Starting /dee2/code/volunteer_pipeline.sh SRR5030860
    current disk space = 160659390464
    free memory = 56711852 
SRR5030860 SRAfilesize
834326d4d4530c5da805057c97e7d881  SRR5030860.sra
SRR5030860.sra file validated
SRR5030860 is single end
SRR5030860 is conventional basespace
SRR5030860 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030860_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	32.48325	34.0	31.0	34.0	31.0	34.0
2	32.72925	34.0	31.0	34.0	31.0	34.0
3	32.8935	34.0	31.0	34.0	31.0	34.0
4	36.264	37.0	37.0	37.0	35.0	37.0
5	36.348	37.0	37.0	37.0	35.0	37.0
6	36.1765	37.0	37.0	37.0	35.0	37.0
7	36.11225	37.0	35.0	37.0	35.0	37.0
8	36.20675	37.0	36.0	37.0	35.0	37.0
9	37.88625	39.0	38.0	39.0	35.0	39.0
10	38.01075	39.0	38.0	39.0	35.0	39.0
11	37.91875	39.0	38.0	39.0	35.0	39.0
12	37.93275	39.0	38.0	39.0	35.0	39.0
13	37.97875	39.0	38.0	39.0	35.0	39.0
14	39.302	41.0	39.0	41.0	36.0	41.0
15	39.26225	41.0	39.0	41.0	36.0	41.0
16	39.30475	41.0	39.0	41.0	36.0	41.0
17	39.43275	41.0	39.0	41.0	36.0	41.0
18	39.41875	41.0	39.0	41.0	36.0	41.0
19	39.26175	41.0	39.0	41.0	36.0	41.0
20	39.14	41.0	39.0	41.0	36.0	41.0
21	39.30725	41.0	39.0	41.0	36.0	41.0
22	39.20675	41.0	39.0	41.0	36.0	41.0
23	38.976	41.0	39.0	41.0	35.0	41.0
24	38.8275	40.0	38.0	41.0	35.0	41.0
25	39.07575	41.0	39.0	41.0	35.0	41.0
26	39.119	41.0	39.0	41.0	35.0	41.0
27	39.13675	41.0	39.0	41.0	36.0	41.0
28	38.95075	40.0	38.0	41.0	35.0	41.0
29	38.08125	40.0	38.0	41.0	33.0	41.0
30	38.31125	40.0	38.0	41.0	33.0	41.0
31	38.60975	40.0	38.0	41.0	34.0	41.0
32	38.85925	40.0	38.0	41.0	35.0	41.0
33	38.0545	40.0	38.0	41.0	33.0	41.0
34	38.08275	40.0	38.0	41.0	33.0	41.0
35	37.975	40.0	37.0	41.0	33.0	41.0
36	35.029	38.0	33.0	40.0	23.0	41.0
37	35.845	38.0	35.0	40.0	30.0	41.0
38	37.073	39.0	37.0	40.0	32.0	41.0
39	37.184	39.0	37.0	40.0	32.0	41.0
40	37.15825	39.0	37.0	41.0	32.0	41.0
41	37.1995	39.0	37.0	41.0	32.0	41.0
42	37.217	40.0	37.0	41.0	32.0	41.0
43	37.07325	40.0	37.0	41.0	32.0	41.0
44	37.1205	40.0	37.0	41.0	32.0	41.0
45	36.8035	39.0	36.0	41.0	31.0	41.0
46	35.22575	38.0	34.0	40.0	27.0	41.0
47	35.608	39.0	35.0	40.0	28.0	41.0
48	35.77625	39.0	35.0	41.0	29.0	41.0
49	34.91	39.0	34.0	40.0	27.0	41.0
50	30.50875	34.0	28.0	38.0	2.0	40.0
>>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
16	1.0
17	1.0
18	2.0
19	3.0
20	6.0
21	5.0
22	6.0
23	7.0
24	12.0
25	21.0
26	22.0
27	18.0
28	29.0
29	33.0
30	56.0
31	51.0
32	96.0
33	102.0
34	154.0
35	183.0
36	301.0
37	535.0
38	988.0
39	1368.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	11.889862327909889	23.67959949937422	46.60826032540676	17.822277847309138
2	21.95	25.224999999999998	20.375	32.45
3	24.725	20.075000000000003	23.45	31.75
4	31.0	25.924999999999997	15.45	27.625
5	20.575	40.525	24.975	13.925
6	33.95	16.625	35.35	14.075
7	19.275000000000002	20.525	25.3	34.9
8	27.0	28.575	14.475	29.95
9	22.6	33.2	28.15	16.05
10	23.575	20.674999999999997	29.725	26.025
11	28.199999999999996	13.525	17.175	41.099999999999994
12	16.5	20.05	30.25	33.2
13	31.874999999999996	19.55	29.775000000000002	18.8
14	28.325	31.5	21.3	18.875
15	33.09154577288644	23.06153076538269	27.238619309654826	16.60830415207604
16	17.325	21.375	23.625	37.675
17	23.075000000000003	21.675	38.5	16.75
18	23.75	18.65	30.5	27.1
19	35.275	15.55	30.7	18.475
20	40.25	17.150000000000002	27.85	14.75
21	24.325	20.05	26.724999999999998	28.9
22	26.275	14.424999999999999	46.625	12.675
23	28.025	14.325	40.575	17.075000000000003
24	48.699999999999996	15.75	25.3	10.25
25	46.775	23.175	16.55	13.5
