Starting /dee2/code/volunteer_pipeline.sh SRR14127856
    current disk space = 639393484
    free memory = 195613992 
SRR14127856 SRAfilesize
b23ec20ac7139653dec7555d79823228  SRR14127856.sra
SRR14127856.sra file validated
SRR14127856 is single end
SRR14127856 is conventional basespace
SRR14127856 read1 length is 51 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR14127856_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	49
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	34.8215	37.0	37.0	37.0	25.0	37.0
2	35.654	37.0	37.0	37.0	37.0	37.0
3	35.935	37.0	37.0	37.0	37.0	37.0
4	36.2375	37.0	37.0	37.0	37.0	37.0
5	36.393	37.0	37.0	37.0	37.0	37.0
6	36.4285	37.0	37.0	37.0	37.0	37.0
7	36.3515	37.0	37.0	37.0	37.0	37.0
8	36.6375	37.0	37.0	37.0	37.0	37.0
9	36.4875	37.0	37.0	37.0	37.0	37.0
10	36.434	37.0	37.0	37.0	37.0	37.0
11	36.465	37.0	37.0	37.0	37.0	37.0
12	36.603	37.0	37.0	37.0	37.0	37.0
13	36.506	37.0	37.0	37.0	37.0	37.0
14	36.4585	37.0	37.0	37.0	37.0	37.0
15	36.418	37.0	37.0	37.0	37.0	37.0
16	36.393	37.0	37.0	37.0	37.0	37.0
17	36.3655	37.0	37.0	37.0	37.0	37.0
18	36.32	37.0	37.0	37.0	37.0	37.0
19	36.514	37.0	37.0	37.0	37.0	37.0
20	36.4305	37.0	37.0	37.0	37.0	37.0
21	36.3995	37.0	37.0	37.0	37.0	37.0
22	36.658	37.0	37.0	37.0	37.0	37.0
23	36.5005	37.0	37.0	37.0	37.0	37.0
24	36.488	37.0	37.0	37.0	37.0	37.0
25	36.5125	37.0	37.0	37.0	37.0	37.0
26	36.47	37.0	37.0	37.0	37.0	37.0
27	36.483	37.0	37.0	37.0	37.0	37.0
28	36.4615	37.0	37.0	37.0	37.0	37.0
29	36.4055	37.0	37.0	37.0	37.0	37.0
30	36.641	37.0	37.0	37.0	37.0	37.0
31	36.5955	37.0	37.0	37.0	37.0	37.0
32	36.5055	37.0	37.0	37.0	37.0	37.0
33	36.5535	37.0	37.0	37.0	37.0	37.0
34	36.385	37.0	37.0	37.0	37.0	37.0
35	36.6065	37.0	37.0	37.0	37.0	37.0
36	36.656	37.0	37.0	37.0	37.0	37.0
37	36.649	37.0	37.0	37.0	37.0	37.0
38	36.5615	37.0	37.0	37.0	37.0	37.0
39	36.4625	37.0	37.0	37.0	37.0	37.0
40	36.4915	37.0	37.0	37.0	37.0	37.0
41	36.4945	37.0	37.0	37.0	37.0	37.0
42	36.493	37.0	37.0	37.0	37.0	37.0
43	36.3825	37.0	37.0	37.0	37.0	37.0
44	36.335	37.0	37.0	37.0	37.0	37.0
45	36.677	37.0	37.0	37.0	37.0	37.0
46	36.736	37.0	37.0	37.0	37.0	37.0
47	36.5	37.0	37.0	37.0	37.0	37.0
48	36.481	37.0	37.0	37.0	37.0	37.0
49	36.5665	37.0	37.0	37.0	37.0	37.0
50	36.4345	37.0	37.0	37.0	37.0	37.0
51	36.4735	37.0	37.0	37.0	37.0	37.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
24	1.0
25	1.0
26	2.0
27	2.0
28	12.0
29	15.0
30	31.0
31	35.0
32	57.0
33	92.0
34	91.0
35	159.0
36	1372.0
37	2130.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	24.825	9.025	61.675000000000004	4.475
2	46.227364185110666	14.537223340040242	10.764587525150905	28.470824949698187
3	14.000000000000002	64.275	6.1	15.625
4	46.175	14.025000000000002	23.925	15.875
5	13.525	46.575	31.525	8.375
6	34.55	10.6	48.475	6.375
7	60.199999999999996	16.0	12.275	11.525
8	13.8	45.675	36.7	3.8249999999999997
9	29.049999999999997	41.725	17.575	11.65
10	59.45	20.025000000000002	13.225000000000001	7.3
11	18.525	10.25	27.6	43.625
12	9.049999999999999	42.675000000000004	32.0	16.275000000000002
13	5.65	16.85	12.775	64.725
14	15.525	31.35	47.199999999999996	5.925
15	75.64999999999999	14.975	5.1	4.275
16	5.8500000000000005	20.9	66.975	6.275
17	27.500000000000004	42.825	20.0	9.675
18	63.824999999999996	10.875	15.15	10.15
19	15.775	9.0	41.075	34.150000000000006
20	23.0	26.724999999999998	44.925	5.35
21	33.95	15.2	16.575	34.275
22	15.225	45.050000000000004	33.4	6.325
