Starting /dee2/code/volunteer_pipeline.sh SRR5030989
    current disk space = 160559906816
    free memory = 73913032 
SRR5030989 SRAfilesize
645430b6fa745b1e0533a9a124670052  SRR5030989.sra
SRR5030989.sra file validated
SRR5030989 is single end
SRR5030989 is conventional basespace
SRR5030989 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030989_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	53
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	32.279	33.0	31.0	34.0	31.0	34.0
2	32.53775	34.0	31.0	34.0	31.0	34.0
3	32.5775	34.0	31.0	34.0	31.0	34.0
4	36.1345	37.0	35.0	37.0	35.0	37.0
5	36.06225	37.0	35.0	37.0	35.0	37.0
6	35.82575	37.0	35.0	37.0	35.0	37.0
7	35.85	37.0	35.0	37.0	35.0	37.0
8	35.91175	37.0	35.0	37.0	35.0	37.0
9	37.446	39.0	37.0	39.0	35.0	39.0
10	37.49025	39.0	37.0	39.0	35.0	39.0
11	37.101	39.0	37.0	39.0	33.0	39.0
12	37.52875	39.0	37.0	39.0	35.0	39.0
13	37.52575	39.0	37.0	39.0	35.0	39.0
14	38.93975	40.0	38.0	41.0	35.0	41.0
15	38.89925	40.0	38.0	41.0	35.0	41.0
16	38.91875	40.0	38.0	41.0	35.0	41.0
17	39.05575	40.0	38.0	41.0	35.0	41.0
18	38.9615	41.0	38.0	41.0	35.0	41.0
19	38.739	40.0	38.0	41.0	34.0	41.0
20	38.731	40.0	38.0	41.0	35.0	41.0
21	38.8485	40.0	38.0	41.0	35.0	41.0
22	38.7685	40.0	38.0	41.0	35.0	41.0
23	38.48725	40.0	38.0	41.0	34.0	41.0
24	38.69775	40.0	38.0	41.0	34.0	41.0
25	38.939	40.0	38.0	41.0	35.0	41.0
26	38.76025	40.0	38.0	41.0	35.0	41.0
27	38.75775	40.0	38.0	41.0	34.0	41.0
28	38.59675	40.0	38.0	41.0	34.0	41.0
29	38.246	40.0	38.0	41.0	33.0	41.0
30	38.18525	40.0	38.0	41.0	33.0	41.0
31	38.393	40.0	38.0	41.0	33.0	41.0
32	38.39525	40.0	38.0	41.0	34.0	41.0
33	38.10875	40.0	38.0	41.0	33.0	41.0
34	38.1825	40.0	38.0	41.0	34.0	41.0
35	38.00875	40.0	38.0	41.0	33.0	41.0
36	37.72175	40.0	37.0	41.0	33.0	41.0
37	37.086	39.0	36.0	41.0	31.0	41.0
38	37.044	39.0	36.0	40.0	31.0	41.0
39	37.4825	39.0	37.0	41.0	32.0	41.0
40	37.596	40.0	37.0	41.0	33.0	41.0
41	37.78	40.0	37.0	41.0	33.0	41.0
42	37.644	40.0	37.0	41.0	33.0	41.0
43	37.66875	40.0	37.0	41.0	33.0	41.0
44	37.50625	40.0	37.0	41.0	33.0	41.0
45	37.475	40.0	37.0	41.0	33.0	41.0
46	37.30175	40.0	37.0	41.0	32.0	41.0
47	36.61075	39.0	35.0	41.0	30.0	41.0
48	36.4215	39.0	35.0	41.0	30.0	41.0
49	36.553	39.0	35.0	41.0	31.0	41.0
50	35.8325	38.0	34.0	40.0	30.0	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	0.0
15	0.0
16	1.0
17	2.0
18	2.0
19	1.0
20	4.0
21	4.0
22	7.0
23	6.0
24	8.0
25	12.0
26	20.0
27	17.0
28	24.0
29	30.0
30	53.0
31	68.0
32	81.0
33	115.0
34	172.0
35	187.0
36	302.0
37	492.0
38	795.0
39	1596.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	12.5	25.2	44.5	17.8
2	24.36764337590784	28.09917355371901	19.659403956924617	27.87377911344853
3	22.85	17.65	24.275	35.225
4	36.6	28.849999999999998	15.55	19.0
5	23.549999999999997	34.275	28.225	13.950000000000001
6	28.249999999999996	16.275000000000002	37.95	17.525
7	21.55	20.225	18.975	39.25
8	21.8	28.9	19.175	30.125
9	23.1	30.7	26.075	20.125
10	23.95	19.5	26.375	30.175
11	34.725	12.950000000000001	17.125	35.199999999999996
12	17.4	21.475	30.225	30.9
13	28.775000000000002	16.275000000000002	35.225	19.725
14	32.425	27.750000000000004	21.3	18.525
15	35.225	21.5	27.55	15.725
16	19.6	16.5	25.775	38.125
17	29.4	23.25	33.45	13.900000000000002
18	29.225	15.375	29.25	26.150000000000002
19	32.75	15.225	34.925	17.1
20	41.4	17.299999999999997	26.724999999999998	14.575
21	25.650000000000002	22.55	24.0	27.800000000000004
22	31.474999999999998	14.95	41.075	12.5
