Starting /dee2/code/volunteer_pipeline.sh SRR30542858
    current disk space = 1193786684
    free memory = 195687656 
SRR30542858 SRAfilesize
2da128d284ea5f50044e33bfc8ff3780  SRR30542858.sra
SRR30542858.sra file validated
SRR30542858 is single end
SRR30542858 is conventional basespace
SRR30542858 read1 length is 36 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR30542858_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	33.302	32.0	32.0	37.0	32.0	37.0
2	34.71425	37.0	32.0	37.0	32.0	37.0
3	36.0185	37.0	37.0	37.0	32.0	37.0
4	36.27525	37.0	37.0	37.0	32.0	37.0
5	36.43225	37.0	37.0	37.0	37.0	37.0
6	36.609	37.0	37.0	37.0	37.0	37.0
7	36.49475	37.0	37.0	37.0	37.0	37.0
8	36.55875	37.0	37.0	37.0	37.0	37.0
9	36.5325	37.0	37.0	37.0	37.0	37.0
10	36.647	37.0	37.0	37.0	37.0	37.0
11	36.6495	37.0	37.0	37.0	37.0	37.0
12	36.56425	37.0	37.0	37.0	37.0	37.0
13	36.53225	37.0	37.0	37.0	37.0	37.0
14	36.6065	37.0	37.0	37.0	37.0	37.0
15	36.6235	37.0	37.0	37.0	37.0	37.0
16	36.55925	37.0	37.0	37.0	37.0	37.0
17	36.5575	37.0	37.0	37.0	37.0	37.0
18	36.55675	37.0	37.0	37.0	37.0	37.0
19	36.60875	37.0	37.0	37.0	37.0	37.0
20	36.59425	37.0	37.0	37.0	37.0	37.0
21	36.583	37.0	37.0	37.0	37.0	37.0
22	36.607	37.0	37.0	37.0	37.0	37.0
23	36.55825	37.0	37.0	37.0	37.0	37.0
24	36.614	37.0	37.0	37.0	37.0	37.0
25	36.4835	37.0	37.0	37.0	37.0	37.0
26	36.5445	37.0	37.0	37.0	37.0	37.0
27	36.552	37.0	37.0	37.0	37.0	37.0
28	36.58825	37.0	37.0	37.0	37.0	37.0
29	36.55725	37.0	37.0	37.0	37.0	37.0
30	36.5295	37.0	37.0	37.0	37.0	37.0
31	36.37025	37.0	37.0	37.0	37.0	37.0
32	36.5565	37.0	37.0	37.0	37.0	37.0
33	36.5195	37.0	37.0	37.0	37.0	37.0
34	36.513	37.0	37.0	37.0	37.0	37.0
35	36.44425	37.0	37.0	37.0	37.0	37.0
36	36.27525	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
22	3.0
23	8.0
24	5.0
25	9.0
26	12.0
27	11.0
28	12.0
29	11.0
30	25.0
31	26.0
32	21.0
33	35.0
34	71.0
35	148.0
36	2864.0
37	739.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	22.525000000000002	20.95	29.15	27.375
2	55.525000000000006	14.499999999999998	14.899999999999999	15.075
3	18.25	33.275	13.925	34.55
4	42.225	15.775	26.200000000000003	15.8
5	31.424999999999997	31.1	17.2	20.275000000000002
6	30.225	13.725000000000001	26.900000000000002	29.15
7	35.05	22.900000000000002	19.75	22.3
8	26.28814407203602	21.76088044022011	37.293646823411706	14.657328664332168
9	18.825	28.725	24.275	28.175
10	37.175000000000004	37.574999999999996	12.725	12.525
11	45.050000000000004	23.775	15.525	15.65
12	30.025000000000002	34.625	18.3	17.05
13	20.8	16.275000000000002	39.65	23.275000000000002
14	20.599999999999998	27.6	28.075	23.724999999999998
15	39.675	26.6	14.625	19.1
16	27.500000000000004	26.174999999999997	34.4	11.924999999999999
17	32.074999999999996	33.775	17.224999999999998	16.925
18	31.574999999999996	17.349999999999998	26.325	24.75
19	35.625	22.0	29.799999999999997	12.575
20	26.950000000000003	20.875	33.5	18.675
21	35.175	19.575	32.925	12.325
22	34.150000000000006	24.675	27.375	13.8
23	19.325	39.525	15.675	25.474999999999998