26	28.725	42.775	14.524999999999999	13.975000000000001
27	18.175	43.7	24.175	13.950000000000001
28	14.099999999999998	25.474999999999998	44.775	15.65
29	12.55	14.95	52.425	20.075000000000003
30	11.875	8.875	35.875	43.375
31	16.025	7.85	42.975	33.15
32	27.950000000000003	8.075000000000001	21.525	42.449999999999996
33	49.75	9.875	16.025	24.349999999999998
34	55.60000000000001	9.225	16.525000000000002	18.65
35	58.75	9.025	20.125	12.1
36	43.025000000000006	10.975	32.15	13.850000000000001
37	43.075	12.5	19.3	25.124999999999996
38	23.275000000000002	15.925	15.225	45.574999999999996
39	18.475	24.099999999999998	11.75	45.675
40	16.175	45.75	12.8	25.275
41	25.5	43.824999999999996	12.875	17.8
42	46.650000000000006	28.225	12.2	12.925
43	46.825	30.45	11.450000000000001	11.275
44	30.625000000000004	45.5	9.3	14.575
45	20.3	46.425	14.274999999999999	19.0
46	13.750000000000002	27.55	20.775	37.925
47	11.625	18.025	36.85	33.5
48	11.875	13.25	20.9	53.974999999999994
49	14.674999999999999	19.825	17.0	48.5
50	20.5	33.900000000000006	15.0	30.599999999999998
>>END_MODULE
>>Per sequence GC content	fail
#GC Content	Count
0	0.0
1	0.0
2	0.0
3	0.0
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.0
10	0.0
11	0.0
12	0.0
13	0.5
14	1.0
15	0.5
16	0.0
17	1.0
18	2.0
19	1.0
20	0.0
21	0.5
22	1.0
23	0.5
24	0.0
25	1.5
26	3.0
27	3.0
28	3.0
29	3.5
30	4.0
31	14.0
32	24.0
33	25.0
34	26.0
35	35.0
36	44.0
37	53.5
38	63.0
39	65.5
40	68.0
41	60.0
42	52.0
43	83.5
44	115.0
45	153.0
46	191.0
47	288.5
48	386.0
49	497.0
50	608.0
51	713.0
52	818.0
53	635.5
54	453.0
55	450.0
56	447.0
57	362.5
58	278.0
59	181.5
60	85.0
61	69.5
62	54.0
63	81.5
64	109.0
65	70.5
66	32.0
67	24.0
68	16.0
69	23.5
70	31.0
71	46.5
72	62.0
73	34.5
74	7.0
75	4.5
76	2.0
77	4.0
78	6.0
79	6.5
80	7.0
81	4.5
82	2.0
83	1.0
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	0.125
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	0.05
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	41.4
#Duplication Level	Percentage of deduplicated	Percentage of total
1	75.60386473429952	31.3
2	9.601449275362318	7.95
3	4.045893719806763	5.025
4	3.140096618357488	5.2
5	1.2077294685990339	2.5
6	1.0869565217391304	2.7
7	0.785024154589372	2.275
8	0.785024154589372	2.6
9	0.5434782608695652	2.025
>10	2.657004830917874	21.0
>50	0.4830917874396135	14.75
>100	0.06038647342995169	2.675
>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	107	2.675	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	96	2.4	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	94	2.35	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	83	2.075	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	76	1.9	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	70	1.7500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	62	1.55	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	56	1.4000000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	53	1.325	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	49	1.225	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	47	1.175	No Hit
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCT	41	1.0250000000000001	RNA PCR Primer, Index 1 (97% over 35bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	37	0.9249999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	32	0.8	RNA PCR Primer, Index 1 (100% over 26bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	31	0.775	No Hit
