Starting /dee2/code/volunteer_pipeline.sh SRR14127850
    current disk space = 649118196
    free memory = 201488800 
SRR14127850 SRAfilesize
7f891bde822263094b9288b56c679891  SRR14127850.sra
SRR14127850.sra file validated
SRR14127850 is single end
SRR14127850 is conventional basespace
SRR14127850 read1 length is 51 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR14127850_1.fastq
File type	Conventional base calls
Encoding	Sanger / Illumina 1.9
Total Sequences	4000
Sequences flagged as poor quality	0
Sequence length	51
%GC	50
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	36.227	37.0	37.0	37.0	37.0	37.0
2	36.0165	37.0	37.0	37.0	37.0	37.0
3	36.1945	37.0	37.0	37.0	37.0	37.0
4	36.3045	37.0	37.0	37.0	37.0	37.0
5	36.5395	37.0	37.0	37.0	37.0	37.0
6	36.3515	37.0	37.0	37.0	37.0	37.0
7	36.3725	37.0	37.0	37.0	37.0	37.0
8	36.575	37.0	37.0	37.0	37.0	37.0
9	36.501	37.0	37.0	37.0	37.0	37.0
10	36.496	37.0	37.0	37.0	37.0	37.0
11	36.606	37.0	37.0	37.0	37.0	37.0
12	36.635	37.0	37.0	37.0	37.0	37.0
13	36.4835	37.0	37.0	37.0	37.0	37.0
14	36.5955	37.0	37.0	37.0	37.0	37.0
15	36.3545	37.0	37.0	37.0	37.0	37.0
16	36.3635	37.0	37.0	37.0	37.0	37.0
17	36.5125	37.0	37.0	37.0	37.0	37.0
18	36.364	37.0	37.0	37.0	37.0	37.0
19	36.623	37.0	37.0	37.0	37.0	37.0
20	36.4795	37.0	37.0	37.0	37.0	37.0
21	36.4865	37.0	37.0	37.0	37.0	37.0
22	36.4935	37.0	37.0	37.0	37.0	37.0
23	36.343	37.0	37.0	37.0	37.0	37.0
24	36.384	37.0	37.0	37.0	37.0	37.0
25	36.462	37.0	37.0	37.0	37.0	37.0
26	36.4185	37.0	37.0	37.0	37.0	37.0
27	36.3215	37.0	37.0	37.0	37.0	37.0
28	36.4555	37.0	37.0	37.0	37.0	37.0
29	36.425	37.0	37.0	37.0	37.0	37.0
30	36.692	37.0	37.0	37.0	37.0	37.0
31	36.6065	37.0	37.0	37.0	37.0	37.0
32	36.4855	37.0	37.0	37.0	37.0	37.0
33	36.5555	37.0	37.0	37.0	37.0	37.0
34	36.529	37.0	37.0	37.0	37.0	37.0
35	36.6065	37.0	37.0	37.0	37.0	37.0
36	36.651	37.0	37.0	37.0	37.0	37.0
37	36.5925	37.0	37.0	37.0	37.0	37.0
38	36.6285	37.0	37.0	37.0	37.0	37.0
39	36.6025	37.0	37.0	37.0	37.0	37.0
40	36.509	37.0	37.0	37.0	37.0	37.0
41	36.513	37.0	37.0	37.0	37.0	37.0
42	36.54475	37.0	37.0	37.0	37.0	37.0
43	36.4295	37.0	37.0	37.0	37.0	37.0
44	36.331	37.0	37.0	37.0	37.0	37.0
45	36.6925	37.0	37.0	37.0	37.0	37.0
46	36.754	37.0	37.0	37.0	37.0	37.0
47	36.617	37.0	37.0	37.0	37.0	37.0
48	36.605	37.0	37.0	37.0	37.0	37.0
49	36.5255	37.0	37.0	37.0	37.0	37.0
50	36.497	37.0	37.0	37.0	37.0	37.0
51	36.4995	37.0	37.0	37.0	37.0	37.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
25	1.0
26	1.0
27	9.0
28	11.0
29	15.0
30	23.0
31	42.0
32	45.0
33	65.0
34	84.0
35	166.0
36	1141.0
37	2397.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	26.1	10.225	57.49999999999999	6.175
2	46.93158953722334	12.122736418511067	11.217303822937625	29.728370221327964
3	12.225	64.67500000000001	7.575	15.525
4	47.225	12.6	26.5	13.675
5	11.825	48.55	30.7	8.924999999999999
6	35.5	10.85	47.325	6.325
7	65.25	12.4	12.950000000000001	9.4
8	13.025	46.75	35.35	4.875
9	30.975	46.0	15.225	7.8
10	63.6	14.299999999999999	14.000000000000002	8.1
11	15.0	8.4	29.099999999999998	47.5
12	9.700000000000001	43.9	30.099999999999998	16.3
13	6.7	16.125	12.1	65.075
14	13.25	32.975	46.925	6.8500000000000005
15	75.8	12.35	7.025	4.825
16	9.1	16.375	68.22500000000001	6.3
17	29.5	47.9	15.125	7.475
18	64.35	12.2	13.65	9.8
19	14.274999999999999	11.025	37.125	37.574999999999996
20	20.75	29.25	42.975	7.025
21	32.975	17.549999999999997	13.925	35.55
