Starting /dee2/code/volunteer_pipeline.sh SRR5030972
    current disk space = 160578486272
    free memory = 73936208 
SRR5030972 SRAfilesize
5b3782e39f363fbfce11d9d9bf08c544  SRR5030972.sra
SRR5030972.sra file validated
SRR5030972 is single end
SRR5030972 is conventional basespace
SRR5030972 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030972_1.fastq
File type	Conventional base calls
Encoding	Sanger / Illumina 1.9
Total Sequences	4000
Sequences flagged as poor quality	0
Sequence length	50
%GC	52
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	32.54275	34.0	31.0	34.0	31.0	34.0
2	32.8295	34.0	31.0	34.0	31.0	34.0
3	32.86075	34.0	31.0	34.0	31.0	34.0
4	36.385	37.0	37.0	37.0	35.0	37.0
5	36.18875	37.0	37.0	37.0	35.0	37.0
6	36.02775	37.0	35.0	37.0	35.0	37.0
7	36.07425	37.0	35.0	37.0	35.0	37.0
8	36.1625	37.0	36.0	37.0	35.0	37.0
9	37.8345	39.0	38.0	39.0	35.0	39.0
10	37.97875	39.0	38.0	39.0	35.0	39.0
11	37.82375	39.0	38.0	39.0	35.0	39.0
12	37.839	39.0	38.0	39.0	35.0	39.0
13	37.8615	39.0	38.0	39.0	35.0	39.0
14	39.12	41.0	39.0	41.0	36.0	41.0
15	39.25925	41.0	39.0	41.0	36.0	41.0
16	39.355	41.0	39.0	41.0	36.0	41.0
17	39.3935	41.0	39.0	41.0	36.0	41.0
18	39.326	41.0	39.0	41.0	36.0	41.0
19	39.041	40.0	39.0	41.0	35.0	41.0
20	39.0325	40.0	39.0	41.0	36.0	41.0
21	39.04275	40.0	39.0	41.0	36.0	41.0
22	39.036	40.0	39.0	41.0	35.0	41.0
23	38.88825	40.0	38.0	41.0	35.0	41.0
24	38.9915	40.0	39.0	41.0	36.0	41.0
25	39.087	41.0	39.0	41.0	36.0	41.0
26	38.772	40.0	38.0	41.0	35.0	41.0
27	38.84475	40.0	38.0	41.0	35.0	41.0
28	38.543	40.0	38.0	41.0	34.0	41.0
29	37.9325	40.0	38.0	41.0	32.0	41.0
30	38.30175	40.0	38.0	41.0	33.0	41.0
31	38.407	40.0	38.0	41.0	34.0	41.0
32	38.31075	40.0	38.0	41.0	34.0	41.0
33	38.47075	40.0	38.0	41.0	34.0	41.0
34	38.411	40.0	38.0	41.0	34.0	41.0
35	38.1835	40.0	38.0	41.0	34.0	41.0
36	37.562	40.0	37.0	41.0	32.0	41.0
37	37.0305	39.0	37.0	41.0	30.0	41.0
38	37.30125	39.0	37.0	41.0	31.0	41.0
39	37.729	40.0	37.0	41.0	33.0	41.0
40	37.8375	40.0	38.0	41.0	33.0	41.0
41	37.839	40.0	38.0	41.0	33.0	41.0
42	37.98675	40.0	38.0	41.0	33.0	41.0
43	38.06	40.0	38.0	41.0	34.0	41.0
44	37.863	40.0	38.0	41.0	33.0	41.0
45	37.621	40.0	37.0	41.0	33.0	41.0
46	37.056	40.0	37.0	41.0	31.0	41.0
47	36.44175	39.0	35.0	41.0	30.0	41.0
48	35.90975	39.0	35.0	41.0	28.0	41.0
49	36.14625	39.0	35.0	40.0	30.0	41.0
50	35.7695	39.0	35.0	40.0	29.0	41.0
>>END_MODULE
>>Per tile sequence quality	pass
#Tile	Base	Mean
1101	1	0.0
1101	2	0.0
1101	3	0.0
1101	4	0.0
1101	5	0.0
1101	6	0.0
1101	7	0.0
1101	8	0.0
1101	9	0.0
1101	10	0.0
1101	11	0.0
1101	12	0.0
1101	13	0.0
1101	14	0.0
1101	15	0.0
1101	16	0.0
1101	17	0.0
1101	18	0.0
1101	19	0.0
1101	20	0.0
1101	21	0.0
1101	22	0.0
1101	23	0.0
1101	24	0.0
1101	25	0.0
1101	26	0.0
1101	27	0.0
1101	28	0.0
1101	29	0.0
1101	30	0.0
1101	31	0.0
1101	32	0.0
1101	33	0.0
1101	34	0.0
1101	35	0.0
1101	36	0.0
1101	37	0.0
1101	38	0.0
1101	39	0.0
1101	40	0.0
1101	41	0.0
1101	42	0.0
1101	43	0.0
1101	44	0.0
1101	45	0.0
1101	46	0.0
1101	47	0.0
1101	48	0.0
1101	49	0.0
1101	50	0.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
13	1.0
14	1.0
15	2.0
16	1.0
17	2.0
18	0.0
19	1.0
20	7.0
21	2.0
22	5.0
23	2.0
24	8.0
25	12.0
26	18.0
27	21.0
28	23.0
29	37.0
30	43.0
31	44.0
32	62.0
33	99.0
34	148.0
35	190.0
36	259.0
37	474.0
38	848.0
39	1690.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	8.231173380035026	26.144608456342254	48.23617713284964	17.38804103077308
2	23.075000000000003	28.275	18.675	29.975
3	24.0	17.8	21.6	36.6
4	33.25	27.224999999999998	14.6	24.925
5	22.35	37.724999999999994	29.175	10.75
6	34.975	13.5	34.025	17.5
7	14.149999999999999	23.799999999999997	21.224999999999998	40.825
8	24.25	28.7	16.5	30.55
9	22.85	33.95	26.724999999999998	16.475
10	22.25	21.375	28.249999999999996	28.125
