Starting /dee2/code/volunteer_pipeline.sh SRR5030880
    current disk space = 160661422080
    free memory = 73946432 
SRR5030880 SRAfilesize
8702966348fa96816e23a676d8cd5de2  SRR5030880.sra
SRR5030880.sra file validated
SRR5030880 is single end
SRR5030880 is conventional basespace
SRR5030880 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030880_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	fail
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	32.31975	33.0	31.0	34.0	31.0	34.0
2	32.70925	34.0	31.0	34.0	31.0	34.0
3	32.74175	34.0	31.0	34.0	31.0	34.0
4	36.2195	37.0	37.0	37.0	35.0	37.0
5	36.2275	37.0	37.0	37.0	35.0	37.0
6	35.9315	37.0	35.0	37.0	35.0	37.0
7	36.0915	37.0	35.0	37.0	35.0	37.0
8	36.13125	37.0	36.0	37.0	35.0	37.0
9	37.86525	39.0	38.0	39.0	35.0	39.0
10	37.8905	39.0	38.0	39.0	35.0	39.0
11	37.78275	39.0	38.0	39.0	35.0	39.0
12	37.9045	39.0	38.0	39.0	35.0	39.0
13	37.873	39.0	38.0	39.0	35.0	39.0
14	39.249	41.0	39.0	41.0	36.0	41.0
15	39.28175	41.0	39.0	41.0	36.0	41.0
16	39.156	40.0	39.0	41.0	36.0	41.0
17	39.2255	41.0	39.0	41.0	36.0	41.0
18	39.25975	41.0	39.0	41.0	36.0	41.0
19	39.1425	40.0	39.0	41.0	36.0	41.0
20	39.13225	40.0	39.0	41.0	36.0	41.0
21	39.214	41.0	39.0	41.0	36.0	41.0
22	39.18175	41.0	39.0	41.0	36.0	41.0
23	39.08	40.0	39.0	41.0	36.0	41.0
24	38.27775	40.0	38.0	41.0	34.0	41.0
25	38.59875	40.0	38.0	41.0	34.0	41.0
26	38.65375	40.0	38.0	41.0	34.0	41.0
27	38.718	40.0	38.0	41.0	35.0	41.0
28	38.661	40.0	38.0	41.0	34.0	41.0
29	38.51575	40.0	38.0	41.0	34.0	41.0
30	38.128	40.0	38.0	41.0	33.0	41.0
31	38.52825	40.0	38.0	41.0	34.0	41.0
32	38.6495	40.0	38.0	41.0	34.0	41.0
33	36.8715	40.0	37.0	41.0	30.0	41.0
34	36.565	40.0	36.0	41.0	30.0	41.0
35	33.0235	38.0	32.0	40.0	15.0	41.0
36	30.10125	37.0	23.0	40.0	8.0	41.0
37	30.482	37.0	25.0	40.0	8.0	41.0
38	32.76175	37.0	31.0	40.0	16.0	41.0
39	32.35225	37.0	31.0	40.0	9.0	41.0
40	33.00225	38.0	33.0	40.0	9.0	41.0
41	30.99825	37.0	28.0	40.0	2.0	41.0
42	32.43325	38.0	31.0	40.0	2.0	41.0
43	30.67075	37.0	28.0	40.0	2.0	41.0
44	31.46775	37.0	30.0	40.0	2.0	41.0
45	29.698	37.0	26.0	40.0	2.0	41.0
46	27.523	35.0	17.0	39.0	2.0	41.0
47	27.56175	35.0	20.0	39.0	2.0	41.0
48	28.0925	35.0	23.0	39.0	2.0	41.0
49	26.3925	35.0	2.0	39.0	2.0	41.0
50	22.97375	30.0	2.0	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	2.0
17	2.0
18	4.0
19	3.0
20	11.0
21	22.0
22	16.0
23	30.0
24	48.0
25	56.0
26	75.0
27	137.0
28	70.0
29	121.0
30	154.0
31	147.0
32	163.0
33	180.0
34	227.0
35	270.0
36	304.0
37	466.0
38	691.0
39	801.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	13.273228149261207	24.36764337590784	43.776609065865266	18.582519408965688
2	27.700000000000003	25.324999999999996	20.25	26.724999999999998
3	22.475	21.349999999999998	21.675	34.5
4	31.45	27.275	15.174999999999999	26.1
5	23.9	37.425000000000004	25.775	12.9
6	31.45	17.224999999999998	35.199999999999996	16.125
7	18.85	21.575	26.25	33.324999999999996
8	28.175	29.575000000000003	17.075000000000003	25.174999999999997
9	18.45	33.0	31.275	17.275
10	23.9	22.825	28.475	24.8
11	37.075	14.174999999999999	15.9	32.85
12	19.075	22.1	27.250000000000004	31.574999999999996
13	28.125	19.25	33.5	19.125
14	29.225	26.424999999999997	24.85	19.5
15	32.95	25.525	25.2	16.325
16	20.225	20.7	24.474999999999998	34.599999999999994
17	24.675	25.55	33.825	15.950000000000001
18	24.375	19.5	30.125	26.0
19	34.125	15.45	30.675	19.75
20	39.825	16.2	28.9	15.075
21	26.474999999999998	21.475	26.474999999999998	25.575
22	29.075	14.249999999999998	42.9	13.775