22	16.8	46.825	27.400000000000002	8.975
23	21.75	62.7	9.45	6.1
24	35.625	28.425	30.625000000000004	5.325
25	14.625	36.25	37.425000000000004	11.700000000000001
26	14.625	14.05	32.7	38.625
27	26.3	9.225	29.625	34.849999999999994
28	51.2	14.099999999999998	3.8249999999999997	30.875000000000004
29	62.475	28.000000000000004	2.375	7.1499999999999995
30	20.65	51.15	2.775	25.424999999999997
31	23.5	50.324999999999996	5.475	20.7
32	41.15	38.15	10.9	9.8
33	35.699999999999996	48.675000000000004	3.95	11.675
34	44.25	28.549999999999997	4.775	22.425
35	12.725	33.475	12.225	41.575
36	7.6	42.15	13.5	36.75
37	17.325	27.200000000000003	4.55	50.925
38	28.875	37.275000000000006	5.75	28.1
39	29.725	22.575	10.6	37.1
40	35.575	25.174999999999997	19.900000000000002	19.35
41	21.85	17.525	39.1	21.525
42	22.53063265816454	17.62940735183796	24.981245311327832	34.858714678669664
43	28.249999999999996	24.325	33.175	14.249999999999998
44	42.075	29.175	10.75	18.0
45	12.025	57.99999999999999	5.949999999999999	24.025
46	5.2	52.825	9.55	32.425
47	3.8249999999999997	24.15	17.4	54.625
48	4.6	19.675	31.674999999999997	44.05
49	13.825000000000001	13.225000000000001	11.65	61.3
50	20.075000000000003	21.349999999999998	14.549999999999999	44.025
51	19.6	35.449999999999996	20.225	24.725
>>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	0.0
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	0.5
27	1.0
28	1.0
29	1.0
30	1.0
31	1.0
32	1.5
33	2.0
34	4.0
35	6.0
36	7.5
37	9.0
38	10.0
39	11.0
40	22.5
41	34.0
42	55.5
43	77.0
44	155.5
45	234.0
46	345.0
47	456.0
48	773.5
49	1091.0
50	1147.0
51	1203.0
52	867.5
53	532.0
54	340.0
55	148.0
56	120.5
57	93.0
58	81.5
59	70.0
60	44.0
61	18.0
62	13.0
63	8.0
64	5.0
65	2.0
66	1.5
67	1.0
68	0.5
69	0.0
70	0.5
71	1.0
72	0.5
73	0.0
74	0.5
75	0.5
76	0.0
77	0.0
78	0.0
79	0.0
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	0.6
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	0.0
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	0.0
27	0.0
28	0.0
29	0.0
30	0.0
31	0.0
32	0.0
33	0.0
34	0.0
35	0.0
36	0.0
37	0.0
38	0.0
39	0.0
40	0.0
41	0.0
42	0.025
43	0.0
44	0.0
45	0.0
46	0.0
47	0.0
48	0.0
49	0.0
50	0.0
51	0.0
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
51	4000.0
>>END_MODULE
>>Sequence Duplication Levels	fail
#Total Deduplicated Percentage	32.725
#Duplication Level	Percentage of deduplicated	Percentage of total
1	78.45683728036668	25.674999999999997
2	10.542398777692895	6.9
3	2.6737967914438503	2.625
4	2.13903743315508	2.8000000000000003
5	0.9931245225362872	1.625
6	0.7639419404125287	1.5
7	0.30557677616501144	0.7000000000000001
8	0.38197097020626436	1.0
9	0.53475935828877	1.575
>10	2.4446142093200915	15.9
>50	0.38197097020626436	8.7
>100	0.38197097020626436	31.0
>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
TGAGATGAAGCACTGTAGCTCTAGATCGGAAGAGCACACGTCTGAACTCCA	447	11.175	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TGAGATGAAGCACTGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAG	243	6.075	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTAGATCGGAAGAGCACACGT	235	5.875	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCAGATCGGAAGAGCACACGTC	187	4.675	No Hit
TGAGATGAAGCACTGTAGCTAGATCGGAAGAGCACACGTCTGAACTCCAGT	128	3.2	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