11	31.574999999999996	9.85	18.3	40.275
12	15.55	16.525000000000002	31.6	36.325
13	30.225	18.275	33.650000000000006	17.849999999999998
14	30.225	32.074999999999996	18.8	18.9
15	35.199999999999996	25.074999999999996	26.6	13.125
16	21.75	19.2	22.1	36.95
17	28.299999999999997	22.3	36.425000000000004	12.975
18	25.45	18.25	29.9	26.400000000000002
19	38.6	13.8	29.45	18.15
20	45.625	14.45	28.625	11.3
21	24.725	21.075	25.974999999999998	28.225
22	30.425	11.924999999999999	48.05	9.6
23	27.224999999999998	12.975	43.925	15.875
24	51.74999999999999	15.299999999999999	26.150000000000002	6.800000000000001
25	49.25	25.724999999999998	15.4	9.625
26	27.700000000000003	45.925	14.6	11.774999999999999
27	14.899999999999999	46.725	25.275	13.100000000000001
28	11.799999999999999	23.075000000000003	48.875	16.25
29	13.0	11.525	56.025000000000006	19.45
30	11.125	6.2	35.625	47.05
31	14.799999999999999	4.9	46.25	34.050000000000004
32	29.575000000000003	4.925	21.9	43.6
33	54.7	9.5	13.3	22.5
34	62.35000000000001	7.449999999999999	16.125	14.075
35	65.5	6.825	18.35	9.325
36	43.0	7.6	35.699999999999996	13.700000000000001
37	43.725	11.4	20.1	24.775
38	23.9	18.425	11.375	46.300000000000004
39	15.024999999999999	24.075	10.575	50.324999999999996
40	15.174999999999999	47.65	11.899999999999999	25.275
41	24.3	49.15	8.75	17.8
42	47.675	29.825000000000003	12.525	9.975000000000001
43	50.875	29.099999999999998	7.9750000000000005	12.049999999999999
44	31.85	47.575	7.175	13.4
45	17.875	49.65	12.775	19.7
46	13.725000000000001	25.575	17.325	43.375
47	8.525	14.374999999999998	39.825	37.275000000000006
48	11.55	12.375	20.7	55.375
49	11.575000000000001	19.45	13.225000000000001	55.75
50	17.125	36.75	14.2	31.924999999999997
>>END_MODULE
>>Per sequence GC content	fail
#GC Content	Count
0	0.0
1	0.5
2	1.0
3	0.5
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.5
10	1.0
11	0.5
12	0.0
13	0.0
14	0.0
15	0.5
16	1.0
17	1.0
18	1.0
19	0.5
20	0.0
21	0.0
22	0.0
23	0.0
24	0.0
25	0.0
26	0.0
27	1.0
28	2.0
29	2.0
30	2.0
31	7.0
32	12.0
33	9.5
34	7.0
35	11.5
36	16.0
37	18.5
38	21.0
39	22.0
40	23.0
41	32.0
42	41.0
43	63.5
44	86.0
45	132.5
46	179.0
47	299.5
48	420.0
49	524.0
50	628.0
51	749.5
52	871.0
53	669.5
54	468.0
55	522.0
56	576.0
57	414.0
58	252.0
59	169.5
60	87.0
61	62.5
62	38.0
63	91.0
64	144.0
65	85.5
66	27.0
67	22.5
68	18.0
69	18.5
70	19.0
71	35.0
72	51.0
73	27.5
74	4.0
75	3.0
76	2.0
77	1.5
78	1.0
79	1.0
80	1.0
81	0.5
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	0.075
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	0.0
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
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
50	4000.0
>>END_MODULE
>>Sequence Duplication Levels	fail
#Total Deduplicated Percentage	37.325
#Duplication Level	Percentage of deduplicated	Percentage of total
1	76.95914266577361	28.725
2	8.506363027461488	6.35
3	4.152712659075687	4.65
4	2.5452109845947755	3.8
5	1.5405224380442064	2.875
6	1.0716677829872738	2.4
7	0.7367716008037508	1.925
8	0.8037508372404554	2.4
9	0.46885465505693236	1.575
>10	2.478231748158071	18.825
>50	0.26791694574681846	5.45
>100	0.46885465505693236	21.025
>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
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	154	3.85	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	143	3.5749999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	118	2.9499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	115	2.875	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	107	2.675	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	102	2.55	RNA PCR Primer, Index 1 (100% over 30bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	102	2.55	No Hit