23	17.95	67.65	8.475000000000001	5.925
24	41.375	26.275	28.9	3.45
25	12.775	43.375	34.55	9.3
26	12.975	12.7	39.425	34.9
27	23.025000000000002	7.3	29.049999999999997	40.625
28	55.65	10.95	3.65	29.75
29	68.77499999999999	24.4	1.625	5.2
30	19.925	56.05	1.675	22.35
31	20.75	57.49999999999999	3.8249999999999997	17.925
32	48.15	34.375	10.85	6.625
33	32.7	55.85	2.25	9.2
34	51.925	24.474999999999998	3.9	19.7
35	11.475	30.725	8.924999999999999	48.875
36	7.000000000000001	48.875	11.975	32.15
37	14.05	25.324999999999996	2.875	57.75
38	25.15	46.050000000000004	3.2750000000000004	25.525
39	26.700000000000003	19.975	9.775	43.55
40	42.525	21.7	16.900000000000002	18.875
41	19.625	15.65	45.5	19.225
42	23.325000000000003	12.4	23.325000000000003	40.949999999999996
43	23.225	22.375	41.175	13.225000000000001
44	48.949999999999996	26.875	10.225	13.950000000000001
45	12.15	60.525	5.525	21.8
46	4.875	60.675000000000004	8.774999999999999	25.674999999999997
47	3.25	20.075000000000003	16.125	60.550000000000004
48	3.675	17.025000000000002	39.35	39.95
49	9.85	10.75	12.65	66.75
50	17.5	16.7	13.075000000000001	52.725
51	16.150000000000002	41.575	20.625	21.65
>>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	0.5
6	1.0
7	1.0
8	1.0
9	0.5
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	0.5
26	0.5
27	0.0
28	0.5
29	1.0
30	0.5
31	0.0
32	0.5
33	1.0
34	1.0
35	1.0
36	3.5
37	6.0
38	4.0
39	2.0
40	17.0
41	32.0
42	71.0
43	110.0
44	208.0
45	306.0
46	450.5
47	595.0
48	900.0
49	1205.0
50	1125.5
51	1046.0
52	743.0
53	440.0
54	274.0
55	108.0
56	89.0
57	70.0
58	58.5
59	47.0
60	31.0
61	15.0
62	10.0
63	5.0
64	4.0
65	3.0
66	3.5
67	4.0
68	2.0
69	0.0
70	0.0
71	0.0
72	0.0
73	0.0
74	0.0
75	0.0
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	0.0
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	28.925
#Duplication Level	Percentage of deduplicated	Percentage of total
1	76.14520311149523	22.025
2	10.717372515125325	6.2
3	3.197925669835782	2.775
4	1.728608470181504	2.0
5	1.4693171996542784	2.125
6	0.7778738115816767	1.35
7	0.5185825410544511	1.05
8	0.6914433880726015	1.6
9	0.17286084701815038	0.44999999999999996
>10	3.543647363872083	20.549999999999997
>50	0.6050129645635264	10.775
>100	0.34572169403630076	15.225
>500	0.08643042350907519	13.875000000000002
>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	555	13.875000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTAGATCGGAAGAGCACACGT	254	6.35	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCAGATCGGAAGAGCACACGTC	127	3.175	No Hit
TGAGATGAAGCACTGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAG	126	3.15	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TGAGATGAAGCACTGTAGCTAGATCGGAAGAGCACACGTCTGAACTCCAGT	102	2.55	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
TGAGATGAAGCACTGTAGCTCCAGATCGGAAGAGCACACGTCTGAACTCCA	69	1.725	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TCAGTGCACTACAGAACTTTGTAGATCGGAAGAGCACACGTCTGAACTCCA	67	1.675	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TAGCTTATCAGACTGATGTTGAAGATCGGAAGAGCACACGTCTGAACTCCA	67	1.675	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTAGATCGGAAGAGCACACGTCTGAACTCCA	62	1.55	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TGAGATGAAGCACTGTAGCTCTTAGATCGGAAGAGCACACGTCTGAACTCC	59	1.4749999999999999	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCTAGATCGGAAGAGCACACGTC	56	1.4000000000000001	No Hit