TGAGATGAAGCACTGTAGCTCCAGATCGGAAGAGCACACGTCTGAACTCCA	96	2.4	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCTAGATCGGAAGAGCACACGTC	75	1.875	No Hit
TTCAAGTAATCCAGGATAGGCTAGATCGGAAGAGCACACGTCTGAACTCCA	61	1.525	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TGAGATGAAGCACTGTAGCTCTTAGATCGGAAGAGCACACGTCTGAACTCC	60	1.5	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
TGAGATGAAGCACTGTAGCTCAAGATCGGAAGAGCACACGTCTGAACTCCA	56	1.4000000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
AAGAAAGTATGCAAGAACTAGATCGGAAGAGCACACGTCTGAACTCCAGTC	46	1.15	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCCAGATCGGAAGAGCACACGT	44	1.0999999999999999	No Hit
TGAGATGAAGCACTGTAGCTTAGATCGGAAGAGCACACGTCTGAACTCCAG	39	0.975	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
AACCCGTAGATCCGATCTTGTAGATCGGAAGAGCACACGTCTGAACTCCAG	34	0.8500000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCAAGATCGGAAGAGCACACGTC	32	0.8	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCAAGATCGGAAGAGCACACGT	31	0.775	No Hit
TGAGATGAAGCACTGTAGCCAGATCGGAAGAGCACACGTCTGAACTCCAGT	27	0.675	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
GTCCAGTTTTCCCAGGAATCCCTAGATCGGAAGAGCACACGTCTGAACTCC	26	0.65	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
TCAGTGCACTACAGAACTTTGTAGATCGGAAGAGCACACGTCTGAACTCCA	22	0.5499999999999999	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TAGCTTATCAGACTGATGTTGACAGATCGGAAGAGCACACGTCTGAACTCC	22	0.5499999999999999	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
TGAGGTAGTAGTTTGTGCTGTTAGATCGGAAGAGCACACGTCTGAACTCCA	21	0.525	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TAGCTTATCAGACTGATGTTGAAGATCGGAAGAGCACACGTCTGAACTCCA	21	0.525	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCAGATCGGAAGAGCACACGTCT	21	0.525	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
TGAGATGAAGCACTGTAGCTAAGATCGGAAGAGCACACGTCTGAACTCCAG	20	0.5	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TTCACAGTGGCTAAGTTCTGCAGATCGGAAGAGCACACGTCTGAACTCCAG	18	0.44999999999999996	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TGAGGTAGTAGATTGTATAGTTAGATCGGAAGAGCACACGTCTGAACTCCA	17	0.42500000000000004	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TGGAATGTAAAGAAGTATGTATAGATCGGAAGAGCACACGTCTGAACTCCA	16	0.4	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TAGCTTATCAGACTGATGTTGAGATCGGAAGAGCACACGTCTGAACTCCAG	15	0.375	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TGAGATGAAGCACTGTAGCAAGATCGGAAGAGCACACGTCTGAACTCCAGT	14	0.35000000000000003	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
TGAGGTAGTAGTTTGTACAGTTAGATCGGAAGAGCACACGTCTGAACTCCA	14	0.35000000000000003	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TGAGATGAAGCACTGTAGCTCTCAGATCGGAAGAGCACACGTCTGAACTCC	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTAGATCGGAAGAGCACACGTCTGAACTCCAG	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GCATTGTGGTTCAGTGGTAGAATTCTCGCCTAGATCGGAAGAGCACACGTC	13	0.325	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCGAGATCGGAAGAGCACACGT	12	0.3	No Hit
TGAGGTAGTAGGTTGTATGGTTAGATCGGAAGAGCACACGTCTGAACTCCA	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TCCCTGTGGTCTAGTGGTTAGGATTCGGCGCTAGATCGGAAGAGCACACGT	11	0.27499999999999997	No Hit
TGAGGTAGTAGGTTGTATAGTTAGATCGGAAGAGCACACGTCTGAACTCCA	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCCAGATCGGAAGAGCACACGTCTGAACTCCA	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TGAGATGAAGCACTGTAGCTCGAGATCGGAAGAGCACACGTCTGAACTCCA	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TACCCTGTAGATCCGAATTTGTAGATCGGAAGAGCACACGTCTGAACTCCA	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
