0.25	No Hit
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACA	9	0.22499999999999998	No Hit
TGAGGTAGTAGGTTGTGTGGTCAGATCGGAAGAGCA	9	0.22499999999999998	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATCAGAT	9	0.22499999999999998	No Hit
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTAGA	9	0.22499999999999998	No Hit
AGAGGTAGTAGGTTGCATAGTTAGATCGGAAGAGCA	9	0.22499999999999998	No Hit
TGAGATGAAGCACTGTAGCTTAGATCGGAAGAGCAC	8	0.2	No Hit
GTAGTCGTGGCCGAGTAGATCGGAAGAGCACACGTC	8	0.2	No Hit
GACTCTTAGCGGTGGATCACTCGGCTCGTGAGATCG	8	0.2	No Hit
TTCACAGTGGCTAAGTTCTGCAGATCGGAAGAGCAC	8	0.2	No Hit
GATCGGAAGAGCACACGTCTGAACTCCAGTCACTAG	8	0.2	TruSeq Adapter, Index 7 (97% over 36bp)
TGAGGTAGTAGTTTGTGCTGTAAGATCGGAAGAGCA	8	0.2	No Hit
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTCTC	8	0.2	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCA	7	0.17500000000000002	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATC	7	0.17500000000000002	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTAGATC	7	0.17500000000000002	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGATT	7	0.17500000000000002	No Hit
CGACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCG	7	0.17500000000000002	No Hit
CGCGACCTCAGATCAGAAGATCGGAAGAGCACACGT	7	0.17500000000000002	No Hit
CGCGACCTCAGATCAGACGAGATCGGAAGAGCACAC	7	0.17500000000000002	No Hit
TGGCTCAGTTCAGCAGGAACAGATCGGAAGAGCACA	7	0.17500000000000002	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAAAGATCG	6	0.15	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATAAGAT	6	0.15	No Hit
TGAGGTAGTAGTTTGTACAGTTAGATCGGAAGAGCA	6	0.15	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAACAGATC	6	0.15	No Hit
AACCCGTAGATCCGATCTTGCAGATCGGAAGAGCAC	6	0.15	No Hit
TGAGGTAGTAGGTTGTATAGTCAGATCGGAAGAGCA	6	0.15	No Hit
TGAGGTAGTAGATTGTATAGTAGATCGGAAGAGCAC	6	0.15	No Hit
ACTGGACTTGGAGTCAGAAGGCAGATCGGAAGAGCA	6	0.15	No Hit
CGCGACCTCAGATCAGGCGTGGCGACCCGCTGAATT	5	0.125	No Hit
TGAGATGAAGCACTGTAGCTAAGATCGGAAGAGCAC	5	0.125	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCTAGATC	5	0.125	No Hit
CCCAGTGTTCAGACTACCTGTTCAGATCGGAAGAGC	5	0.125	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAAGA	5	0.125	No Hit
CGCGACCTCAGATCAGACGAAGATCGGAAGAGCACA	5	0.125	No Hit
TCCCTGTGGTCTAGTGGTTAGGATTCGGCGCTCTCA	5	0.125	No Hit
TGAGGTAGTAGGTTGTATGGTAAGATCGGAAGAGCA	5	0.125	No Hit
TGAAATGATGGCAATCATCTTTCGGGACTGACCTGA	5	0.125	No Hit
GGTAGCGTGGCCGAGCAGATCGGAAGAGCACACGTC	5	0.125	No Hit
>>END_MODULE
>>Adapter Content	fail
#Position	Illumina Universal Adapter	Illumina Small RNA 3' Adapter	Illumina Small RNA 5' Adapter	Nextera Transposase Sequence	SOLID Small RNA Adapter
1	6.9	0.0	0.0	0.0	0.0
2	6.975	0.0	0.0	0.0	0.0
3	7.0	0.0	0.0	0.0	0.0
4	7.0	0.0	0.0	0.0	0.0
5	7.075	0.0	0.0	0.0	0.0
6	7.1	0.0	0.0	0.0	0.0
7	7.1	0.0	0.0	0.0	0.0
8	7.1	0.0	0.0	0.0	0.0
9	7.15	0.0	0.0	0.0	0.0
10	8.4	0.0	0.0	0.0	0.0
11	8.625	0.0	0.0	0.0	0.0
12	8.825	0.0	0.0	0.0	0.0
13	9.15	0.0	0.0	0.0	0.0
14	9.825	0.0	0.0	0.0	0.0
15	11.625	0.0	0.0	0.0	0.0
16	12.375	0.0	0.0	0.0	0.0
17	14.125	0.0	0.0	0.0	0.0
18	15.55	0.0	0.0	0.0	0.0
19	18.0	0.0	0.0	0.0	0.0
20	20.525	0.0	0.0	0.0	0.0
21	25.15	0.0	0.0	0.0	0.0
22	30.45	0.0	0.0	0.0	0.0
23	44.325	0.0	0.0	0.0	0.0
24	53.05	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
GAGGTAG	45	1.1683369E-8	30.000002	2
GTATGGT	30	2.707939E-5	30.000002	15
TGGTTAG	30	2.707939E-5	30.000002	18
TAGTGGT	30	2.707939E-5	30.000002	13
TTGTATG	30	2.707939E-5	30.000002	13
AGTGGTT	30	2.707939E-5	30.000002	14
TGAGGTA	45	1.1683369E-8	30.000002	1
CAGATCA	30	2.707939E-5	30.000002	9
TGTATGG	30	2.707939E-5	30.000002	14
AGATCAG	30	2.707939E-5	30.000002	10
GGTTGTA	35	2.0637017E-6	30.0	11
TGGTTAT	25	3.5274107E-4	30.0	16
TAGTGTA	25	3.5274107E-4	30.0	8
CAGTCAC	25	3.5274107E-4	30.0	28
AGTAGGT	35	2.0637017E-6	30.0	7
CCAGTCA	25	3.5274107E-4	30.0	27
GTGTAGT	25	3.5274107E-4	30.0	10
ATGGTTA	25	3.5274107E-4	30.0	17
CTCCAGT	25	3.5274107E-4	30.0	25
TCCAGTC	25	3.5274107E-4	30.0	26
>>END_MODULE
Read 41680 spots for SRR30542860.sra
Written 41680 spots for SRR30542860.sra
Read 41676 spots for SRR30542860.sra
Written 41676 spots for SRR30542860.sra
Read 41676 spots for SRR30542860.sra
Written 41676 spots for SRR30542860.sra
Read 41676 spots for SRR30542860.sra
Written 41676 spots for SRR30542860.sra
Read 41676 spots for SRR30542860.sra
Written 41676 spots for SRR30542860.sra
Read 41676 spots for SRR30542860.sra
Written 41676 spots for SRR30542860.sra
Read 41676 spots for SRR30542860.sra
Written 41676 spots for SRR30542860.sra
Read 41676 spots for SRR30542860.sra
Written 41676 spots for SRR30542860.sra
SRR ids: ['SRR30542860.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_trxp92pv
SRR30542860.sra spots: 333412
blocks: [[1, 41676], [41677, 83352], [83353, 125028], [125029, 166704], [166705, 208380], [208381, 250056], [250057, 291732], [291733, 333412]]
SRR30542860 file size 47496
SRR30542860 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	/usr/local/bin/skewer -f sanger -l 18 -q 10 -k inf -t 8 -o SRR30542860 SRR30542860_1.fastq
Input file:	SRR30542860_1.fastq
trimmed:	SRR30542860-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
-- maximum error ratio allowed (-r):	0.100
-- maximum indel error ratio allowed (-d):	0.030
-- end quality threshold (-q):		10
-- minimum read length allowed after trimming (-l):	18
-- file format (-f):		Sanger/Illumina 1.8+ FASTQ 
-- minimum overlap length for adapter detection (-k):	inf
-- number of concurrent threads (-t):	8
Thu Nov  6 06:57:46 2025 >> started