TGAGGTAGTAGTTTGTGCTGTTAGATCGGAAGAGCACACGTCTGAACTCCA	51	1.275	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TGAGATGAAGCACTGTAGCTCAAGATCGGAAGAGCACACGTCTGAACTCCA	48	1.2	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCCAGATCGGAAGAGCACACGT	47	1.175	No Hit
AACCCGTAGATCCGATCTTGTAGATCGGAAGAGCACACGTCTGAACTCCAG	44	1.0999999999999999	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TAGCTTATCAGACTGATGTTGACAGATCGGAAGAGCACACGTCTGAACTCC	38	0.95	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
TAGCTTATCAGACTGATGTTGAGATCGGAAGAGCACACGTCTGAACTCCAG	37	0.9249999999999999	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TGAGGTAGTAGATTGTATAGTTAGATCGGAAGAGCACACGTCTGAACTCCA	37	0.9249999999999999	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCAGATCGGAAGAGCACACGTCT	36	0.8999999999999999	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
AAGAAAGTATGCAAGAACTAGATCGGAAGAGCACACGTCTGAACTCCAGTC	34	0.8500000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCAGATCGGAAGAGCACA	33	0.8250000000000001	No Hit
TGAGATGAAGCACTGTAGCTTAGATCGGAAGAGCACACGTCTGAACTCCAG	28	0.7000000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TGAGGTAGTAGTTTGTACAGTTAGATCGGAAGAGCACACGTCTGAACTCCA	28	0.7000000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCAAGATCGGAAGAGCACACGT	25	0.625	No Hit
GGAGATGAAGCACTGTAGCTCTAGATCGGAAGAGCACACGTCTGAACTCCA	22	0.5499999999999999	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TTCACAGTGGCTAAGTTCTGCAGATCGGAAGAGCACACGTCTGAACTCCAG	21	0.525	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCAAGATCGGAAGAGCACACGTC	19	0.475	No Hit
TGAGATGAAGCACTGTAGCCAGATCGGAAGAGCACACGTCTGAACTCCAGT	18	0.44999999999999996	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
TTCAAGTAATTCAGGATAGGTTAGATCGGAAGAGCACACGTCTGAACTCCA	17	0.42500000000000004	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TTCAAGTAATCCAGGATAGGAGATCGGAAGAGCACACGTCTGAACTCCAGT	15	0.375	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
TGGAATGTAAAGAAGTATGTATAGATCGGAAGAGCACACGTCTGAACTCCA	15	0.375	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TCAGTGCACTACAGAACTTTGCAGATCGGAAGAGCACACGTCTGAACTCCA	15	0.375	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TAGCTTATCAGACTGATGTTGACTAGATCGGAAGAGCACACGTCTGAACTC	15	0.375	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGTAGATCGGAAGAGCACACGTCT	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
TTCAAGTAATCCAGGATAGGCCAGATCGGAAGAGCACACGTCTGAACTCCA	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TGAGGTAGTAGGTTGTATGGTTAGATCGGAAGAGCACACGTCTGAACTCCA	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TGAGAACTGAATTCCATGGGTTAGATCGGAAGAGCACACGTCTGAACTCCA	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TGAGGTAGTAGGTTGTATAGTTAGATCGGAAGAGCACACGTCTGAACTCCA	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TACCCTGTAGAACCGAATTTGTAGATCGGAAGAGCACACGTCTGAACTCCA	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCTAGATCGGAAGAGCACA	12	0.3	No Hit
TTCACAGTGGCTAAGTTCTGTAGATCGGAAGAGCACACGTCTGAACTCCAG	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
AACCCGTAGATCCGATCTTGTGAAGATCGGAAGAGCACACGTCTGAACTCC	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
TGAGGTAGTAGTTTGTGCTGTCAGATCGGAAGAGCACACGTCTGAACTCCA	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GTCCAGTTTTCCCAGGAATCCCTAGATCGGAAGAGCACACGTCTGAACTCC	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
TGTAAACATCCTCGACTGGAAGAGATCGGAAGAGCACACGTCTGAACTCCA	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCGAGATCGGAAGAGCACACGT	11	0.27499999999999997	No Hit
