Starting /dee2/code/volunteer_pipeline.sh SRR5030998
    current disk space = 160563904512
    free memory = 73928072 
SRR5030998 SRAfilesize
44297aca77dd8e00ded6c6746526a7f9  SRR5030998.sra
SRR5030998.sra file validated
SRR5030998 is single end
SRR5030998 is conventional basespace
SRR5030998 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030998_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	32.24675	33.0	31.0	34.0	31.0	34.0
2	32.49125	34.0	31.0	34.0	31.0	34.0
3	32.49725	34.0	31.0	34.0	31.0	34.0
4	36.1445	37.0	35.0	37.0	35.0	37.0
5	36.0095	37.0	35.0	37.0	35.0	37.0
6	35.81875	37.0	35.0	37.0	33.0	37.0
7	35.7675	37.0	35.0	37.0	35.0	37.0
8	35.861	37.0	35.0	37.0	35.0	37.0
9	37.4655	39.0	37.0	39.0	35.0	39.0
10	37.3485	39.0	37.0	39.0	33.0	39.0
11	37.03775	39.0	37.0	39.0	33.0	39.0
12	37.48925	39.0	37.0	39.0	34.0	39.0
13	37.51	39.0	37.0	39.0	34.0	39.0
14	38.86575	40.0	38.0	41.0	35.0	41.0
15	38.8125	40.0	38.0	41.0	35.0	41.0
16	38.7445	40.0	38.0	41.0	35.0	41.0
17	38.87125	40.0	38.0	41.0	35.0	41.0
18	38.82625	40.0	38.0	41.0	35.0	41.0
19	38.52925	40.0	38.0	41.0	34.0	41.0
20	38.563	40.0	38.0	41.0	34.0	41.0
21	38.6875	40.0	38.0	41.0	34.0	41.0
22	38.759	40.0	38.0	41.0	35.0	41.0
23	38.29975	40.0	38.0	41.0	33.0	41.0
24	38.69175	40.0	38.0	41.0	34.0	41.0
25	38.82975	40.0	38.0	41.0	35.0	41.0
26	38.70625	40.0	38.0	41.0	35.0	41.0
27	38.67175	40.0	38.0	41.0	34.0	41.0
28	38.48125	40.0	38.0	41.0	34.0	41.0
29	38.09975	40.0	38.0	41.0	33.0	41.0
30	38.05075	40.0	38.0	41.0	33.0	41.0
31	38.293	40.0	38.0	41.0	34.0	41.0
32	38.22725	40.0	38.0	41.0	34.0	41.0
33	37.4955	40.0	37.0	41.0	32.0	41.0
34	37.569	40.0	37.0	41.0	32.0	41.0
35	37.345	39.0	37.0	40.0	31.0	41.0
36	37.409	39.0	37.0	40.0	32.0	41.0
37	36.89675	39.0	36.0	40.0	30.0	41.0
38	37.02625	39.0	36.0	40.0	31.0	41.0
39	37.454	39.0	37.0	41.0	32.0	41.0
40	37.573	40.0	37.0	41.0	33.0	41.0
41	37.70625	40.0	37.0	41.0	33.0	41.0
42	37.64975	40.0	37.0	41.0	33.0	41.0
43	37.5705	40.0	37.0	41.0	32.0	41.0
44	37.62425	40.0	37.0	41.0	33.0	41.0
45	37.5	40.0	37.0	41.0	33.0	41.0
46	37.20825	40.0	36.0	41.0	32.0	41.0
47	36.39075	39.0	35.0	41.0	30.0	41.0
48	36.30025	39.0	35.0	41.0	30.0	41.0
49	36.321	39.0	35.0	41.0	30.0	41.0
50	35.644	38.0	34.0	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
11	1.0
12	0.0
13	1.0
14	1.0
15	3.0
16	0.0
17	0.0
18	3.0
19	5.0
20	4.0
21	4.0
22	1.0
23	5.0
24	9.0
25	14.0
26	12.0
27	18.0
28	30.0
29	41.0
30	66.0
31	72.0
32	82.0
33	117.0
34	167.0
35	216.0
36	318.0
37	469.0
38	809.0
39	1532.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	11.05	24.25	47.0	17.7
2	24.831038798498124	25.556946182728414	18.197747183979978	31.414267834793492
3	24.075	19.900000000000002	22.225	33.800000000000004
4	33.225	26.650000000000002	16.975	23.150000000000002
5	23.375	37.225	27.400000000000002	12.0
6	35.275	13.8	34.55	16.375
7	19.25	21.6	21.15	38.0
8	24.099999999999998	27.400000000000002	19.05	29.45
9	23.5	30.775000000000002	27.900000000000002	17.825
10	22.025	23.125	27.700000000000003	27.150000000000002
11	31.724999999999998	11.325000000000001	18.575	38.375
12	16.75	18.95	30.375000000000004	33.925
13	31.874999999999996	16.975	32.574999999999996	18.575
14	29.725	31.8	20.5	17.974999999999998
15	37.5	22.625	25.8	14.075
16	19.950000000000003	18.65	24.825	36.575
17	27.200000000000003	22.85	36.275	13.675
18	24.95	16.975	29.675	28.4
19	35.75	14.725	32.074999999999996	17.45
20	42.8	16.5	26.724999999999998	13.975000000000001
21	24.825	21.725	26.200000000000003	27.250000000000004
22	29.65	14.099999999999998	44.925	11.325000000000001
23	26.75	14.399999999999999	41.025	17.825
24	48.949999999999996	15.775	25.974999999999998	9.3