23	26.525	13.625000000000002	42.075	17.775
24	48.225	14.975	26.275	10.525
25	49.35	23.25	15.8	11.600000000000001
26	30.0	41.55	15.125	13.325000000000001
27	18.25	42.6	23.025000000000002	16.125
28	14.299999999999999	23.525	44.175	18.0
29	15.675	13.425	51.37500000000001	19.525000000000002
30	11.924999999999999	8.425	33.4	46.25
31	15.55	6.65	42.475	35.325
32	28.325	6.6000000000000005	24.175	40.9
33	50.275000000000006	10.325	14.2	25.2
34	57.699999999999996	8.275	17.724999999999998	16.3
35	61.7	8.85	18.125	11.325000000000001
36	41.425	9.975000000000001	34.925	13.675
37	41.525	13.325000000000001	22.025	23.125
38	25.525	18.05	13.700000000000001	42.725
39	16.975	22.625	12.725	47.675
40	17.2	44.975	14.099999999999998	23.724999999999998
41	23.9	45.824999999999996	10.2	20.075000000000003
42	45.4	27.800000000000004	14.475	12.325
43	49.75	26.8	9.9	13.55
44	32.574999999999996	42.725	10.0	14.7
45	20.0	46.075	15.299999999999999	18.625
46	19.35	24.95	16.325	39.375
47	12.825000000000001	14.774999999999999	36.675000000000004	35.725
48	13.8	12.9	21.224999999999998	52.075
49	14.674999999999999	19.650000000000002	16.05	49.625
50	18.95	35.525	14.124999999999998	31.4
>>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	0.0
14	0.0
15	0.0
16	0.0
17	0.0
18	0.0
19	0.0
20	0.0
21	0.5
22	1.0
23	1.0
24	1.0
25	1.0
26	1.0
27	2.5
28	4.0
29	2.5
30	1.0
31	6.0
32	11.0
33	12.5
34	14.0
35	18.5
36	23.0
37	31.0
38	39.0
39	39.5
40	40.0
41	45.5
42	51.0
43	80.0
44	109.0
45	145.5
46	182.0
47	287.0
48	392.0
49	476.5
50	561.0
51	695.5
52	830.0
53	608.0
54	386.0
55	453.0
56	520.0
57	396.5
58	273.0
59	185.5
60	98.0
61	82.0
62	66.0
63	126.5
64	187.0
65	115.0
66	43.0
67	27.0
68	11.0
69	25.5
70	40.0
71	73.0
72	106.0
73	55.5
74	5.0
75	4.0
76	3.0
77	2.0
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	0.0
2	0.17500000000000002
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	39.324999999999996
#Duplication Level	Percentage of deduplicated	Percentage of total
1	75.58804831532105	29.725
2	9.917355371900827	7.8
3	3.4965034965034967	4.125
4	3.0514939605848697	4.8
5	1.7164653528289893	3.375
6	0.9535918626827717	2.25
7	0.8900190718372537	2.45
8	0.5721551176096631	1.7999999999999998
9	0.25429116338207247	0.8999999999999999
>10	2.9879211697393515	21.349999999999998
>50	0.3814367450731087	12.2
>100	0.19071837253655435	9.225
>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
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	141	3.5249999999999995	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	114	2.85	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	114	2.85	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	100	2.5	No Hit
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	86	2.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	81	2.025	RNA PCR Primer, Index 1 (100% over 30bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	80	2.0	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	76	1.9	RNA PCR Primer, Index 1 (100% over 28bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	65	1.625	No Hit
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	48	1.2	RNA PCR Primer, Index 1 (100% over 28bp)
GGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	44	1.0999999999999999	No Hit
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGA	36	0.8999999999999999	RNA PCR Primer, Index 7 (97% over 35bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	31	0.775	RNA PCR Primer, Index 1 (100% over 29bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	31	0.775	No Hit