24	37.325	37.875	12.8	12.0
25	25.35	38.675	18.55	17.424999999999997
26	19.379844961240313	21.080270067516878	29.83245811452863	29.707426856714182
27	21.975	17.349999999999998	19.025	41.65
28	32.875	22.650000000000002	9.15	35.325
29	45.25	32.4	6.625	15.725
30	32.45	40.475	7.75	19.325
31	23.240671174555473	38.39218632607062	23.165539694465316	15.20160280490859
32	38.4	32.125	11.05	18.425
33	26.224999999999998	48.475	9.475	15.825
34	32.574999999999996	35.25	6.575	25.6
35	20.075000000000003	33.7	17.625	28.599999999999998
36	16.162121591193397	35.851888916687514	15.46159619714786	32.524393294971226
>>END_MODULE
>>Per sequence GC content	warn
#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	0.5
11	1.0
12	1.0
13	0.5
14	0.0
15	0.5
16	1.0
17	1.0
18	2.5
19	4.0
20	4.0
21	5.0
22	6.0
23	6.0
24	6.0
25	6.0
26	5.5
27	5.0
28	5.0
29	8.0
30	11.0
31	11.0
32	11.0
33	11.0
34	11.0
35	23.0
36	35.0
37	35.0
38	83.5
39	132.0
40	157.0
41	182.0
42	182.0
43	365.5
44	549.0
45	549.0
46	542.0
47	535.0
48	535.0
49	543.0
50	551.0
51	578.0
52	605.0
53	605.0
54	512.0
55	419.0
56	419.0
57	383.5
58	348.0
59	348.0
60	367.0
61	386.0
62	386.0
63	261.5
64	137.0
65	85.5
66	34.0
67	34.0
68	30.0
69	26.0
70	26.0
71	19.5
72	13.0
73	13.0
74	7.0
75	1.0
76	1.5
77	2.0
78	2.0
79	1.0
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	0.05
9	0.0
10	0.0
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	0.0
23	0.0
24	0.0
25	0.0
26	0.025
27	0.0
28	0.0
29	0.0
30	0.0
31	0.17500000000000002
32	0.0
33	0.0
34	0.0
35	0.0
36	0.075
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
36	4000.0
>>END_MODULE
>>Sequence Duplication Levels	warn
#Total Deduplicated Percentage	51.37500000000001
#Duplication Level	Percentage of deduplicated	Percentage of total
1	86.81265206812651	44.6
2	6.034063260340632	6.2
3	1.8004866180048662	2.775
4	1.3625304136253042	2.8000000000000003
5	0.7785888077858881	2.0
6	0.583941605839416	1.7999999999999998
7	0.34063260340632606	1.225
8	0.145985401459854	0.6
9	0.38929440389294406	1.7999999999999998
>10	1.3625304136253042	13.850000000000001
>50	0.291970802919708	11.025
>100	0.09732360097323602	11.325000000000001
>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
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACAC	236	5.8999999999999995	TruSeq Adapter, Index 5 (100% over 35bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATT	217	5.425	No Hit
GGAAGAGCACACGTCTGAACTCCAGTCACACTTGAA	92	2.3	TruSeq Adapter, Index 8 (100% over 36bp)
TGAGGTAGTAGTTTGTGCTGTTAGATCGGAAGAGCA	78	1.95	No Hit
GTTTCCGTAGTGTAGTGGTTATCAGATCGGAAGAGC	74	1.8499999999999999	No Hit
TGAGGTAGTAGGTTGTATGGTTAGATCGGAAGAGCA	68	1.7000000000000002	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTAGAT	65	1.625	No Hit
TGAGGTAGTAGATTGTATAGTTAGATCGGAAGAGCA	64	1.6	No Hit
CGCGACCTCAGATCAGACGTAGATCGGAAGAGCACA	42	1.05	No Hit
TAGCTTATCAGACTGATGTTGACAGATCGGAAGAGC	39	0.975	No Hit
GGGGATGTAGCTCAGTGGTAGATCGGAAGAGCACAC	34	0.8500000000000001	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATA	34	0.8500000000000001	No Hit