GCATGGGTGGTTCAGTGGTAGAATTCTCGCCAGATCGGAAGAGCACACGTC	11	0.27499999999999997	No Hit
GCATGGGTGGTTCAGTGGTAGAATTCTCGCCTAGATCGGAAGAGCACACGT	11	0.27499999999999997	No Hit
TCGTACCGTGAGTAATAATGCAGATCGGAAGAGCACACGTCTGAACTCCAG	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GGAGATGAAGCACTGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAG	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
ACAGTAGTCTGCACATTGGTTAGATCGGAAGAGCACACGTCTGAACTCCAG	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TAGCACCATCTGAAATCGGTTAGATCGGAAGAGCACACGTCTGAACTCCAG	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TGAGATGAAGCACTGTAGCAAGATCGGAAGAGCACACGTCTGAACTCCAGT	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
TGGAATGTAAAGAAGTATGTAGATCGGAAGAGCACACGTCTGAACTCCAGT	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
TGAGATGAAGCACTGTAGCTCGAGATCGGAAGAGCACACGTCTGAACTCCA	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TGAGATGAAGCACTGTAGCTAAGATCGGAAGAGCACACGTCTGAACTCCAG	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TGAGATGAAGCACTGTAGCTCTCAGATCGGAAGAGCACACGTCTGAACTCC	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
TAGCTTATCAGACTGATGTTAAGATCGGAAGAGCACACGTCTGAACTCCAG	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
CCCAGTGTTCAGACTACCTGTTAGATCGGAAGAGCACACGTCTGAACTCCA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTAGATCGGAAGAGCACACGTCTGAACTCCAG	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TGTAAACATCCTTGACTGGAAGCTAGATCGGAAGAGCACACGTCTGAACTC	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
TACCCTGTAGATCCGAATTTGTAGATCGGAAGAGCACACGTCTGAACTCCA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TGTAAACATCCCCGACTGGAAGCTAGATCGGAAGAGCACACGTCTGAACTC	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
AACCCGTAGATCCGATCTTGTGAGATCGGAAGAGCACACGTCTGAACTCCA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TAACACTGTCTGGTAACGATGTAGATCGGAAGAGCACACGTCTGAACTCCA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TCGTACCGTGAGTAATAATGAGATCGGAAGAGCACACGTCTGAACTCCAGT	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
AAGAAAGTATGCAAGAACCAGATCGGAAGAGCACACGTCTGAACTCCAGTC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
TGAGGTAGTAGTTTGTGCTGTTAAGATCGGAAGAGCACACGTCTGAACTCC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
TGTAAACATCCTCGACTGGAAGCTAGATCGGAAGAGCACACGTCTGAACTC	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)
TTCAAGTAATCCAGGATAGGCTTAGATCGGAAGAGCACACGTCTGAACTCC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
TGTAAACATCCTCGACTGGAAAGATCGGAAGAGCACACGTCTGAACTCCAG	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCAGATCGGAAGAGCACAC	6	0.15	No Hit
TGAGATGAAGCACTGTAGCTTTAGATCGGAAGAGCACACGTCTGAACTCCA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TGAGGTAGTAGTTTGTGCTGTTTAGATCGGAAGAGCACACGTCTGAACTCC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCAGATCGGAAGAGCACACGTCTGAACTCCAG	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TCCCTGAGACCCTAACTTGTGAAGATCGGAAGAGCACACGTCTGAACTCCA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GCCCGGCTAGCTCAGTCGGTAGAGCATGAGACTAGATCGGAAGAGCACACG	6	0.15	No Hit
TGTAAACATCCTCGACTGGAAGCAGATCGGAAGAGCACACGTCTGAACTCC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
TCGTACCGTGAGTAATAATGCGAGATCGGAAGAGCACACGTCTGAACTCCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TGAGGTAGTAGGTTGTGTGGTTAGATCGGAAGAGCACACGTCTGAACTCCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TAGCTTATCAGACTGATGTTAGATCGGAAGAGCACACGTCTGAACTCCAGT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