25	46.775	24.55	17.0	11.675
26	27.900000000000002	42.65	15.5	13.950000000000001
27	17.25	42.775	24.224999999999998	15.75
28	14.025000000000002	22.650000000000002	45.475	17.849999999999998
29	14.625	12.6	52.47500000000001	20.3
30	11.899999999999999	7.6	35.85	44.65
31	16.075	5.949999999999999	43.7	34.275
32	30.175	6.15	22.525000000000002	41.15
33	50.925	10.0	15.125	23.95
34	57.4	8.075000000000001	18.25	16.275000000000002
35	60.0	8.5	20.0	11.5
36	42.025	8.674999999999999	34.475	14.825
37	42.15	12.85	21.3	23.7
38	25.474999999999998	17.224999999999998	12.85	44.45
39	16.975	23.674999999999997	12.9	46.45
40	17.125	45.925	13.075000000000001	23.875
41	24.95	45.175	10.875	19.0
42	45.225	27.500000000000004	15.45	11.825
43	48.35	27.250000000000004	10.225	14.174999999999999
44	32.300000000000004	43.7	9.775	14.224999999999998
45	21.375	44.95	14.299999999999999	19.375
46	17.65	24.099999999999998	18.15	40.1
47	12.15	15.6	37.45	34.8
48	14.475	13.3	20.275000000000002	51.949999999999996
49	15.125	19.125	15.5	50.24999999999999
50	19.825	33.35	15.65	31.175000000000004
>>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	1.0
12	2.0
13	1.0
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	0.5
24	1.0
25	1.0
26	1.0
27	1.0
28	1.0
29	3.0
30	5.0
31	10.5
32	16.0
33	16.5
34	17.0
35	20.5
36	24.0
37	28.5
38	33.0
39	38.0
40	43.0
41	54.5
42	66.0
43	77.5
44	89.0
45	143.0
46	197.0
47	294.5
48	392.0
49	481.0
50	570.0
51	681.0
52	792.0
53	623.0
54	454.0
55	486.0
56	518.0
57	401.5
58	285.0
59	187.5
60	90.0
61	72.5
62	55.0
63	103.0
64	151.0
65	100.0
66	49.0
67	30.5
68	12.0
69	24.0
70	36.0
71	61.5
72	87.0
73	47.0
74	7.0
75	3.5
76	0.0
77	1.5
78	3.0
79	3.0
80	3.0
81	2.0
82	1.0
83	0.5
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	0.125
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	37.9
#Duplication Level	Percentage of deduplicated	Percentage of total
1	74.67018469656992	28.299999999999997
2	9.498680738786279	7.199999999999999
3	4.8153034300791555	5.475
4	2.5725593667546174	3.9
5	1.8469656992084433	3.5000000000000004
6	1.1873350923482848	2.7
7	0.7255936675461742	1.925
8	0.5277044854881267	1.6
9	0.395778364116095	1.35
>10	3.2321899736147754	24.575
>50	0.1978891820580475	5.949999999999999
>100	0.32981530343007914	13.525
>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
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	114	2.85	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	114	2.85	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	109	2.725	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	103	2.5749999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	101	2.5250000000000004	No Hit
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	97	2.4250000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	81	2.025	RNA PCR Primer, Index 1 (100% over 30bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	60	1.5	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	49	1.225	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	46	1.15	RNA PCR Primer, Index 1 (100% over 28bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	42	1.05	No Hit
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	41	1.0250000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGT	41	1.0250000000000001	RNA PCR Primer, Index 1 (97% over 35bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	37	0.9249999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	35	0.8750000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	34	0.8500000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	31	0.775	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	28	0.7000000000000001	No Hit