Thu Nov  6 06:57:46 2025 >> done (0.119s)
333412 reads processed; of these:
   550 ( 0.16%) short reads filtered out after trimming by size control
 25382 ( 7.61%) empty reads filtered out after trimming by size control
307480 (92.22%) reads available; of these:
    33 ( 0.01%) trimmed reads available after processing
307447 (99.99%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 35	    33	  0.01%
 36	307447	 99.99%
307480 reads passed initial QC


criterion=sequence-density
sequence-density=50.59
sequence-density-rank=1
fanout-score=27.23
fanout-score-rank=1
prefix-density=57.59
prefix-fanout=23.9
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACTAGCTTAT


criterion=fanout-score
sequence-density=50.59
sequence-density-rank=1
fanout-score=27.23
fanout-score-rank=1
prefix-density=57.59
prefix-fanout=23.9
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACTAGCTTAT
Potential 3prime adapter identified. Now checking if in reference sequence
Warning: gzbuffer added in zlib v1.2.3.5. Unable to change buffer size from default of 8192.
1 reads; of these:
  1 (100.00%) were unpaired; of these:
    1 (100.00%) aligned 0 times
    0 (0.00%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
0.00% overall alignment rate
Adapter seq not found in reference. Now shuffling file before clipping
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	/usr/local/bin/skewer -f sanger -l 18 -t 8 -x AGATCGGAAGAGCACACGTCTGAACTCCAGTCACTAGCTTAT -o SRR30542860 -
Input file:	STDIN
trimmed:	SRR30542860-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	AGATCGGAAGAGCACACGTCTGAACTCCAGTCACTAGCTTAT
-- maximum error ratio allowed (-r):	0.100
-- maximum indel error ratio allowed (-d):	0.030
-- minimum read length allowed after trimming (-l):	18
-- file format (-f):		Sanger/Illumina 1.8+ FASTQ 
-- minimum overlap length for adapter detection (-k):	3
-- number of concurrent threads (-t):	8
Thu Nov  6 06:57:47 2025 >> started