CGCGACCTCAGATCGGAAGAGCACACGTCTGAACTC	27	0.675	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
TGGAATGTAAGGAAGTGTGTGGAGATCGGAAGAGCA	25	0.625	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATAGATC	25	0.625	No Hit
TGAGATGAAGCACTGTAGCTCAGATCGGAAGAGCAC	23	0.575	No Hit
TGAGGTAGTAGGTTGTATAGTTAGATCGGAAGAGCA	23	0.575	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAAAG	23	0.575	No Hit
CGCGACCTCAGATCAGATCGGAAGAGCACACGTCTG	22	0.5499999999999999	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
GTTTCCGTAGTGTAGTGGTTATTAGATCGGAAGAGC	22	0.5499999999999999	No Hit
CGCGACCTCAGATCAGACGTGGCAGATCGGAAGAGC	21	0.525	No Hit
TGAGGTAGTAGGTTGTGTGGTTAGATCGGAAGAGCA	18	0.44999999999999996	No Hit
AACCCGTAGATCCGATCTTGTAGATCGGAAGAGCAC	16	0.4	No Hit
TTCAAGTAATCCAGGATAGGCTAGATCGGAAGAGCA	16	0.4	No Hit
CTAGACTGAGGCTCCTTGAGGAGATCGGAAGAGCAC	15	0.375	No Hit
TGAGATGAAGCACTGTAGCTTAGATCGGAAGAGCAC	13	0.325	No Hit
CGACTCTTAGCGGTGGATCACTCGGCTCGTGAGATC	13	0.325	No Hit
CGCGACCTCAGATCAGACGCAGATCGGAAGAGCACA	13	0.325	No Hit
TAGCTTATCAGACTGATGTTGACTAGATCGGAAGAG	13	0.325	No Hit
TCGATGTGGTGCTGCCGCGTTCTCTTCGGGCCGGGG	12	0.3	No Hit
TGAGATGAAGCACTGTAGCTCTAGATCGGAAGAGCA	12	0.3	No Hit
TGAGGTAGTAGATTGTATAGTCAGATCGGAAGAGCA	11	0.27499999999999997	No Hit
GGCTTTTTAAGTCGGATGTGAGATCGGAAGAGCACA	11	0.27499999999999997	No Hit
TTCACAGTGGCTAAGTTCTGCAGATCGGAAGAGCAC	11	0.27499999999999997	No Hit
TGAGGTAGTAGTTTGTACAGTTAGATCGGAAGAGCA	10	0.25	No Hit
TCAGTGCACTACAGAACTTTGTAGATCGGAAGAGCA	10	0.25	No Hit
TAGCTTATCAGACTGATGTTGATAGATCGGAAGAGC	9	0.22499999999999998	No Hit
TGAGGTAGTAGTTTGTGCTGTCAGATCGGAAGAGCA	9	0.22499999999999998	No Hit
CGCGACCTCAGATCAGACAGATCGGAAGAGCACACG	9	0.22499999999999998	No Hit
GTCTACGGCCATACCACCCTGAACGCGCCCGATCTC	9	0.22499999999999998	No Hit
ACTGGACTTGGAGTCAGAAGGTAGATCGGAAGAGCA	9	0.22499999999999998	No Hit
AGCTACATCTGGCTACTGGGTCTCTAGATCGGAAGA	9	0.22499999999999998	No Hit
TGAAATGATGGCAATCATCTTTCGGGACTGACCTGA	9	0.22499999999999998	No Hit
ACTGGACTTGGAGTCAGAAGGCAGATCGGAAGAGCA	9	0.22499999999999998	No Hit
CGCGACCTCAGATCAGACGTGGTAGATCGGAAGAGC	8	0.2	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGATT	8	0.2	No Hit
TGGAATGTAAGGAAGTGTGTGAGATCGGAAGAGCAC	8	0.2	No Hit
CTCTGTGCTGATTGTCATGTTCTGATCAGATCGGAA	7	0.17500000000000002	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCTAGATC	7	0.17500000000000002	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATCAGAT	7	0.17500000000000002	No Hit
TAGCTTATCAGACTGATGTTGACAAGATCGGAAGAG	7	0.17500000000000002	No Hit
GTTTCCGTAGTGTAGTGGTTATAAGATCGGAAGAGC	7	0.17500000000000002	No Hit
AGCTACATTGTCTGCTGGGTTTCAGATCGGAAGAGC	7	0.17500000000000002	No Hit
GGTAGCGTGGCCGAGCAGATCGGAAGAGCACACGTC	7	0.17500000000000002	No Hit
CGCGACCTCAGATTAGATCGGAAGAGCACACGTCTG	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
TGAGGTAGTAGTTTGTGCTGTAGATCGGAAGAGCAC	6	0.15	No Hit
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACA	6	0.15	No Hit
CGCGACCTAAGATCGGAAGAGCACACGTCTGAACTC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
GTAGTCGTGGCCGAGTAGATCGGAAGAGCACACGTC	6	0.15	No Hit