TTCACAGTGGCTAAGTTCTGAGATCGGAAGAGCACACGTCTGAACTCCAGT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
TGTAAACATCCTCGACTGGAAGATCGGAAGAGCACACGTCTGAACTCCAGT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
TCAGTGCATGACAGAACTTGGAGATCGGAAGAGCACACGTCTGAACTCCAG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TCCTTCATTCCACCGGAGTCTGTAGATCGGAAGAGCACACGTCTGAACTCC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
TAGCTTATCAGACTGATGTTGACAAGATCGGAAGAGCACACGTCTGAACTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
TGAGATGAAGCACTGTAGCTTTTAGATCGGAAGAGCACACGTCTGAACTCC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
GTCCAGTTTTCCCAGGAATCCAGATCGGAAGAGCACACGTCTGAACTCCAG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GCATTGTGGTTCAGTGGTAGAATTCTCGCCTAGATCGGAAGAGCACACGTC	5	0.125	No Hit
GTGAAATGTTTAGGACCACTAGAGATCGGAAGAGCACACGTCTGAACTCCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTAGATCGGAAGAGCACACG	5	0.125	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGAAGATCGGAAGAGCACACGTCT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
CGCGACCTCAGATCAGACGTAGATCGGAAGAGCACACGTCTGAACTCCAGT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
TGGCTCAGTTCAGCAGGAACAGTAGATCGGAAGAGCACACGTCTGAACTCC	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	0.125	0.0	0.0	0.0	0.0
2	0.125	0.0	0.0	0.0	0.0
3	0.125	0.0	0.0	0.0	0.0
4	0.125	0.0	0.0	0.0	0.0
5	0.125	0.0	0.0	0.0	0.0
6	0.125	0.0	0.0	0.0	0.0
7	0.15	0.0	0.0	0.0	0.0
8	0.15	0.0	0.0	0.0	0.0
9	0.25	0.0	0.0	0.0	0.0
10	0.325	0.0	0.0	0.0	0.0
11	0.625	0.0	0.0	0.0	0.0
12	0.825	0.0	0.0	0.0	0.0
13	1.05	0.0	0.0	0.0	0.0
14	1.625	0.0	0.0	0.0	0.0
15	2.075	0.0	0.0	0.0	0.0
16	2.8	0.0	0.0	0.0	0.0
17	3.35	0.0	0.0	0.0	0.0
18	3.825	0.0	0.0	0.0	0.0
19	4.45	0.0	0.0	0.0	0.0
20	6.275	0.0	0.0	0.0	0.0
21	12.6	0.0	0.0	0.0	0.0
22	26.4	0.0	0.0	0.0	0.0
23	63.425	0.0	0.0	0.0	0.0
24	71.425	0.0	0.0	0.0	0.0
25	73.95	0.0	0.0	0.0	0.0
26	74.4	0.0	0.0	0.0	0.0
27	74.625	0.0	0.0	0.0	0.0
28	75.1	0.0	0.0	0.0	0.0
29	75.475	0.0	0.0	0.0	0.0
30	75.725	0.0	0.0	0.0	0.0
31	77.725	0.0	0.0	0.0	0.0
32	84.425	0.0	0.0	0.0	0.0
33	94.375	0.0	0.0	0.0	0.0
34	95.2	0.0	0.0	0.0	0.0
35	95.75	0.0	0.0	0.0	0.0
36	97.325	0.0	0.0	0.0	0.0
37	97.525	0.0	0.0	0.0	0.0
38	97.7	0.0	0.0	0.0	0.0
39	97.75	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TAGCTCT	115	0.0	45.000004	16
CTACAGA	20	6.222983E-4	45.0	9
TGCACTA	20	6.222983E-4	45.0	5
GAGGTAG	20	6.222983E-4	45.0	2
GTAGAAT	80	0.0	45.0	18
ACTGTAG	160	0.0	45.0	12
TGGTTCA	80	0.0	45.0	8
AGCTCTA	105	0.0	45.0	17
GTGCACT	20	6.222983E-4	45.0	4
ACAGAAC	20	6.222983E-4	45.0	11
TACAGAA	20	6.222983E-4	45.0	10
CGCCTAG	25	3.236105E-5	45.0	28
GCCTAGA	25	3.236105E-5	45.0	29
ATTGGTG	70	0.0	45.0	3
AGTGGTA	80	0.0	45.0	14
GAAGCAC	160	0.0	45.0	7
TAGCTCA	20	6.222983E-4	45.0	16
CGCCAGA	20	6.222983E-4	45.0	28
ATGAAGC	160	0.0	45.0	5
CACTGTA	160	0.0	45.0	11
>>END_MODULE
Rejected 2130714 READS because READLEN < 1
Read 2130714 spots for SRR14127856.sra
Written 2130714 spots for SRR14127856.sra
Rejected 2130714 READS because READLEN < 1
Read 2130714 spots for SRR14127856.sra
Written 2130714 spots for SRR14127856.sra
Rejected 2130714 READS because READLEN < 1
Read 2130714 spots for SRR14127856.sra
Written 2130714 spots for SRR14127856.sra
Rejected 2130714 READS because READLEN < 1