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	61	1.525	RNA PCR Primer, Index 1 (100% over 27bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCT	54	1.35	RNA PCR Primer, Index 1 (97% over 35bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	52	1.3	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	51	1.275	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	44	1.0999999999999999	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	42	1.05	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	36	0.8999999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	35	0.8750000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	30	0.75	RNA PCR Primer, Index 1 (100% over 33bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	27	0.675	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	27	0.675	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	27	0.675	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	25	0.625	RNA PCR Primer, Index 1 (100% over 26bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	25	0.625	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	25	0.625	RNA PCR Primer, Index 1 (100% over 27bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	24	0.6	RNA PCR Primer, Index 1 (100% over 27bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	23	0.575	No Hit
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTATACATCTC	23	0.575	RNA PCR Primer, Index 39 (100% over 44bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	21	0.525	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	20	0.5	RNA PCR Primer, Index 1 (100% over 29bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	19	0.475	No Hit
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	19	0.475	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	19	0.475	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	19	0.475	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 29bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	15	0.375	RNA PCR Primer, Index 1 (100% over 31bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	15	0.375	RNA PCR Primer, Index 1 (100% over 26bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 30bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	13	0.325	RNA PCR Primer, Index 1 (100% over 30bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	12	0.3	No Hit
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	12	0.3	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	10	0.25	No Hit
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	10	0.25	No Hit
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGCATTCTCGGGTGCC	9	0.22499999999999998	No Hit
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTTGGAATTCTCGGGTGCC	9	0.22499999999999998	No Hit
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	9	0.22499999999999998	No Hit
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TATTGCACTCGTCCCGGCCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	8	0.2	RNA PCR Primer, Index 1 (100% over 25bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	8	0.2	No Hit
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTCTTGGAATTCTCGGGTG	8	0.2	No Hit
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	7	0.17500000000000002	No Hit
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TAGCACCATCTGAAATCGGTTATGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	7	0.17500000000000002	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATGGAATTCTCGGGTGCCAAG	7	0.17500000000000002	No Hit
CTAGACTGAGGCTCCTTGAGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TATTGCACTTGTCCCGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
AAGCCCTTACCCCAAAAAGCATTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGCGGGGCTAGGGCTAACAGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	6	0.15	No Hit