TGGAAGACTAGTGATTTTGTTGTTAGATCGGAAGAG	6	0.15	No Hit
ATCACATTGCCAGGGATTACCACTAGATCGGAAGAG	6	0.15	No Hit
GACTCTTAGCGGTGGATCACTCGGCTCGTGCGAGAT	6	0.15	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAACA	6	0.15	No Hit
TCCCTGTGGTCTAGTGGTTAGGATTCGGCGCTCTCA	6	0.15	No Hit
TGAGGTAGTAGATTGTATAGTAGATCGGAAGAGCAC	6	0.15	No Hit
TGGCTCAGTTCAGCAGGAACAGAGATCGGAAGAGCA	6	0.15	No Hit
AGATCGGAAAGCACACGTCTGAACTCCAGTCACACT	5	0.125	TruSeq Adapter, Index 8 (96% over 29bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAGAT	5	0.125	No Hit
TGAGGTAGTAGGTTGTATGGTCAGATCGGAAGAGCA	5	0.125	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAAGATCGG	5	0.125	No Hit
TCTCTGTGCTGATTGTCATGTTCTGATCAGATCGGA	5	0.125	No Hit
GTGGACGGTGTGAGGCTAGATCGGAAGAGCACACGT	5	0.125	No Hit
CGACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCG	5	0.125	No Hit
GGCCGGTACAGTGAAACTAGATCGGAAGAGCACACG	5	0.125	No Hit
GTGAAATGATGGCAATCATCTTTCGGGACTGACCTG	5	0.125	No Hit
CCGCGACCTCAGATCAGACGTGGCGACCCGCTGAAT	5	0.125	No Hit
AGCTACATTGTCTGCTGGGTTTAGATCGGAAGAGCA	5	0.125	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCTA	5	0.125	No Hit
GACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGA	5	0.125	No Hit
TGAGGTAGTAGTTTGTGCTGTAAGATCGGAAGAGCA	5	0.125	No Hit
TGAGATGAAGCACTGTAGCTAGATCGGAAGAGCACA	5	0.125	No Hit
ACAGTAGTCTGCACATTGGTTAGATCGGAAGAGCAC	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	6.45	0.0	0.0	0.0	0.0
2	6.575	0.0	0.0	0.0	0.0
3	6.575	0.0	0.0	0.0	0.0
4	6.65	0.0	0.0	0.0	0.0
5	6.7	0.0	0.0	0.0	0.0
6	6.7	0.0	0.0	0.0	0.0
7	6.775	0.0	0.0	0.0	0.0
8	6.8	0.0	0.0	0.0	0.0
9	6.925	0.0	0.0	0.0	0.0
10	8.2	0.0	0.0	0.0	0.0
11	8.475	0.0	0.0	0.0	0.0
12	8.8	0.0	0.0	0.0	0.0
13	9.4	0.0	0.0	0.0	0.0
14	10.15	0.0	0.0	0.0	0.0
15	11.775	0.0	0.0	0.0	0.0
16	12.875	0.0	0.0	0.0	0.0
17	14.625	0.0	0.0	0.0	0.0
18	16.1	0.0	0.0	0.0	0.0
19	18.275	0.0	0.0	0.0	0.0
20	21.125	0.0	0.0	0.0	0.0
21	25.55	0.0	0.0	0.0	0.0
22	31.625	0.0	0.0	0.0	0.0
23	46.0	0.0	0.0	0.0	0.0
24	54.15	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
CGCGACC	55	6.366463E-11	30.000002	1
GCGACCT	55	6.366463E-11	30.000002	2
AGACGTG	45	1.1683369E-8	30.000002	15
GACGTGG	45	1.1683369E-8	30.000002	16
TCAGACG	55	6.366463E-11	30.000002	13
CCTCAGA	55	6.366463E-11	30.000002	6
CAGATCA	55	6.366463E-11	30.000002	9
ACCTCAG	55	6.366463E-11	30.000002	5
GACCTCA	55	6.366463E-11	30.000002	4
AGATCAG	55	6.366463E-11	30.000002	10
CGACCTC	55	6.366463E-11	30.000002	3
ACGTGGC	45	1.1683369E-8	30.000002	17
GTAGATT	35	2.0637017E-6	30.0	8
CGCTGAA	35	2.0637017E-6	30.0	28
GAGGTAG	85	0.0	30.0	2
GTTTGTG	25	3.5274107E-4	30.0	11
GTATGGT	25	3.5274107E-4	30.0	15
GGTTGTA	25	3.5274107E-4	30.0	11
TTGTATG	25	3.5274107E-4	30.0	13
TTGTATA	35	2.0637017E-6	30.0	13
>>END_MODULE
Read 39705 spots for SRR30542858.sra
Written 39705 spots for SRR30542858.sra
Read 39705 spots for SRR30542858.sra
Written 39705 spots for SRR30542858.sra
Read 39705 spots for SRR30542858.sra
Written 39705 spots for SRR30542858.sra
Read 39709 spots for SRR30542858.sra
Written 39709 spots for SRR30542858.sra