AACCCGTAGATCCGATCTTGTGAAGATCGGAAGAGCACACGTCTGAACTCC	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTAGATCGGAAGAGCACACG	10	0.25	No Hit
GCATTGTGGTTCAGTGGTAGAATTCTCGCCAGATCGGAAGAGCACACGTCT	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
TTCAAGTAATCCAGGATAGGAGATCGGAAGAGCACACGTCTGAACTCCAGT	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
TCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTAGATCGG	9	0.22499999999999998	No Hit
TGAGATGAAGCACTGTAGCTTTAGATCGGAAGAGCACACGTCTGAACTCCA	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
ACAGTAGTCTGCACATTGGTTAGATCGGAAGAGCACACGTCTGAACTCCAG	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
AAGAAAGTATGCAAGAACCAGATCGGAAGAGCACACGTCTGAACTCCAGTC	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
TGAGGTAGTAGTTTGTACAGTAGATCGGAAGAGCACACGTCTGAACTCCAG	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCAGATCGGAAGAGCACAC	8	0.2	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCAGATCGGAAGAGCACA	8	0.2	No Hit
TTCAAGTAATTCAGGATAGGTTAGATCGGAAGAGCACACGTCTGAACTCCA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GCCCGGCTAGCTCAGTCGGTAGAGCATGAGACTAGATCGGAAGAGCACACG	8	0.2	No Hit
TCGTACCGTGAGTAATAATGCAGATCGGAAGAGCACACGTCTGAACTCCAG	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TCGTACCGTGAGTAATAATGCGAGATCGGAAGAGCACACGTCTGAACTCCA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TCCTTCATTCCACCGGAGTCTGTAGATCGGAAGAGCACACGTCTGAACTCC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
GCATGGGTGGTTCAGTGGTAGAATTCTCGCCTAGATCGGAAGAGCACACGT	7	0.17500000000000002	No Hit
GGAATACCGGGTGCTGTAGGCTTTAGATCGGAAGAGCACACGTCTGAACTC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
TGAGATGAAGCACTGTAGCTCTAAGATCGGAAGAGCACACGTCTGAACTCC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
AAGAAAGTATGCAAGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
TGAGGTAGTAGTTTGTGCTGTTTAGATCGGAAGAGCACACGTCTGAACTCC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
TGTAAACATCCTCGACTGGAAGAGATCGGAAGAGCACACGTCTGAACTCCA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TGAGATGAAGCACTGTAGCCCAGATCGGAAGAGCACACGTCTGAACTCCAG	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
ATCACATTGCCAGGGATTTCCAGATCGGAAGAGCACACGTCTGAACTCCAG	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TGAGATGAAGCACTGTAGCTTTTAGATCGGAAGAGCACACGTCTGAACTCC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
TCAGTGCACTACAGAACTTTGCAGATCGGAAGAGCACACGTCTGAACTCCA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
CGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTAGATCGGA	6	0.15	No Hit
CGCGACCTCAGATCAGACGTAGATCGGAAGAGCACACGTCTGAACTCCAGT	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGTAGATCGGAAGAGCACACGTCT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
TGAGATGAAGCACTGTAGCGCTAGATCGGAAGAGCACACGTCTGAACTCCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TCGTACCGTGAGTAATAATGCAAGATCGGAAGAGCACACGTCTGAACTCCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TACCCTGTAGAACCGAATTTGTAGATCGGAAGAGCACACGTCTGAACTCCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTCAGATCGGAAGAGCACACGTCTGAACTCCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GTCCAGTTTTCCCAGGAATCCCAGATCGGAAGAGCACACGTCTGAACTCCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