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGACTGGAATTCTCGGGT	6	0.15	No Hit
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGAATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
CTATACGACCTGCTGCCTTTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATGGTTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
AGCCGCCTGGATACCGCAGCTAGGAATAATGGAATTCTCGGGTGCCAAGG	5	0.125	Illumina Small RNA Adapter 2 (100% over 21bp)
TCACAGTGAACCGGTCTCTTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTGTGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGGAATTCTCGGGTGCCAA	5	0.125	No Hit
TCACAGTGAACCGGTCTCTTATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTAT	5	0.125	RNA PCR Primer, Index 2 (97% over 37bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGTGGAATTCTCGGGTGCC	5	0.125	No Hit
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
GTGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCA	5	0.125	No Hit
TGAGATGAAGCACTGTAGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
CACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC	5	0.125	RNA PCR Primer, Index 2 (100% over 34bp)
CGCGACCTCAGATCAGATGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	5	0.125	RNA PCR Primer, Index 1 (100% over 33bp)
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTCTCTGGAATTCTCGGGT	5	0.125	No Hit
TGACTTGATGAAAGTACTTTTGAACCCTTTTCCATCTGATGTGGAATTCT	5	0.125	No Hit
TATTGCACTCGTCCCGGCCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
ACTAATCCTAGCCCTAGCCCTACACAAATATAATTATACTATTATATGGA	5	0.125	No Hit
TCGGATCCGTCTGAGCTTGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TTGTGCTTGATCTAACCATGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
>>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	0.0	0.1	0.0	0.0	0.0
2	0.0	0.1	0.0	0.0	0.0
3	0.0	0.225	0.0	0.0	0.0
4	0.0	0.3	0.0	0.0	0.0
5	0.0	0.325	0.0	0.0	0.0
6	0.0	0.45	0.0	0.0	0.0
7	0.0	1.1	0.0	0.0	0.0
8	0.0	1.35	0.0	0.0	0.0
9	0.0	1.4	0.0	0.0	0.0
10	0.0	1.475	0.0	0.0	0.0
11	0.0	1.625	0.0	0.0	0.0
12	0.0	1.825	0.0	0.0	0.0
13	0.0	2.05	0.0	0.0	0.0
14	0.0	2.65	0.0	0.0	0.0
15	0.0	3.025	0.0	0.0	0.0
16	0.0	4.75	0.0	0.0	0.0
17	0.0	5.4	0.0	0.0	0.0
18	0.0	6.675	0.0	0.0	0.0
19	0.0	7.45	0.0	0.0	0.0
20	0.0	8.925	0.0	0.0	0.0
21	0.0	14.75	0.0	0.0	0.0
22	0.0	26.55	0.0	0.0	0.0
23	0.0	55.95	0.0	0.0	0.0
24	0.0	69.425	0.0	0.0	0.0
25	0.0	74.975	0.0	0.0	0.0
26	0.0	76.5	0.0	0.0	0.0
27	0.0	77.325	0.0	0.0	0.0
28	0.0	77.9	0.0	0.0	0.0
29	0.0	78.575	0.0	0.0	0.0
30	0.0	79.075	0.0	0.0	0.0
31	0.0	79.875	0.0	0.0	0.0
32	0.0	80.925	0.0	0.0	0.0
33	0.0	82.0	0.0	0.0	0.0
34	0.0	85.925	0.0	0.0	0.0
35	0.0	86.95	0.0	0.0	0.0
36	0.0	87.85	0.0	0.0	0.0
37	0.0	88.7	0.0	0.0	0.0
38	0.0	89.175	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TTGCACT	20	6.952051E-4	44.000004	3
CTGAGCT	40	5.315087E-9	44.000004	11
CTTTAAC	20	6.952051E-4	44.000004	12
CCCGGCC	20	6.952051E-4	44.000004	13
ATAGGCT	20	6.952051E-4	44.000004	16
GAGCTTG	40	5.315087E-9	44.000004	13
GGATCCG	40	5.315087E-9	44.000004	3
CCGTCTG	40	5.315087E-9	44.000004	7
TCGGATC	40	5.315087E-9	44.000004	1
CATTCAA	40	5.315087E-9	44.000004	3
CGGATCC	40	5.315087E-9	44.000004	2
TATTGCA	20	6.952051E-4	44.000004	1
ACATTCA	40	5.315087E-9	44.000004	2
GAGTTGG	20	6.952051E-4	44.000004	20
GGATAGG	20	6.952051E-4	44.000004	14
CTTGGCT	20	6.952051E-4	44.000004	16
TAACCTG	20	6.952051E-4	44.000004	15
GTCCCGG	20	6.952051E-4	44.000004	11
ATTGCAC	20	6.952051E-4	44.000004	2
GATCCGT	40	5.315087E-9	44.000004	4
>>END_MODULE
Read 173874 spots for SRR5030972.sra
Written 173874 spots for SRR5030972.sra
Read 173874 spots for SRR5030972.sra
Written 173874 spots for SRR5030972.sra
Read 173874 spots for SRR5030972.sra
Written 173874 spots for SRR5030972.sra
Read 173874 spots for SRR5030972.sra