Read 39705 spots for SRR30542858.sra
Written 39705 spots for SRR30542858.sra
Read 39705 spots for SRR30542858.sra
Written 39705 spots for SRR30542858.sra
Read 39705 spots for SRR30542858.sra
Written 39705 spots for SRR30542858.sra
Read 39705 spots for SRR30542858.sra
Written 39705 spots for SRR30542858.sra
SRR ids: ['SRR30542858.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_onk4_9qn
SRR30542858.sra spots: 317644
blocks: [[1, 39705], [39706, 79410], [79411, 119115], [119116, 158820], [158821, 198525], [198526, 238230], [238231, 277935], [277936, 317644]]
SRR30542858 file size 45244
SRR30542858 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 SRR30542858 SRR30542858_1.fastq
Input file:	SRR30542858_1.fastq
trimmed:	SRR30542858-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 06:33:05 2025 >> started

Thu Nov  6 06:33:05 2025 >> done (0.258s)
317644 reads processed; of these:
   614 ( 0.19%) short reads filtered out after trimming by size control
 20710 ( 6.52%) empty reads filtered out after trimming by size control
296320 (93.29%) reads available; of these:
    32 ( 0.01%) trimmed reads available after processing
296288 (99.99%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 35	    32	  0.01%
 36	296288	 99.99%
296320 reads passed initial QC


criterion=sequence-density
sequence-density=52.16
sequence-density-rank=1
fanout-score=27.29
fanout-score-rank=1
prefix-density=59.70
prefix-fanout=23.8
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACACTTGAATC


criterion=fanout-score
sequence-density=52.16
sequence-density-rank=1
fanout-score=27.29
fanout-score-rank=1
prefix-density=59.70
prefix-fanout=23.8
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACACTTGAATC
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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACACTTGAATC -o SRR30542858 -
Input file:	STDIN
trimmed:	SRR30542858-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	AGATCGGAAGAGCACACGTCTGAACTCCAGTCACACTTGAATC
-- 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 06:33:06 2025 >> started

Thu Nov  6 06:33:06 2025 >> done (0.197s)
285138 reads processed; of these:
 30424 (10.67%) short reads filtered out after trimming by size control
   312 ( 0.11%) empty reads filtered out after trimming by size control
254402 (89.22%) reads available; of these:
185253 (72.82%) trimmed reads available after processing
 69149 (27.18%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  6498	  2.55%
 19	  9582	  3.77%
 20	 13846	  5.44%
 21	 18446	  7.25%
 22	 44143	 17.35%
 23	 26863	 10.56%
 24	  9540	  3.75%
 25	  5203	  2.05%
 26	  4620	  1.82%
 27	  5533	  2.17%
 28	  6079	  2.39%
 29	  4987	  1.96%
 30	  5677	  2.23%
 31	  9376	  3.69%
 32	 10329	  4.06%
 33	  4531	  1.78%
 34	     0	  0.00%
 35	     4	  0.00%
 36	 69145	 27.18%


criterion=sequence-density
sequence-density=4.34
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=10
prefix-density=0.00
prefix-fanout=1.0
sequence=TGAGGTAGTAGGTTGTATGGTTAGATCGGA