Thu Nov  6 06:57:47 2025 >> done (0.101s)
295422 reads processed; of these:
 30900 (10.46%) short reads filtered out after trimming by size control
   490 ( 0.17%) empty reads filtered out after trimming by size control
264032 (89.37%) reads available; of these:
190507 (72.15%) trimmed reads available after processing
 73525 (27.85%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  7007	  2.65%
 19	  7983	  3.02%
 20	 13878	  5.26%
 21	 17174	  6.50%
 22	 45638	 17.29%
 23	 28185	 10.67%
 24	  8610	  3.26%
 25	  5351	  2.03%
 26	  4470	  1.69%
 27	  5232	  1.98%
 28	  6044	  2.29%
 29	  5068	  1.92%
 30	  5825	  2.21%
 31	 11010	  4.17%
 32	 14014	  5.31%
 33	  5018	  1.90%
 34	     0	  0.00%
 35	    10	  0.00%
 36	 73515	 27.84%


criterion=sequence-density
sequence-density=5.94
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=11
prefix-density=0.00
prefix-fanout=1.0
sequence=TGAGGTAGTAGGTTGTATGGTTAGATCGGA


criterion=fanout-score
sequence-density=2.54
sequence-density-rank=5
fanout-score=17.17
fanout-score-rank=1
prefix-density=2.89
prefix-fanout=15.1
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACTAGCTTAT
                                 Started job on |	Nov 06 06:57:54
                             Started mapping on |	Nov 06 06:57:54
                                    Finished on |	Nov 06 06:58:01
       Mapping speed, Million of reads per hour |	141.99

                          Number of input reads |	276090
                      Average input read length |	27
                                    UNIQUE READS:
                   Uniquely mapped reads number |	76081
                        Uniquely mapped reads % |	27.56%
                          Average mapped length |	24.30
                       Number of splices: Total |	585
            Number of splices: Annotated (sjdb) |	115
                       Number of splices: GT/AG |	532
                       Number of splices: GC/AG |	15
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	38
                      Mismatch rate per base, % |	0.45%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.28
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.00
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	101239
             % of reads mapped to multiple loci |	36.67%
        Number of reads mapped to too many loci |	67819
             % of reads mapped to too many loci |	24.56%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	9.91%
                     % of reads unmapped: other |	1.30%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	98770	98770	98770
N_multimapping	101239	101239	101239
N_noFeature	22524	26427	72063
N_ambiguous	1480	1364	1
UnstrandedReadsAssigned:52077 PositiveStrandReadsAssigned:48290 NegativeStrandReadsAssigned:4017
Dataset is classified positive stranded
MeadianReadLen=26 20thPercentileLength=22 echo kmer=19
SRR30542860 Starting Kallisto single end mapping to ensembl reference transcriptome. kmer=19

[quant] fragment length distribution is truncated gaussian with mean = 100, sd = 20
[index] k-mer length: 19
[index] number of targets: 31,715
[index] number of k-mers: 49,362,984
[index] number of equivalence classes: 166,181
[quant] running in single-end mode
[quant] will process file 1: SRR30542860-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 276,090 reads, 7,870 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 581 rounds

  31716 SRR30542860.ke.tsv
  32883 SRR30542860.se.tsv
  64599 total
==> SRR30542860.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
ENSRNOT00000047550.4	955	856	10	1086.14
ENSRNOT00000040993.4	1039	940	19	1879.25
ENSRNOT00000050156.3	1545	1446	71	4565.08
ENSRNOT00000043693.3	684	585	13	2066.08
ENSRNOT00000046201.3	204	105	8	7083.69
ENSRNOT00000046108.3	681	582	9	1437.73
ENSRNOT00000049683.3	784	685	5	678.638
ENSRNOT00000041241.3	348	249	2	746.774
ENSRNOT00000044582.3	297	198	9	4226.06

==> SRR30542860.se.tsv <==
ENSRNOG00000046319	0
ENSRNOG00000047964	0
ENSRNOG00000050370	0
ENSRNOG00000032365	0
ENSRNOG00000040300	0
ENSRNOG00000058808	0
ENSRNOG00000061316	1
ENSRNOG00000050129	0
ENSRNOG00000040316	0
ENSRNOG00000023659	0
SRR30542860 completed mapping pipeline successfully