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	30	0.75	RNA PCR Primer, Index 1 (100% over 29bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	30	0.75	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	27	0.675	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	26	0.65	RNA PCR Primer, Index 1 (100% over 28bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	25	0.625	RNA PCR Primer, Index 1 (100% over 33bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	25	0.625	RNA PCR Primer, Index 1 (100% over 26bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	24	0.6	RNA PCR Primer, Index 1 (100% over 28bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	24	0.6	No Hit
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	23	0.575	RNA PCR Primer, Index 1 (100% over 26bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTCGTATGC	19	0.475	RNA PCR Primer, Index 9 (100% over 50bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	16	0.4	RNA PCR Primer, Index 1 (100% over 27bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	16	0.4	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	15	0.375	RNA PCR Primer, Index 1 (100% over 27bp)
TACCCTGTAGAACCGAATTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	14	0.35000000000000003	No Hit
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	13	0.325	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTC	12	0.3	RNA PCR Primer, Index 9 (100% over 44bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 26bp)
CCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGAT	11	0.27499999999999997	RNA PCR Primer, Index 9 (100% over 36bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	10	0.25	No Hit
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGACTGGAATTCTCGGGT	10	0.25	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGT	10	0.25	No Hit
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	10	0.25	RNA PCR Primer, Index 1 (100% over 31bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCTGGAATTCTCGGGTGC	10	0.25	No Hit
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TGCGGGGCTAGGGCTAACAGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	8	0.2	RNA PCR Primer, Index 1 (100% over 25bp)
TCCAGCATCAGTGATTTTGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	8	0.2	No Hit
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	8	0.2	No Hit
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	8	0.2	No Hit
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCCAGGAACTCCAGTCACGA	7	0.17500000000000002	RNA PCR Primer, Index 9 (97% over 35bp)
TACCCTGTAGATCCGAATTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCTGGAATTCTCGGGTG	7	0.17500000000000002	No Hit
AACATTCAACGCTGTCGGTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	7	0.17500000000000002	No Hit
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	7	0.17500000000000002	No Hit
CACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAAT	7	0.17500000000000002	No Hit
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
CTAGACTGAGGCTCCTTGAGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTAATGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TATTGCACTTGTCCCGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGGTAGTTCAATGGTAGAATTCTCGCCTCCCTGGAATTCTCGGGTG	6	0.15	No Hit
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGATGAAGCACTGTAGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTCTTGGAATTCTCGGGTG	6	0.15	No Hit