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	26	0.65	RNA PCR Primer, Index 1 (100% over 33bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	26	0.65	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	23	0.575	RNA PCR Primer, Index 1 (100% over 26bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTAGCTATCTCGTATGC	23	0.575	RNA PCR Primer, Index 38 (100% over 50bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	23	0.575	RNA PCR Primer, Index 1 (100% over 27bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
GGTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCG	20	0.5	No Hit
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	20	0.5	RNA PCR Primer, Index 1 (100% over 26bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTAGCTATCTC	20	0.5	RNA PCR Primer, Index 38 (100% over 44bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	19	0.475	No Hit
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	19	0.475	RNA PCR Primer, Index 1 (100% over 28bp)
GCGGATGATGACACCTGGGTATGCTGCACACTCCCGACTGCGTCGTGGGG	18	0.44999999999999996	No Hit
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 26bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	17	0.42500000000000004	No Hit
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	16	0.4	No Hit
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
CACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGT	13	0.325	No Hit
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	13	0.325	No Hit
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 30bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (96% over 28bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (96% over 28bp)
TGAACTGATGATATCATTTCTTTCCCCGTCAGATCGACCCTGTTGATCTC	10	0.25	No Hit
CACCCTGATGAACTGAATACCGCCCCAGTCTGATAGCTGTGGAGAAAGGT	10	0.25	No Hit
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	10	0.25	No Hit
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	9	0.22499999999999998	No Hit
TCACAGTGAACCGGTCTCTTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	9	0.22499999999999998	No Hit
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
GCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 32bp)
GTAAATGATGAGATTCCATTGGTCCGTGTTTCTGAACTACATGATTTTCC	9	0.22499999999999998	No Hit
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTAATGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
CATTATTACTTTTGGTACGCGTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
GACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGCT	8	0.2	No Hit
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
AGCCCATGATGGTATGAGAGTAGTGGACAGAAGGGATTTCTGAAAAACAC	8	0.2	No Hit
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	8	0.2	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTTGGAATTCTCGGGTGCCA	8	0.2	No Hit
CGCACGGGGTCGGCGGCGATGTCGGCTGGAATTCTCGGGTGCCAAGGAAC	8	0.2	RNA PCR Primer, Index 1 (100% over 24bp)
ATACATGATGATCTCACACAACTTGAACTCTCTCACTGATTACTTGATGA	8	0.2	No Hit
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAC	7	0.17500000000000002	No Hit
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
CTATACGACCTGCTGCCTTTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TTGCAATGATGACTTATATATCTGTCAATCCCCTGAGAGATCACTGACGA	7	0.17500000000000002	No Hit
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGAAATCAAA	7	0.17500000000000002	No Hit
AACCCGTAGATCCGAACTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTATGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
CCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTA	6	0.15	RNA PCR Primer, Index 2 (97% over 36bp)