criterion=fanout-score
sequence-density=2.53
sequence-density-rank=6
fanout-score=15.98
fanout-score-rank=1
prefix-density=2.81
prefix-fanout=14.4
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACACTTGAATC
                                 Started job on |	Nov 06 06:33:13
                             Started mapping on |	Nov 06 06:33:14
                                    Finished on |	Nov 06 06:33:23
       Mapping speed, Million of reads per hour |	106.23

                          Number of input reads |	265584
                      Average input read length |	27
                                    UNIQUE READS:
                   Uniquely mapped reads number |	89396
                        Uniquely mapped reads % |	33.66%
                          Average mapped length |	24.66
                       Number of splices: Total |	616
            Number of splices: Annotated (sjdb) |	148
                       Number of splices: GT/AG |	562
                       Number of splices: GC/AG |	11
                       Number of splices: AT/AC |	1
               Number of splices: Non-canonical |	42
                      Mismatch rate per base, % |	0.41%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.22
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.33
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	87693
             % of reads mapped to multiple loci |	33.02%
        Number of reads mapped to too many loci |	54020
             % of reads mapped to too many loci |	20.34%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	11.11%
                     % of reads unmapped: other |	1.87%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	88495	88495	88495
N_multimapping	87693	87693	87693
N_noFeature	32183	36737	84734
N_ambiguous	1951	1842	1
UnstrandedReadsAssigned:55262 PositiveStrandReadsAssigned:50817 NegativeStrandReadsAssigned:4661
Dataset is classified positive stranded
MeadianReadLen=25 20thPercentileLength=22 echo kmer=19
SRR30542858 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: SRR30542858-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 265,584 reads, 8,780 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 666 rounds

  31716 SRR30542858.ke.tsv
  32883 SRR30542858.se.tsv
  64599 total
==> SRR30542858.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
ENSRNOT00000047550.4	955	856	2	215.217
ENSRNOT00000040993.4	1039	940	9	881.932
ENSRNOT00000050156.3	1545	1446	68	4331.73
ENSRNOT00000043693.3	684	585	17	2676.79
ENSRNOT00000046201.3	204	105	7	6140.86
ENSRNOT00000046108.3	681	582	4	633.079
ENSRNOT00000049683.3	784	685	13	1748.13
ENSRNOT00000041241.3	348	249	0	0
ENSRNOT00000044582.3	297	198	2	930.434

==> SRR30542858.se.tsv <==
ENSRNOG00000046319	0
ENSRNOG00000047964	0
ENSRNOG00000050370	0
ENSRNOG00000032365	0
ENSRNOG00000040300	0
ENSRNOG00000058808	0
ENSRNOG00000061316	0
ENSRNOG00000050129	0
ENSRNOG00000040316	0
ENSRNOG00000023659	0
SRR30542858 completed mapping pipeline successfully