Read 2130714 spots for SRR14127856.sra
Written 2130714 spots for SRR14127856.sra
Rejected 2130714 READS because READLEN < 1
Read 2130714 spots for SRR14127856.sra
Written 2130714 spots for SRR14127856.sra
Rejected 2130714 READS because READLEN < 1
Read 2130714 spots for SRR14127856.sra
Written 2130714 spots for SRR14127856.sra
Rejected 2130714 READS because READLEN < 1
Read 2130714 spots for SRR14127856.sra
Written 2130714 spots for SRR14127856.sra
Rejected 2130715 READS because READLEN < 1
Read 2130715 spots for SRR14127856.sra
Written 2130715 spots for SRR14127856.sra
SRR ids: ['SRR14127856.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_50fvjl1q
SRR14127856.sra spots: 17045713
blocks: [[1, 2130714], [2130715, 4261428], [4261429, 6392142], [6392143, 8522856], [8522857, 10653570], [10653571, 12784284], [12784285, 14914998], [14914999, 17045713]]
SRR14127856 file size 2425292
SRR14127856 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 SRR14127856 SRR14127856_1.fastq
Input file:	SRR14127856_1.fastq
trimmed:	SRR14127856-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 20:20:07 2025 >> started

Tue Dec  2 20:20:15 2025 >> done (7.987s)
17045713 reads processed; of these:
  670891 ( 3.94%) short reads filtered out after trimming by size control
   21133 ( 0.12%) empty reads filtered out after trimming by size control
16353689 (95.94%) reads available; of these:
  531120 ( 3.25%) trimmed reads available after processing
15822569 (96.75%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  107629	  0.66%
 19	  423491	  2.59%
 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	15822569	 96.75%
16353689 reads passed initial QC


criterion=sequence-density
sequence-density=94.71
sequence-density-rank=1
fanout-score=16.32
fanout-score-rank=1
prefix-density=95.30
prefix-fanout=16.2
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCTTGTAATCTCGTATGCCGTCT


criterion=fanout-score
sequence-density=94.71
sequence-density-rank=1
fanout-score=16.32
fanout-score-rank=1
prefix-density=95.30
prefix-fanout=16.2
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCTTGTAATCTCGTATGCCGTCT
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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCTTGTAATCTCGTATGCCGTCT -o SRR14127856 -
Input file:	STDIN
trimmed:	SRR14127856-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCTTGTAATCTCGTATGCCGTCT
-- 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 20:20:33 2025 >> started

Tue Dec  2 20:20:49 2025 >> done (15.406s)
16009401 reads processed; of these:
    5682 ( 0.04%) short reads filtered out after trimming by size control
      43 ( 0.00%) empty reads filtered out after trimming by size control
16003676 (99.96%) reads available; of these:
15421977 (96.37%) trimmed reads available after processing
  581699 ( 3.63%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  103521	  0.65%
 19	  421195	  2.63%
 20	 1002172	  6.26%
 21	 2369238	 14.80%
 22	 6345840	 39.65%
 23	 1429488	  8.93%
 24	  410819	  2.57%
 25	   65728	  0.41%
 26	   50054	  0.31%
 27	   51950	  0.32%
 28	   67248	  0.42%
 29	   55065	  0.34%
 30	  328970	  2.06%
 31	 1085811	  6.78%
 32	 1543757	  9.65%
 33	  120868	  0.76%
 34	  130423	  0.81%
 35	  215768	  1.35%
 36	   30736	  0.19%
 37	   35666	  0.22%
 38	   21818	  0.14%
 39	   14350	  0.09%
 40	    9511	  0.06%
 41	    4487	  0.03%
 42	    3657	  0.02%
 43	    4420	  0.03%