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
CGACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGC	6	0.15	No Hit
TCTTAGATCGATGTGGTGCTCCGGAGTTCTCTTCGGGCCAGGGCCTAAGC	6	0.15	No Hit
TATTGCACTTGTCCCGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	6	0.15	No Hit
CTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC	6	0.15	RNA PCR Primer, Index 2 (100% over 34bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	6	0.15	No Hit
GGCTTTGGTGACTCTAGATAACCTCGGGCCGATCGCACGCCCTTGGAATT	6	0.15	No Hit
ACTAATCCTAGCCCTAGCCCTACACAAATATAATTATACTGGAATTCTCG	6	0.15	No Hit
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	6	0.15	No Hit
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
GTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCGG	6	0.15	No Hit
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCCTGTACTGAGCTGCCCCGAGATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTTGGAATTCTCGGGTGCCA	5	0.125	No Hit
GCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAATTC	5	0.125	No Hit
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TAGCACCATCTGAAATCGGTTATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
GAAGGATCATTATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTAGC	5	0.125	RNA PCR Primer, Index 38 (100% over 38bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
ATCATGATGGGCTCCTCGGTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TATGCAAGGGCAAGCTCTCTTCATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGCATTCTCGGGTGCC	5	0.125	No Hit
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	5	0.125	RNA PCR Primer, Index 1 (100% over 31bp)
CTGCGTTCGCGCTCTCCCCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCAGTGCACTACAGAACTTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTC	5	0.125	No Hit
ACTAATCCTAGCCCTAGCCCTACACAAATATAATTATACTATTATTGGAA	5	0.125	No Hit
AATCGTACAGGGTCATCCACTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ACGAACGAGACTCTGGCATGCTAACTAGTTACGCGACCCCCTGGAATTCT	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	0.0	0.625	0.0	0.0	0.0
2	0.0	0.625	0.0	0.0	0.0
3	0.0	0.7	0.0	0.0	0.0
4	0.0	0.8	0.0	0.0	0.0
5	0.0	0.85	0.0	0.0	0.0
6	0.0	0.9	0.0	0.0	0.0
7	0.0	1.525	0.0	0.0	0.0
8	0.0	1.8	0.0	0.0	0.0
9	0.0	1.975	0.0	0.0	0.0
10	0.0	2.275	0.0	0.0	0.0
11	0.0	2.45	0.0	0.0	0.0
12	0.0	2.675	0.0	0.0	0.0
13	0.0	3.05	0.0	0.0	0.0
14	0.0	3.325	0.0	0.0	0.0
15	0.0	3.7	0.0	0.0	0.0
16	0.0	5.3	0.0	0.0	0.0
17	0.0	5.95	0.0	0.0	0.0
18	0.0	7.05	0.0	0.0	0.0
19	0.0	7.95	0.0	0.0	0.0
20	0.0	8.525	0.0	0.0	0.0
21	0.0	12.925	0.0	0.0	0.0
22	0.0	23.675	0.0	0.0	0.0
23	0.0	49.225	0.0	0.0	0.0
24	0.0	60.05	0.0	0.0	0.0
25	0.0	66.2	0.0	0.0	0.0
26	0.0	67.325	0.0	0.0	0.0
27	0.0	68.125	0.0	0.0	0.0
28	0.0	68.675	0.0	0.0	0.0
29	0.0	69.1	0.0	0.0	0.0
30	0.0	69.6	0.0	0.0	0.0
31	0.0	70.175	0.0	0.0	0.0
32	0.0	71.025	0.0	0.0	0.0
33	0.0	72.325	0.0	0.0	0.0
34	0.0	74.475	0.0	0.0	0.0
35	0.0	75.525	0.0	0.0	0.0
36	0.0	76.25	0.0	0.0	0.0
37	0.0	77.05	0.0	0.0	0.0
38	0.0	77.575	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TCGGATC	20	6.952051E-4	44.000004	1
CGGATCC	20	6.952051E-4	44.000004	2
CTTGGCT	20	6.952051E-4	44.000004	16
GCTTGGC	20	6.952051E-4	44.000004	15
CTGTTGG	20	6.952051E-4	44.000004	19
AACGCTG	25	3.6958358E-5	44.0	8
GGTGAGT	25	3.6958358E-5	44.0	17
ACGCTGT	25	3.6958358E-5	44.0	9
TTCAACG	25	3.6958358E-5	44.0	5
TCGGTGA	25	3.6958358E-5	44.0	15
GAGCTTG	25	3.6958358E-5	44.0	13
GGATCCG	25	3.6958358E-5	44.0	3
CCGTCTG	25	3.6958358E-5	44.0	7
CATTCAA	25	3.6958358E-5	44.0	3
TCAACGC	25	3.6958358E-5	44.0	6
ACATTCA	25	3.6958358E-5	44.0	2