Written 173874 spots for SRR5030972.sra
Read 173874 spots for SRR5030972.sra
Written 173874 spots for SRR5030972.sra
Read 173874 spots for SRR5030972.sra
Written 173874 spots for SRR5030972.sra
Read 173874 spots for SRR5030972.sra
Written 173874 spots for SRR5030972.sra
Read 173874 spots for SRR5030972.sra
Written 173874 spots for SRR5030972.sra
Read 173874 spots for SRR5030972.sra
Written 173874 spots for SRR5030972.sra
Read 173874 spots for SRR5030972.sra
Written 173874 spots for SRR5030972.sra
Read 173879 spots for SRR5030972.sra
Written 173879 spots for SRR5030972.sra
Read 173874 spots for SRR5030972.sra
Written 173874 spots for SRR5030972.sra
SRR ids: ['SRR5030972.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_e5bxrid4
SRR5030972.sra spots: 2086493
blocks: [[1, 173874], [173875, 347748], [347749, 521622], [521623, 695496], [695497, 869370], [869371, 1043244], [1043245, 1217118], [1217119, 1390992], [1390993, 1564866], [1564867, 1738740], [1738741, 1912614], [1912615, 2086493]]
SRR5030972 file size 360562
SRR5030972 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030972 SRR5030972_1.fastq
Input file:	SRR5030972_1.fastq
trimmed:	SRR5030972-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 (auto detected)
-- minimum overlap length for adapter detection (-k):	inf
-- number of concurrent threads (-t):	12
Wed Mar  4 06:57:08 2020 >> started

Wed Mar  4 06:57:09 2020 >> done (1.340s)
2086493 reads processed; of these:
    137 ( 0.01%) short reads filtered out after trimming by size control
      3 ( 0.00%) empty reads filtered out after trimming by size control
2086353 (99.99%) reads available; of these:
 141894 ( 6.80%) trimmed reads available after processing
1944459 (93.20%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     43	  0.00%
 19	     66	  0.00%
 20	    103	  0.00%
 21	    145	  0.01%
 22	    235	  0.01%
 23	    295	  0.01%
 24	    314	  0.02%
 25	    402	  0.02%
 26	    323	  0.02%
 27	    519	  0.02%
 28	    564	  0.03%
 29	    805	  0.04%
 30	    561	  0.03%
 31	    608	  0.03%
 32	    650	  0.03%
 33	    873	  0.04%
 34	   1162	  0.06%
 35	   1988	  0.10%
 36	   1929	  0.09%
 37	   1884	  0.09%
 38	   2030	  0.10%
 39	   2335	  0.11%
 40	   2547	  0.12%
 41	   2816	  0.13%
 42	   3875	  0.19%
 43	   5273	  0.25%
 44	   7388	  0.35%
 45	   9484	  0.45%
 46	  14826	  0.71%
 47	  15080	  0.72%
 48	  27144	  1.30%
 49	  35627	  1.71%
 50	1944459	 93.20%
2086353 reads passed initial QC


criterion=sequence-density
sequence-density=89.01
sequence-density-rank=1
fanout-score=20.08
fanout-score-rank=1
prefix-density=91.13
prefix-fanout=19.6
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTATACATCTCGTATGCC


criterion=fanout-score
sequence-density=89.01
sequence-density-rank=1
fanout-score=20.08
fanout-score-rank=1
prefix-density=91.13
prefix-fanout=19.6
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTATACATCTCGTATGCC
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:	skewer -l 18 -t 12 -x TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTATACATCTCGTATGCC -o SRR5030972 -
Input file:	STDIN
trimmed:	SRR5030972-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTATACATCTCGTATGCC
-- 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):		Unknown format (auto detected)
-- minimum overlap length for adapter detection (-k):	3
-- number of concurrent threads (-t):	12
Wed Mar  4 06:57:21 2020 >> started

Wed Mar  4 06:57:25 2020 >> done (3.104s)
2039990 reads processed; of these:
 144118 ( 7.06%) short reads filtered out after trimming by size control
   6982 ( 0.34%) empty reads filtered out after trimming by size control
1888890 (92.59%) reads available; of these:
1832655 (97.02%) trimmed reads available after processing