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCTGGCTCCGTGTCTTCACTCCCTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTTGGAATTCTCGGGTGCCA	6	0.15	No Hit
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGTGGTTCAGTGGTAGAATTCTCGCCTGCTGGAATTCTCGGGTGCC	5	0.125	No Hit
TCCTGTACTGAGCTGCCCCGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCCAGCATCAGTGATTTTGTTGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTTGGAATTCTCGGGTGCCA	5	0.125	No Hit
GTCAGGATGGCCGAGCGGTCTAAGGCTGGAATTCTCGGGTGCCAAGGAAC	5	0.125	RNA PCR Primer, Index 1 (100% over 24bp)
GCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAATTC	5	0.125	No Hit
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCC	5	0.125	No Hit
CATTATTACTTTTGGTACGCGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGCTGGAATTCTCGGGTGCC	5	0.125	No Hit
TCGGATCCGTCTGAGCTTGGCTTTTTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TTTGGCAATGGTAGAACTCACACCGTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	5	0.125	No Hit
TATTGCACTCGTCCCGGCCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCATTGTTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	5	0.125	No Hit
CACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATC	5	0.125	RNA PCR Primer, Index 9 (100% over 37bp)
TTCAAGTAATTCAGGATAGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AGAATTGTGGCTGGACATCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTTGGAATTCTCGGGTGCC	5	0.125	No Hit
CGCGACCTCAGATCAGATGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	5	0.125	RNA PCR Primer, Index 1 (100% over 33bp)
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTCTCTGGAATTCTCGGGT	5	0.125	No Hit
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTC	5	0.125	No Hit
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	5	0.125	No Hit
ATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCTGGAATTCTCGGGTGCC	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	0.475	0.0	0.0	0.0
2	0.0	0.55	0.0	0.0	0.0
3	0.0	0.675	0.0	0.0	0.0
4	0.0	0.725	0.0	0.0	0.0
5	0.0	0.75	0.0	0.0	0.0
6	0.0	0.8	0.0	0.0	0.0
7	0.0	1.3	0.0	0.0	0.0
8	0.0	1.525	0.0	0.0	0.0
9	0.0	1.675	0.0	0.0	0.0
10	0.0	1.775	0.0	0.0	0.0
11	0.0	1.925	0.0	0.0	0.0
12	0.0	2.325	0.0	0.0	0.0
13	0.0	2.675	0.0	0.0	0.0
14	0.0	3.05	0.0	0.0	0.0
15	0.0	3.75	0.0	0.0	0.0
16	0.0	5.425	0.0	0.0	0.0
17	0.0	5.95	0.0	0.0	0.0
18	0.0	7.175	0.0	0.0	0.0
19	0.0	7.9	0.0	0.0	0.0
20	0.0	8.825	0.0	0.0	0.0
21	0.0	13.725	0.0	0.0	0.0
22	0.0	23.375	0.0	0.0	0.0
23	0.0	48.875	0.0	0.0	0.0
24	0.0	61.45	0.0	0.0	0.0
25	0.0	66.55	0.0	0.0	0.0
26	0.0	68.1	0.0	0.0	0.0
27	0.0	68.975	0.0	0.0	0.0
28	0.0	69.625	0.0	0.0	0.0
29	0.0	70.25	0.0	0.0	0.0
30	0.0	70.775	0.0	0.0	0.0
31	0.0	71.55	0.0	0.0	0.0
32	0.0	73.775	0.0	0.0	0.0
33	0.0	74.8	0.0	0.0	0.0
34	0.0	79.05	0.0	0.0	0.0
35	0.0	80.525	0.0	0.0	0.0
36	0.0	81.975	0.0	0.0	0.0
37	0.0	83.5	0.0	0.0	0.0
38	0.0	83.975	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
GAGTGGA	40	5.315087E-9	44.000004	20
ACATTCA	65	0.0	44.000004	2
GCTTGGC	20	6.952051E-4	44.000004	15
GTCGGTG	65	0.0	44.000004	14
AACATTC	65	0.0	44.000004	1
TGTCGGT	65	0.0	44.000004	13
AACGCTG	60	0.0	44.0	8
GGTGAGT	50	1.4551915E-11	44.0	17
ACGCTGT	60	0.0	44.0	9
TTCAACG	60	0.0	44.0	5
TCGGTGA	55	0.0	44.0	15
TCGGATC	25	3.6958358E-5	44.0	1
CATTCAA	60	0.0	44.0	3
TCAACGC	60	0.0	44.0	6
GTGAGTG	35	1.02281774E-7	44.0	18
GCTGTCG	60	0.0	44.0	11
CGGTGAG	50	1.4551915E-11	44.0	16
CTGTCGG	60	0.0	44.0	12
CTGTTGG	25	3.6958358E-5	44.0	19