GCTGTCG	25	3.6958358E-5	44.0	11
GATCCGT	25	3.6958358E-5	44.0	4
CGGTGAG	25	3.6958358E-5	44.0	16
TCCGTCT	25	3.6958358E-5	44.0	6
>>END_MODULE
Read 192423 spots for SRR5030860.sra
Written 192423 spots for SRR5030860.sra
Read 192423 spots for SRR5030860.sra
Written 192423 spots for SRR5030860.sra
Read 192423 spots for SRR5030860.sra
Written 192423 spots for SRR5030860.sra
Read 192423 spots for SRR5030860.sra
Written 192423 spots for SRR5030860.sra
Read 192423 spots for SRR5030860.sra
Written 192423 spots for SRR5030860.sra
Read 192423 spots for SRR5030860.sra
Written 192423 spots for SRR5030860.sra
Read 192423 spots for SRR5030860.sra
Written 192423 spots for SRR5030860.sra
Read 192423 spots for SRR5030860.sra
Written 192423 spots for SRR5030860.sra
Read 192423 spots for SRR5030860.sra
Written 192423 spots for SRR5030860.sra
Read 192423 spots for SRR5030860.sra
Written 192423 spots for SRR5030860.sra
Read 192423 spots for SRR5030860.sra
Written 192423 spots for SRR5030860.sra
Read 192425 spots for SRR5030860.sra
Written 192425 spots for SRR5030860.sra
SRR ids: ['SRR5030860.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_3q_ej28u
SRR5030860.sra spots: 2309078
blocks: [[1, 192423], [192424, 384846], [384847, 577269], [577270, 769692], [769693, 962115], [962116, 1154538], [1154539, 1346961], [1346962, 1539384], [1539385, 1731807], [1731808, 1924230], [1924231, 2116653], [2116654, 2309078]]
SRR5030860 file size 399136
SRR5030860 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030860 SRR5030860_1.fastq
Input file:	SRR5030860_1.fastq
trimmed:	SRR5030860-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 06:31:00 2020 >> started

Wed Mar  4 06:31:01 2020 >> done (1.660s)
2309078 reads processed; of these:
    118 ( 0.01%) short reads filtered out after trimming by size control
      1 ( 0.00%) empty reads filtered out after trimming by size control
2308959 (99.99%) reads available; of these:
 134679 ( 5.83%) trimmed reads available after processing
2174280 (94.17%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     37	  0.00%
 19	     41	  0.00%
 20	    111	  0.00%
 21	    115	  0.00%
 22	    220	  0.01%
 23	    245	  0.01%
 24	    325	  0.01%
 25	    405	  0.02%
 26	    364	  0.02%
 27	    464	  0.02%
 28	    643	  0.03%
 29	    831	  0.04%
 30	    581	  0.03%
 31	    777	  0.03%
 32	    753	  0.03%
 33	   1058	  0.05%
 34	   1883	  0.08%
 35	   1920	  0.08%
 36	   1611	  0.07%
 37	   1713	  0.07%
 38	   1841	  0.08%
 39	   2206	  0.10%
 40	   2275	  0.10%
 41	   2502	  0.11%
 42	   3203	  0.14%
 43	   4298	  0.19%
 44	   7365	  0.32%
 45	   9749	  0.42%
 46	   9124	  0.40%
 47	  13534	  0.59%
 48	  25897	  1.12%
 49	  38588	  1.67%
 50	2174280	 94.17%
2308959 reads passed initial QC


criterion=sequence-density
sequence-density=77.47
sequence-density-rank=1
fanout-score=20.41
fanout-score-rank=1
prefix-density=79.41
prefix-fanout=19.9
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTAGCTATCTCGTATGCC


criterion=fanout-score
sequence-density=77.47
sequence-density-rank=1
fanout-score=20.41
fanout-score-rank=1
prefix-density=79.41
prefix-fanout=19.9
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTAGCTATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTAGCTATCTCGTATGCC -o SRR5030860 -
Input file:	STDIN
trimmed:	SRR5030860-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTAGCTATCTCGTATGCC
-- 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 06:31:14 2020 >> started