ATTCCTGGAAATACTGTTCTAGATCGGAAGAGCACACGTCTGAACTCCAGT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
TNAGATGAAGCACTGTAGCTCTAGATCGGAAGAGCACACGTCTGAACTCCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCAGATCGGAAGAGCACACGT	5	0.125	No Hit
TGAGATGAAGCACTGTAGCAGATCGGAAGAGCACACGTCTGAACTCCAGTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
TTCAAGTAATCCAGGATAGGCAGATCGGAAGAGCACACGTCTGAACTCCAG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TCCCTGAGACCCTAACTTGTGAAGATCGGAAGAGCACACGTCTGAACTCCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TGAGGTAGTAGTTTGTGCTGTTAAGATCGGAAGAGCACACGTCTGAACTCC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
>>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	0.05	0.0	0.0	0.0	0.0
2	0.05	0.0	0.0	0.0	0.0
3	0.05	0.0	0.0	0.0	0.0
4	0.05	0.0	0.0	0.0	0.0
5	0.05	0.0	0.0	0.0	0.0
6	0.1	0.0	0.0	0.0	0.0
7	0.175	0.0	0.0	0.0	0.0
8	0.275	0.0	0.0	0.0	0.0
9	0.325	0.0	0.0	0.0	0.0
10	0.55	0.0	0.0	0.0	0.0
11	1.125	0.0	0.0	0.0	0.0
12	1.75	0.0	0.0	0.0	0.0
13	2.325	0.0	0.0	0.0	0.0
14	3.275	0.0	0.0	0.0	0.0
15	4.3	0.0	0.0	0.0	0.0
16	5.45	0.0	0.0	0.0	0.0
17	6.325	0.0	0.0	0.0	0.0
18	7.325	0.0	0.0	0.0	0.0
19	8.45	0.0	0.0	0.0	0.0
20	10.975	0.0	0.0	0.0	0.0
21	17.8	0.0	0.0	0.0	0.0
22	32.8	0.0	0.0	0.0	0.0
23	61.625	0.0	0.0	0.0	0.0
24	68.9	0.0	0.0	0.0	0.0
25	70.675	0.0	0.0	0.0	0.0
26	71.15	0.0	0.0	0.0	0.0
27	71.425	0.0	0.0	0.0	0.0
28	71.95	0.0	0.0	0.0	0.0
29	72.45	0.0	0.0	0.0	0.0
30	72.875	0.0	0.0	0.0	0.0
31	74.425	0.0	0.0	0.0	0.0
32	83.475	0.0	0.0	0.0	0.0
33	93.375	0.0	0.0	0.0	0.0
34	94.55	0.0	0.0	0.0	0.0
35	95.3	0.0	0.0	0.0	0.0
36	96.05	0.0	0.0	0.0	0.0
37	96.225	0.0	0.0	0.0	0.0
38	96.55	0.0	0.0	0.0	0.0
39	96.9	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
AGCTCTT	20	6.222983E-4	45.0	17
CATTGGT	70	0.0	45.0	2
AGCTAGA	25	3.236105E-5	45.0	17
ATTGGTG	70	0.0	45.0	3
TAGCTAG	25	3.236105E-5	45.0	16
TCTCGCC	50	1.0913936E-11	45.0	25
TTGGTGG	70	0.0	45.0	4
GGTGGTT	75	0.0	45.0	6
GCTCTTA	20	6.222983E-4	45.0	18
TGGTGGT	70	0.0	45.0	5
GCATTGG	70	0.0	45.0	1
GTAGCTA	25	3.236105E-5	45.0	15
CTCGCCA	25	3.236105E-5	45.0	26
TCTTAGA	20	6.222983E-4	45.0	20
ACTGTAG	150	0.0	43.5	12
CACTGTA	150	0.0	43.5	11
AGCACTG	150	0.0	43.5	9
GCACTGT	150	0.0	43.5	10
CTGTAGC	150	0.0	43.5	13
GAAGCAC	145	0.0	43.448273	7
>>END_MODULE
Rejected 1990780 READS because READLEN < 1
Read 1990780 spots for SRR14127850.sra
Written 1990780 spots for SRR14127850.sra
Rejected 1990780 READS because READLEN < 1
Read 1990780 spots for SRR14127850.sra
Written 1990780 spots for SRR14127850.sra
Rejected 1990780 READS because READLEN < 1
Read 1990780 spots for SRR14127850.sra
Written 1990780 spots for SRR14127850.sra
Rejected 1990780 READS because READLEN < 1
Read 1990780 spots for SRR14127850.sra
Written 1990780 spots for SRR14127850.sra
Rejected 1990780 READS because READLEN < 1
Read 1990780 spots for SRR14127850.sra
Written 1990780 spots for SRR14127850.sra
Rejected 1990780 READS because READLEN < 1
Read 1990780 spots for SRR14127850.sra
Written 1990780 spots for SRR14127850.sra
Rejected 1990780 READS because READLEN < 1
Read 1990780 spots for SRR14127850.sra
Written 1990780 spots for SRR14127850.sra
Rejected 1990780 READS because READLEN < 1
Read 1990780 spots for SRR14127850.sra
Written 1990780 spots for SRR14127850.sra
SRR ids: ['SRR14127850.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_65y_a9jm
SRR14127850.sra spots: 15926240