 44	    7412	  0.05%
 45	    4456	  0.03%
 46	     673	  0.00%
 47	     409	  0.00%
 48	    1239	  0.01%
 49	       0	  0.00%
 50	       0	  0.00%
 51	   66927	  0.42%


criterion=sequence-density
sequence-density=16.81
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=9
prefix-density=0.00
prefix-fanout=1.0
sequence=GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGC


criterion=fanout-score
sequence-density=0.38
sequence-density-rank=18
fanout-score=88.00
fanout-score-rank=1
prefix-density=32.21
prefix-fanout=1.0
sequence=GCACTGTAGCTTTT
                                 Started job on |	Dec 02 20:21:04
                             Started mapping on |	Dec 02 20:21:04
                                    Finished on |	Dec 02 20:22:03
       Mapping speed, Million of reads per hour |	997.50

                          Number of input reads |	16347964
                      Average input read length |	24
                                    UNIQUE READS:
                   Uniquely mapped reads number |	10002298
                        Uniquely mapped reads % |	61.18%
                          Average mapped length |	21.56
                       Number of splices: Total |	10010
            Number of splices: Annotated (sjdb) |	4773
                       Number of splices: GT/AG |	9713
                       Number of splices: GC/AG |	92
                       Number of splices: AT/AC |	2
               Number of splices: Non-canonical |	203
                      Mismatch rate per base, % |	0.10%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.47
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.34
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	2999621
             % of reads mapped to multiple loci |	18.35%
        Number of reads mapped to too many loci |	2952211
             % of reads mapped to too many loci |	18.06%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	2.36%
                     % of reads unmapped: other |	0.05%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	3346045	3346045	3346045
N_multimapping	2999621	2999621	2999621
N_noFeature	232215	797055	9428333
N_ambiguous	186969	177831	13
UnstrandedReadsAssigned:9583114 PositiveStrandReadsAssigned:9027412 NegativeStrandReadsAssigned:573952
Dataset is classified positive stranded
MeadianReadLen=22 20thPercentileLength=21 echo kmer=19
SRR14127856 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: SRR14127856-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 16,347,964 reads, 381,746 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 820 rounds

  31716 SRR14127856.ke.tsv
  32883 SRR14127856.se.tsv
  64599 total
==> SRR14127856.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
ENSRNOT00000047550.4	955	856	2424	4265.53
ENSRNOT00000040993.4	1039	940	1860	2980.57
ENSRNOT00000050156.3	1545	1446	13045	13589.1
ENSRNOT00000043693.3	684	585	3221	8293.72
ENSRNOT00000046201.3	204	105	640	9181.32
ENSRNOT00000046108.3	681	582	2341	6058.89
ENSRNOT00000049683.3	784	685	3268	7186.31
ENSRNOT00000041241.3	348	249	290	1754.34
ENSRNOT00000044582.3	297	198	501	3811.42

==> SRR14127856.se.tsv <==
ENSRNOG00000046319	0
ENSRNOG00000047964	0
ENSRNOG00000050370	0
ENSRNOG00000032365	0
ENSRNOG00000040300	0
ENSRNOG00000058808	0
ENSRNOG00000061316	2
ENSRNOG00000050129	0
ENSRNOG00000040316	0
ENSRNOG00000023659	0
SRR14127856 completed mapping pipeline successfully