Wed Mar  4 06:31:18 2020 >> done (3.459s)
2249755 reads processed; of these:
 147453 ( 6.55%) short reads filtered out after trimming by size control
  12316 ( 0.55%) empty reads filtered out after trimming by size control
2089986 (92.90%) reads available; of these:
1809431 (86.58%) trimmed reads available after processing
 280555 (13.42%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  16825	  0.81%
 19	  22552	  1.08%
 20	 108886	  5.21%
 21	 240206	 11.49%
 22	 578660	 27.69%
 23	 257542	 12.32%
 24	 124199	  5.94%
 25	  34102	  1.63%
 26	  18478	  0.88%
 27	  13740	  0.66%
 28	  15296	  0.73%
 29	  11976	  0.57%
 30	  15681	  0.75%
 31	  19327	  0.92%
 32	  22752	  1.09%
 33	  55822	  2.67%
 34	  20245	  0.97%
 35	  16992	  0.81%
 36	  20074	  0.96%
 37	  11226	  0.54%
 38	  11950	  0.57%
 39	  13087	  0.63%
 40	  20504	  0.98%
 41	  27864	  1.33%
 42	  32306	  1.55%
 43	  23431	  1.12%
 44	  17617	  0.84%
 45	  24491	  1.17%
 46	  18061	  0.86%
 47	  14415	  0.69%
 48	   2929	  0.14%
 49	   8554	  0.41%
 50	 250196	 11.97%


criterion=sequence-density
sequence-density=5.87
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=17
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.01
sequence-density-rank=39
fanout-score=85.59
fanout-score-rank=1
prefix-density=1.07
prefix-fanout=1.0
sequence=ATTGTATAGTTTAACAGTCTACAGCCATGGTCGT
                                 Started job on |	Mar 04 06:31:38
                             Started mapping on |	Mar 04 06:31:39
                                    Finished on |	Mar 04 06:32:02
       Mapping speed, Million of reads per hour |	336.39

                          Number of input reads |	2149190
                      Average input read length |	29
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1193915
                        Uniquely mapped reads % |	55.55%
                          Average mapped length |	27.90
                       Number of splices: Total |	1106
            Number of splices: Annotated (sjdb) |	174
                       Number of splices: GT/AG |	1031
                       Number of splices: GC/AG |	16
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	59
                      Mismatch rate per base, % |	0.21%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.59
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.08
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	650735
             % of reads mapped to multiple loci |	30.28%
        Number of reads mapped to too many loci |	46399
             % of reads mapped to too many loci |	2.16%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	11.34%
                     % of reads unmapped: other |	0.67%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	304540	304540	304540
N_multimapping	650735	650735	650735
N_noFeature	56240	71881	856639
N_ambiguous	660049	371367	14399
UnstrandedReadsAssigned:477626 PositiveStrandReadsAssigned:750667 NegativeStrandReadsAssigned:322877
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5030860 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: SRR5030860-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,149,190 reads, 534,635 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,093 rounds

 109283 SRR5030860.ke.tsv
  52636 SRR5030860.se.tsv
 161919 total
==> SRR5030860.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

==> SRR5030860.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030860 completed mapping pipeline successfully