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	25	0.625	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	25	0.625	RNA PCR Primer, Index 1 (100% over 26bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	24	0.6	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	24	0.6	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	23	0.575	RNA PCR Primer, Index 1 (100% over 28bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTCCGCATCTCGTATGC	21	0.525	RNA PCR Primer, Index 18 (100% over 50bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	21	0.525	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	21	0.525	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	20	0.5	RNA PCR Primer, Index 1 (100% over 26bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	20	0.5	RNA PCR Primer, Index 1 (100% over 33bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	15	0.375	No Hit
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	15	0.375	RNA PCR Primer, Index 1 (100% over 26bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	14	0.35000000000000003	No Hit
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	13	0.325	RNA PCR Primer, Index 1 (100% over 31bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	13	0.325	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	13	0.325	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	13	0.325	RNA PCR Primer, Index 1 (100% over 26bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGT	13	0.325	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCTGGAATTCTCGGGTGC	13	0.325	No Hit
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	12	0.3	No Hit
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	12	0.3	No Hit
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	12	0.3	No Hit
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCTGGAATTCTCGGGTG	11	0.27499999999999997	No Hit
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	9	0.22499999999999998	No Hit
TCCCTGTGGTCTAGTGGTTAGGATTCGGCGCTCTCTGGAATTCTCGGGTG	9	0.22499999999999998	No Hit
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGCTGGAATTCTCGGGTGCC	9	0.22499999999999998	No Hit
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	9	0.22499999999999998	No Hit
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
GGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	8	0.2	No Hit
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTCTCTGGAATTCTCGGGT	8	0.2	No Hit
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGACTGGAATTCTCGGGT	8	0.2	No Hit
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
ATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCTGGAATTCTCGGGTGCC	8	0.2	No Hit
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
GACCCTGTTGATCTCAAATACTAATTGCCAGTTTTGTCTGATGTGGAATT	7	0.17500000000000002	No Hit
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TGCGGGGCTAGGGCTAACAGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
CACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAAT	7	0.17500000000000002	No Hit
TATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAATTCTCGGGTGCC	7	0.17500000000000002	No Hit
ACTAATCCTAGCCCTAGCCCTACACTGGAATTCTCGGGTGCCAAGGAACT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 25bp)
TTCCCTTTGTCATCCTATGCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTTGGAATTCTCGGGTGCCA	6	0.15	No Hit
CCTCGACACAAGGGTTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	6	0.15	RNA PCR Primer, Index 1 (100% over 31bp)
TATTGCACTTGTCCCGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	6	0.15	No Hit
TCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCC	6	0.15	No Hit
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTCACTGGAATTCTCGGGT	6	0.15	No Hit
TCGGATCCGTCTGAGCTTGGCTTTTTGGAATTCTCGGGTGCCAAGGAACT	6	0.15	RNA PCR Primer, Index 1 (100% over 25bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTCCGCATCTC	6	0.15	RNA PCR Primer, Index 18 (100% over 44bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTC	6	0.15	No Hit
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTCTTGGAATTCTCGGGTG	6	0.15	No Hit
TGTAAACATCCTCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
AGCAGCATTGTACAGGGCTATGTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATGGAATTCTCGGGTGCCAAG	6	0.15	No Hit
CTAGACTGAGGCTCCTTGAGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
CTGGCCCTCTCTGCCCTTCCGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTC	5	0.125	RNA PCR Primer, Index 1 (97% over 36bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCT	5	0.125	No Hit
CACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGT	5	0.125	No Hit
TGGGGGGCCCAAGTCCTTCTGATCGAGGCCTGGAATTCTCGGGTGCCAAG	5	0.125	No Hit
AGCTACATTGTCTGCTGGGTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTAATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
GCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAATTC	5	0.125	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGTGGAATTCTCGGGTGCC	5	0.125	No Hit
TGAGGTAGGAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTTTAACCTGTGTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTTGGAATTCTCGGGTGCC	5	0.125	No Hit
TAGCACCATCTGAAATCGGTTATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGACTTGATGAAAGTACTTTTGAACCCTTTTCCATCTGATGTGGAATTCT	5	0.125	No Hit
AGAGGTAGTAGGTTGCATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	5	0.125	No Hit
TCACAGTGAACCGGTCTCTTTATTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
CATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTCCGCATCTCGTAT	5	0.125	RNA PCR Primer, Index 18 (100% over 48bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	5	0.125	No Hit
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGGAATTCTCGGGTGCCA	5	0.125	No Hit
ACTAATCCTAGCCCTAGCCCTACACAAATATAATTATACTATTATATGGA	5	0.125	No Hit
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
>>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	0.575	0.0	0.0	0.0
2	0.0	0.6	0.0	0.0	0.0
3	0.0	0.775	0.0	0.0	0.0
4	0.0	0.825	0.0	0.0	0.0
5	0.0	0.875	0.0	0.0	0.0
6	0.0	0.975	0.0	0.0	0.0
7	0.0	1.175	0.0	0.0	0.0
8	0.0	1.3	0.0	0.0	0.0
9	0.0	1.4	0.0	0.0	0.0
10	0.0	1.5	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	2.15	0.0	0.0	0.0
14	0.0	2.4	0.0	0.0	0.0
15	0.0	2.675	0.0	0.0	0.0
16	0.0	3.95	0.0	0.0	0.0
17	0.0	4.625	0.0	0.0	0.0
18	0.0	5.825	0.0	0.0	0.0
19	0.0	6.35	0.0	0.0	0.0
20	0.0	7.4	0.0	0.0	0.0
21	0.0	12.3	0.0	0.0	0.0
22	0.0	23.075	0.0	0.0	0.0
23	0.0	48.875	0.0	0.0	0.0
24	0.0	60.825	0.0	0.0	0.0
25	0.0	66.325	0.0	0.0	0.0
26	0.0	68.075	0.0	0.0	0.0
27	0.0	68.925	0.0	0.0	0.0
28	0.0	69.45	0.0	0.0	0.0
29	0.0	70.125	0.0	0.0	0.0
30	0.0	70.75	0.0	0.0	0.0
31	0.0	71.85	0.0	0.0	0.0
32	0.0	73.025	0.0	0.0	0.0
33	0.0	74.3	0.0	0.0	0.0
34	0.0	78.825	0.0	0.0	0.0
35	0.0	80.1	0.0	0.0	0.0
36	0.0	81.575	0.0	0.0	0.0
37	0.0	83.3	0.0	0.0	0.0
38	0.0	83.875	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
GAGGTAG	20	6.952051E-4	44.000004	2
CTGGAAG	20	6.952051E-4	44.000004	16
GGAAGCT	20	6.952051E-4	44.000004	18
GACTGGA	20	6.952051E-4	44.000004	14
TGAGGTA	20	6.952051E-4	44.000004	1
TTGGCTT	20	6.952051E-4	44.000004	17
TGGAAGC	20	6.952051E-4	44.000004	17
AGGTAGT	20	6.952051E-4	44.000004	3
ACTGGAA	20	6.952051E-4	44.000004	15