TGAGTGG	35	1.02281774E-7	44.0	19
>>END_MODULE
Read 189184 spots for SRR5030989.sra
Written 189184 spots for SRR5030989.sra
Read 189184 spots for SRR5030989.sra
Written 189184 spots for SRR5030989.sra
Read 189184 spots for SRR5030989.sra
Written 189184 spots for SRR5030989.sra
Read 189184 spots for SRR5030989.sra
Written 189184 spots for SRR5030989.sra
Read 189184 spots for SRR5030989.sra
Written 189184 spots for SRR5030989.sra
Read 189184 spots for SRR5030989.sra
Written 189184 spots for SRR5030989.sra
Read 189184 spots for SRR5030989.sra
Written 189184 spots for SRR5030989.sra
Read 189184 spots for SRR5030989.sra
Written 189184 spots for SRR5030989.sra
Read 189184 spots for SRR5030989.sra
Written 189184 spots for SRR5030989.sra
Read 189184 spots for SRR5030989.sra
Written 189184 spots for SRR5030989.sra
Read 189187 spots for SRR5030989.sra
Written 189187 spots for SRR5030989.sra
Read 189184 spots for SRR5030989.sra
Written 189184 spots for SRR5030989.sra
SRR ids: ['SRR5030989.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_6a3tince
SRR5030989.sra spots: 2270211
blocks: [[1, 189184], [189185, 378368], [378369, 567552], [567553, 756736], [756737, 945920], [945921, 1135104], [1135105, 1324288], [1324289, 1513472], [1513473, 1702656], [1702657, 1891840], [1891841, 2081024], [2081025, 2270211]]
SRR5030989 file size 392406
SRR5030989 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030989 SRR5030989_1.fastq
Input file:	SRR5030989_1.fastq
trimmed:	SRR5030989-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 07:00:54 2020 >> started

Wed Mar  4 07:00:57 2020 >> done (2.749s)
2270211 reads processed; of these:
    301 ( 0.01%) short reads filtered out after trimming by size control
      9 ( 0.00%) empty reads filtered out after trimming by size control
2269901 (99.99%) reads available; of these:
 140650 ( 6.20%) trimmed reads available after processing
2129251 (93.80%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     64	  0.00%
 19	     83	  0.00%
 20	    141	  0.01%
 21	    174	  0.01%
 22	    319	  0.01%
 23	    336	  0.01%
 24	    374	  0.02%
 25	    539	  0.02%
 26	    431	  0.02%
 27	    514	  0.02%
 28	    654	  0.03%
 29	    971	  0.04%
 30	    691	  0.03%
 31	    792	  0.03%
 32	    832	  0.04%
 33	   1003	  0.04%
 34	   1355	  0.06%
 35	   2473	  0.11%
 36	   2172	  0.10%
 37	   2536	  0.11%
 38	   2465	  0.11%
 39	   2552	  0.11%
 40	   2921	  0.13%
 41	   3045	  0.13%
 42	   3998	  0.18%
 43	   5873	  0.26%
 44	   7385	  0.33%
 45	   9800	  0.43%
 46	  15007	  0.66%
 47	  15969	  0.70%
 48	  23845	  1.05%
 49	  31336	  1.38%
 50	2129251	 93.80%
2269901 reads passed initial QC


criterion=sequence-density
sequence-density=83.31
sequence-density-rank=1
fanout-score=21.66
fanout-score-rank=1
prefix-density=85.49
prefix-fanout=21.1
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTCGTATGCC


criterion=fanout-score
sequence-density=83.31
sequence-density-rank=1
fanout-score=21.66
fanout-score-rank=1
prefix-density=85.49
prefix-fanout=21.1
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTCGTATGCC -o SRR5030989 -
Input file:	STDIN
trimmed:	SRR5030989-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTCGTATGCC
-- 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 07:03:26 2020 >> started

Wed Mar  4 07:03:32 2020 >> done (5.450s)
2215856 reads processed; of these:
 159782 ( 7.21%) short reads filtered out after trimming by size control