  56235 ( 2.98%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  12132	  0.64%
 19	  24649	  1.30%
 20	 116087	  6.15%
 21	 233378	 12.36%
 22	 620988	 32.88%
 23	 270154	 14.30%
 24	 114639	  6.07%
 25	  30861	  1.63%
 26	  16427	  0.87%
 27	  13731	  0.73%
 28	  15608	  0.83%
 29	  10995	  0.58%
 30	  17403	  0.92%
 31	  18305	  0.97%
 32	  24789	  1.31%
 33	  89995	  4.76%
 34	  25518	  1.35%
 35	  19725	  1.04%
 36	  23104	  1.22%
 37	  10185	  0.54%
 38	  10854	  0.57%
 39	  10429	  0.55%
 40	  16116	  0.85%
 41	  20340	  1.08%
 42	  21856	  1.16%
 43	  14919	  0.79%
 44	  10404	  0.55%
 45	  12811	  0.68%
 46	   9731	  0.52%
 47	   6993	  0.37%
 48	    625	  0.03%
 49	   1117	  0.06%
 50	  44022	  2.33%


criterion=sequence-density
sequence-density=7.47
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=13
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTT


criterion=fanout-score
sequence-density=2.19
sequence-density-rank=5
fanout-score=20.23
fanout-score-rank=1
prefix-density=2.26
prefix-fanout=19.6
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTATACATCTCGTATGC
                                 Started job on |	Mar 04 06:57:46
                             Started mapping on |	Mar 04 06:57:46
                                    Finished on |	Mar 04 06:58:12
       Mapping speed, Million of reads per hour |	267.96

                          Number of input reads |	1935253
                      Average input read length |	26
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1019117
                        Uniquely mapped reads % |	52.66%
                          Average mapped length |	23.95
                       Number of splices: Total |	1102
            Number of splices: Annotated (sjdb) |	324
                       Number of splices: GT/AG |	1047
                       Number of splices: GC/AG |	16
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	39
                      Mismatch rate per base, % |	0.16%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.68
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.00
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	653818
             % of reads mapped to multiple loci |	33.78%
        Number of reads mapped to too many loci |	41504
             % of reads mapped to too many loci |	2.14%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	10.78%
                     % of reads unmapped: other |	0.63%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	262318	262318	262318
N_multimapping	653818	653818	653818
N_noFeature	41675	52968	686906
N_ambiguous	588989	305857	8183
UnstrandedReadsAssigned:388453 PositiveStrandReadsAssigned:660292 NegativeStrandReadsAssigned:324028
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=21 echo kmer=19
SRR5030972 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: 109,282
[index] number of k-mers: 92,755,666
[index] number of equivalence classes: 769,752
[quant] running in single-end mode
[quant] will process file 1: SRR5030972-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 1,935,253 reads, 510,379 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,124 rounds

 109283 SRR5030972.ke.tsv
  52636 SRR5030972.se.tsv
 161919 total
==> SRR5030972.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
ENSMUST00000177564.1	16	4.59059	0	0
ENSMUST00000196221.1	9	3.70903	0	0
ENSMUST00000179664.1	11	4.02702	0	0
ENSMUST00000178537.1	12	4.16231	0	0
ENSMUST00000178862.1	14	4.39563	0	0
ENSMUST00000179520.1	11	4.02702	0	0
ENSMUST00000179883.1	16	4.59059	0	0
ENSMUST00000195858.1	10	3.87667	0	0
ENSMUST00000179932.1	12	4.16231	0	0

==> SRR5030972.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030972 completed mapping pipeline successfully