TAAACAT	25	3.6958358E-5	44.0	3
AAACATC	25	3.6958358E-5	44.0	4
ACATCCT	25	3.6958358E-5	44.0	6
CTTGGCT	30	1.9515464E-6	44.0	16
GCTTGGC	35	1.02281774E-7	44.0	15
GTAAACA	25	3.6958358E-5	44.0	2
AACATCC	25	3.6958358E-5	44.0	5
CTGAGCT	45	1.506669E-8	39.111115	11
GAGCTTG	45	1.506669E-8	39.111115	13
GGATCCG	45	1.506669E-8	39.111115	3
CCGTCTG	45	1.506669E-8	39.111115	7
>>END_MODULE
Read 246778 spots for SRR5030998.sra
Written 246778 spots for SRR5030998.sra
Read 246778 spots for SRR5030998.sra
Written 246778 spots for SRR5030998.sra
Read 246778 spots for SRR5030998.sra
Written 246778 spots for SRR5030998.sra
Read 246778 spots for SRR5030998.sra
Written 246778 spots for SRR5030998.sra
Read 246778 spots for SRR5030998.sra
Written 246778 spots for SRR5030998.sra
Read 246778 spots for SRR5030998.sra
Written 246778 spots for SRR5030998.sra
Read 246778 spots for SRR5030998.sra
Written 246778 spots for SRR5030998.sra
Read 246778 spots for SRR5030998.sra
Written 246778 spots for SRR5030998.sra
Read 246778 spots for SRR5030998.sra
Written 246778 spots for SRR5030998.sra
Read 246778 spots for SRR5030998.sra
Written 246778 spots for SRR5030998.sra
Read 246784 spots for SRR5030998.sra
Written 246784 spots for SRR5030998.sra
Read 246778 spots for SRR5030998.sra
Written 246778 spots for SRR5030998.sra
SRR ids: ['SRR5030998.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_7cflmza0
SRR5030998.sra spots: 2961342
blocks: [[1, 246778], [246779, 493556], [493557, 740334], [740335, 987112], [987113, 1233890], [1233891, 1480668], [1480669, 1727446], [1727447, 1974224], [1974225, 2221002], [2221003, 2467780], [2467781, 2714558], [2714559, 2961342]]
SRR5030998 file size 512198
SRR5030998 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030998 SRR5030998_1.fastq
Input file:	SRR5030998_1.fastq
trimmed:	SRR5030998-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 07:03:03 2020 >> started

Wed Mar  4 07:03:05 2020 >> done (1.768s)
2961342 reads processed; of these:
    310 ( 0.01%) short reads filtered out after trimming by size control
      9 ( 0.00%) empty reads filtered out after trimming by size control
2961023 (99.99%) reads available; of these:
 204781 ( 6.92%) trimmed reads available after processing
2756242 (93.08%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	    100	  0.00%
 19	    113	  0.00%
 20	    195	  0.01%
 21	    271	  0.01%
 22	    415	  0.01%
 23	    506	  0.02%
 24	    533	  0.02%
 25	    667	  0.02%
 26	    646	  0.02%
 27	    724	  0.02%
 28	    906	  0.03%
 29	   1273	  0.04%
 30	   1033	  0.03%
 31	   1084	  0.04%
 32	   1367	  0.05%
 33	   1456	  0.05%
 34	   1585	  0.05%
 35	   2802	  0.09%
 36	   2618	  0.09%
 37	   3091	  0.10%
 38	   3416	  0.12%
 39	   3587	  0.12%
 40	   4124	  0.14%
 41	   4241	  0.14%
 42	   5664	  0.19%
 43	   8418	  0.28%
 44	  11749	  0.40%
 45	  14690	  0.50%
 46	  21639	  0.73%
 47	  23484	  0.79%
 48	  34583	  1.17%
 49	  47801	  1.61%
 50	2756242	 93.08%
2961023 reads passed initial QC


criterion=sequence-density
sequence-density=82.21
sequence-density-rank=1
fanout-score=22.13
fanout-score-rank=1
prefix-density=85.13
prefix-fanout=21.4
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTCCGCATCTCGTATGCC


criterion=fanout-score
sequence-density=82.21
sequence-density-rank=1
fanout-score=22.13
fanout-score-rank=1
prefix-density=85.13
prefix-fanout=21.4
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTCCGCATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTCCGCATCTCGTATGCC -o SRR5030998 -
Input file:	STDIN
trimmed:	SRR5030998-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTCCGCATCTCGTATGCC
-- 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 07:03:20 2020 >> started

Wed Mar  4 07:03:24 2020 >> done (4.375s)
2889673 reads processed; of these:
 161643 ( 5.59%) short reads filtered out after trimming by size control
  15493 ( 0.54%) empty reads filtered out after trimming by size control
2712537 (93.87%) reads available; of these:
2540408 (93.65%) trimmed reads available after processing
 172129 ( 6.35%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  13378	  0.49%
 19	  28659	  1.06%
 20	 133908	  4.94%
 21	 288250	 10.63%
 22	 761731	 28.08%
 23	 353124	 13.02%
 24	 164481	  6.06%
 25	  45751	  1.69%
 26	  25144	  0.93%
 27	  19844	  0.73%
 28	  23088	  0.85%
 29	  17849	  0.66%
 30	  27070	  1.00%
 31	  44224	  1.63%
 32	  35444	  1.31%
 33	 128175	  4.73%
 34	  47069	  1.74%
 35	  40374	  1.49%
 36	  51584	  1.90%
 37	  20141	  0.74%
 38	  22740	  0.84%
 39	  20400	  0.75%
 40	  30264	  1.12%
 41	  39475	  1.46%
 42	  47085	  1.74%
 43	  33473	  1.23%
 44	  24277	  0.89%
 45	  32372	  1.19%
 46	  24585	  0.91%
 47	  17377	  0.64%
 48	   1979	  0.07%
 49	   4135	  0.15%
 50	 145087	  5.35%


criterion=sequence-density
sequence-density=6.26
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=15
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.63
sequence-density-rank=23
fanout-score=12.24
fanout-score-rank=1
prefix-density=7.67
prefix-fanout=1.0
sequence=TGAGCTTGGCTTTT
                                 Started job on |	Mar 04 07:03:47
                             Started mapping on |	Mar 04 07:03:47
                                    Finished on |	Mar 04 07:04:12
       Mapping speed, Million of reads per hour |	400.88

                          Number of input reads |	2783887
                      Average input read length |	28
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1402791
                        Uniquely mapped reads % |	50.39%
                          Average mapped length |	25.57
                       Number of splices: Total |	1552
            Number of splices: Annotated (sjdb) |	295
                       Number of splices: GT/AG |	1454
                       Number of splices: GC/AG |	17
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	81
                      Mismatch rate per base, % |	0.23%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.82
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.11
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	923577
             % of reads mapped to multiple loci |	33.18%
        Number of reads mapped to too many loci |	83181
             % of reads mapped to too many loci |	2.99%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	12.73%
                     % of reads unmapped: other |	0.71%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	457519	457519	457519
N_multimapping	923577	923577	923577
N_noFeature	93026	113388	961003
N_ambiguous	777468	400556	17291
UnstrandedReadsAssigned:532297 PositiveStrandReadsAssigned:888847 NegativeStrandReadsAssigned:424497
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5030998 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: SRR5030998-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,783,887 reads, 672,259 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,171 rounds

 109283 SRR5030998.ke.tsv
  52636 SRR5030998.se.tsv
 161919 total
==> SRR5030998.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

==> SRR5030998.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030998 completed mapping pipeline successfully