  11934 ( 0.54%) empty reads filtered out after trimming by size control
2044140 (92.25%) reads available; of these:
1901440 (93.02%) trimmed reads available after processing
 142700 ( 6.98%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  11536	  0.56%
 19	  23516	  1.15%
 20	 111028	  5.43%
 21	 216538	 10.59%
 22	 556404	 27.22%
 23	 269616	 13.19%
 24	 125345	  6.13%
 25	  35669	  1.74%
 26	  19635	  0.96%
 27	  15679	  0.77%
 28	  16407	  0.80%
 29	  13273	  0.65%
 30	  20657	  1.01%
 31	  45017	  2.20%
 32	  26470	  1.29%
 33	 105270	  5.15%
 34	  33516	  1.64%
 35	  29019	  1.42%
 36	  31990	  1.56%
 37	  14046	  0.69%
 38	  16948	  0.83%
 39	  13590	  0.66%
 40	  18419	  0.90%
 41	  24234	  1.19%
 42	  28770	  1.41%
 43	  21245	  1.04%
 44	  15193	  0.74%
 45	  23838	  1.17%
 46	  19493	  0.95%
 47	  13947	  0.68%
 48	   1266	  0.06%
 49	   2304	  0.11%
 50	 124262	  6.08%


criterion=sequence-density
sequence-density=2.49
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=16
prefix-density=0.00
prefix-fanout=1.0
sequence=TGTAAACATCCT


criterion=fanout-score
sequence-density=0.61
sequence-density-rank=24
fanout-score=11.98
fanout-score-rank=1
prefix-density=7.34
prefix-fanout=1.0
sequence=TGAGCTTGGCTAT
                                 Started job on |	Mar 04 07:04:01
                             Started mapping on |	Mar 04 07:04:02
                                    Finished on |	Mar 04 07:04:28
       Mapping speed, Million of reads per hour |	290.52

                          Number of input reads |	2098185
                      Average input read length |	28
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1047102
                        Uniquely mapped reads % |	49.91%
                          Average mapped length |	25.01
                       Number of splices: Total |	1239
            Number of splices: Annotated (sjdb) |	185
                       Number of splices: GT/AG |	1165
                       Number of splices: GC/AG |	15
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	59
                      Mismatch rate per base, % |	0.22%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.84
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.00
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	669938
             % of reads mapped to multiple loci |	31.93%
        Number of reads mapped to too many loci |	64955
             % of reads mapped to too many loci |	3.10%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	13.90%
                     % of reads unmapped: other |	1.17%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	381145	381145	381145
N_multimapping	669938	669938	669938
N_noFeature	77261	91951	702804
N_ambiguous	556344	250272	9363
UnstrandedReadsAssigned:413497 PositiveStrandReadsAssigned:704879 NegativeStrandReadsAssigned:334935
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5030989 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: SRR5030989-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,098,185 reads, 493,303 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,124 rounds

 109283 SRR5030989.ke.tsv
  52636 SRR5030989.se.tsv
 161919 total
==> SRR5030989.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

==> SRR5030989.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	1
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030989 completed mapping pipeline successfully