blocks: [[1, 1990780], [1990781, 3981560], [3981561, 5972340], [5972341, 7963120], [7963121, 9953900], [9953901, 11944680], [11944681, 13935460], [13935461, 15926240]]
SRR14127850 file size 2264592
SRR14127850 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 SRR14127850 SRR14127850_1.fastq
Input file:	SRR14127850_1.fastq
trimmed:	SRR14127850-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
Tue Dec  2 20:25:52 2025 >> started

Tue Dec  2 20:25:55 2025 >> done (3.105s)
15926240 reads processed; of these:
 1176675 ( 7.39%) short reads filtered out after trimming by size control
   11415 ( 0.07%) empty reads filtered out after trimming by size control
14738150 (92.54%) reads available; of these:
  594677 ( 4.03%) trimmed reads available after processing
14143473 (95.97%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  165038	  1.12%
 19	  429639	  2.92%
 20	       0	  0.00%
 21	       0	  0.00%
 22	       0	  0.00%
 23	       0	  0.00%
 24	       0	  0.00%
 25	       0	  0.00%
 26	       0	  0.00%
 27	       0	  0.00%
 28	       0	  0.00%
 29	       0	  0.00%
 30	       0	  0.00%
 31	       0	  0.00%
 32	       0	  0.00%
 33	       0	  0.00%
 34	       0	  0.00%
 35	       0	  0.00%
 36	       0	  0.00%
 37	       0	  0.00%
 38	       0	  0.00%
 39	       0	  0.00%
 40	       0	  0.00%
 41	       0	  0.00%
 42	       0	  0.00%
 43	       0	  0.00%
 44	       0	  0.00%
 45	       0	  0.00%
 46	       0	  0.00%
 47	       0	  0.00%
 48	       0	  0.00%
 49	       0	  0.00%
 50	       0	  0.00%
 51	14143473	 95.97%
14738150 reads passed initial QC


criterion=sequence-density
sequence-density=93.20
sequence-density-rank=1
fanout-score=15.17
fanout-score-rank=3
prefix-density=94.11
prefix-fanout=15.0
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGCCGTCT


criterion=fanout-score
sequence-density=1.14
sequence-density-rank=12
fanout-score=32.10
fanout-score-rank=1
prefix-density=35.83
prefix-fanout=1.0
sequence=AGCACTGTAGCCAGATCGGA
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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGCCGTCT -o SRR14127850 -
Input file:	STDIN
trimmed:	SRR14127850-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	AGATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGCCGTCT
-- 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
Tue Dec  2 20:26:23 2025 >> started

Tue Dec  2 20:26:31 2025 >> done (8.841s)
14424572 reads processed; of these:
    7251 ( 0.05%) short reads filtered out after trimming by size control
      16 ( 0.00%) empty reads filtered out after trimming by size control
14417305 (99.95%) reads available; of these:
13787795 (95.63%) trimmed reads available after processing
  629510 ( 4.37%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  159361	  1.11%
 19	  425687	  2.95%
 20	 1135830	  7.88%
 21	 2361663	 16.38%
 22	 4678744	 32.45%
 23	 1069819	  7.42%
 24	  289805	  2.01%
 25	   80378	  0.56%
 26	   61274	  0.43%
 27	   66500	  0.46%
 28	   76004	  0.53%
 29	   63577	  0.44%
 30	  205059	  1.42%
 31	 1512998	 10.49%
 32	 1509100	 10.47%
 33	  191414	  1.33%
 34	   97123	  0.67%
 35	   98104	  0.68%
 36	   47969	  0.33%
 37	   38466	  0.27%
 38	   33923	  0.24%
 39	   28661	  0.20%
 40	   20040	  0.14%
 41	   17333	  0.12%
 42	   11108	  0.08%
 43	   24673	  0.17%
 44	   35673	  0.25%
 45	   14086	  0.10%
 46	    4795	  0.03%
 47	    1960	  0.01%
 48	    2198	  0.02%
 49	       0	  0.00%
 50	       0	  0.00%
 51	   53980	  0.37%


criterion=sequence-density
sequence-density=19.24
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=14
prefix-density=0.00
prefix-fanout=1.0
sequence=GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCAC


criterion=fanout-score
sequence-density=0.24
sequence-density-rank=33
fanout-score=154.84
fanout-score-rank=1
prefix-density=35.94
prefix-fanout=1.0
sequence=AGCACTGTAGCGCT
                                 Started job on |	Dec 02 20:26:52
                             Started mapping on |	Dec 02 20:26:52
                                    Finished on |	Dec 02 20:27:43
       Mapping speed, Million of reads per hour |	1039.83

                          Number of input reads |	14730883
                      Average input read length |	25
                                    UNIQUE READS:
                   Uniquely mapped reads number |	8431786
                        Uniquely mapped reads % |	57.24%
                          Average mapped length |	21.51
                       Number of splices: Total |	11370
            Number of splices: Annotated (sjdb) |	7078
                       Number of splices: GT/AG |	11095
                       Number of splices: GC/AG |	73
                       Number of splices: AT/AC |	6
               Number of splices: Non-canonical |	196
                      Mismatch rate per base, % |	0.10%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.28
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.25
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	2705443
             % of reads mapped to multiple loci |	18.37%
        Number of reads mapped to too many loci |	3221744
             % of reads mapped to too many loci |	21.87%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	2.45%
                     % of reads unmapped: other |	0.07%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	3593654	3593654	3593654
N_multimapping	2705443	2705443	2705443
N_noFeature	264453	578970	8099127
N_ambiguous	114595	96423	33
UnstrandedReadsAssigned:8052738 PositiveStrandReadsAssigned:7756393 NegativeStrandReadsAssigned:332626
Dataset is classified positive stranded
MeadianReadLen=22 20thPercentileLength=21 echo kmer=19
SRR14127850 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: SRR14127850-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 14,730,883 reads, 402,107 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 848 rounds

  31716 SRR14127850.ke.tsv
  32883 SRR14127850.se.tsv
  64599 total
==> SRR14127850.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
ENSRNOT00000047550.4	955	856	9752	20146.3
ENSRNOT00000040993.4	1039	940	10518	19787
ENSRNOT00000050156.3	1545	1446	39520	48330.7
ENSRNOT00000043693.3	684	585	9285	28067.3
ENSRNOT00000046201.3	204	105	975	16420.6
ENSRNOT00000046108.3	681	582	8153	24772.4
ENSRNOT00000049683.3	784	685	11132	28738
ENSRNOT00000041241.3	348	249	1087	7719.77
ENSRNOT00000044582.3	297	198	1292	11539.1

==> SRR14127850.se.tsv <==
ENSRNOG00000046319	0
ENSRNOG00000047964	0
ENSRNOG00000050370	0
ENSRNOG00000032365	0
ENSRNOG00000040300	0
ENSRNOG00000058808	0
ENSRNOG00000061316	1
ENSRNOG00000050129	0
ENSRNOG00000040316	0
ENSRNOG00000023659	0
SRR14127850 completed mapping pipeline successfully