23	25.724999999999998	15.65	40.575	18.05
24	46.9	13.8	26.525	12.775
25	45.6	22.95	16.6	14.85
26	28.299999999999997	39.050000000000004	15.775	16.875
27	18.35	42.8	20.7	18.15
28	15.575	25.5	42.15	16.775000000000002
29	16.150000000000002	14.174999999999999	50.849999999999994	18.825
30	13.725000000000001	9.175	35.35	41.75
31	16.900000000000002	7.9	43.475	31.724999999999998
32	28.525	7.9750000000000005	23.225	40.275
33	46.35	12.925	15.174999999999999	25.55
34	55.175	9.175	17.0	18.65
35	54.449999999999996	9.825000000000001	21.325	14.399999999999999
36	58.225	10.174999999999999	16.7	14.899999999999999
37	37.775	14.374999999999998	21.925	25.924999999999997
38	26.5	17.1	13.925	42.475
39	18.425	24.75	13.3	43.525000000000006
40	18.875	42.525	14.499999999999998	24.099999999999998
41	27.0	40.125	12.8	20.075000000000003
42	45.0	28.000000000000004	14.499999999999998	12.5
43	41.775	33.1	11.575000000000001	13.55
44	31.474999999999998	43.925	10.05	14.549999999999999
45	22.25	43.725	11.799999999999999	22.225
46	17.299999999999997	28.325	23.925	30.45
47	13.100000000000001	17.325	32.225	37.35
48	14.725	14.025000000000002	21.7	49.55
49	15.525	25.3	14.825	44.35
50	30.607651912978245	23.40585146286572	11.077769442360589	34.90872718179545
>>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	0.5
16	1.0
17	0.5
18	0.0
19	0.0
20	0.0
21	0.5
22	1.0
23	1.5
24	2.0
25	1.5
26	1.0
27	1.0
28	1.0
29	2.5
30	4.0
31	5.5
32	7.0
33	14.0
34	21.0
35	35.5
36	50.0
37	71.0
38	92.0
39	79.5
40	67.0
41	70.5
42	74.0
43	92.0
44	110.0
45	159.5
46	209.0
47	247.0
48	285.0
49	388.0
50	491.0
51	619.5
52	748.0
53	631.0
54	514.0
55	470.0
56	426.0
57	365.5
58	305.0
59	236.0
60	167.0
61	129.5
62	92.0
63	129.0
64	166.0
65	107.0
66	48.0
67	30.0
68	12.0
69	21.5
70	31.0
71	41.0
72	51.0
73	31.5
74	12.0
75	6.5
76	1.0
77	3.0
78	5.0
79	3.5
80	2.0
81	3.0
82	4.0
83	2.0
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	0.17500000000000002
2	0.0
3	0.0
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.0
10	0.0
11	0.0
12	0.0
13	0.0
14	0.0
15	0.0
16	0.0
17	0.0
18	0.0
19	0.0
20	0.0
21	0.0
22	0.0
23	0.0
24	0.0
25	0.0
26	0.0
27	0.0
28	0.0
29	0.0
30	0.0
31	0.0
32	0.0
33	0.0
34	0.0
35	0.0
36	0.0
37	0.0
38	0.0
39	0.0
40	0.0
41	0.0
42	0.0
43	0.0
44	0.0
45	0.0
46	0.0
47	0.0
48	0.0
49	0.0
50	0.025
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
50	4000.0
>>END_MODULE
>>Sequence Duplication Levels	warn
#Total Deduplicated Percentage	54.50000000000001
#Duplication Level	Percentage of deduplicated	Percentage of total
1	81.88073394495413	44.625
2	7.477064220183487	8.15
3	3.6238532110091746	5.925
4	1.1926605504587156	2.6
5	1.3302752293577982	3.6249999999999996
6	0.6880733944954129	2.25
7	0.6880733944954129	2.625
8	0.41284403669724773	1.7999999999999998
9	0.45871559633027525	2.25
>10	2.1100917431192663	19.825
>50	0.09174311926605505	3.675
>100	0.045871559633027525	2.65
>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	106	2.65	RNA PCR Primer, Index 1 (100% over 27bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	90	2.25	No Hit
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	57	1.425	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	39	0.975	RNA PCR Primer, Index 1 (96% over 28bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	30	0.75	No Hit
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGACGACATCTCGTATGC	28	0.7000000000000001	RNA PCR Primer, Index 41 (100% over 50bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	27	0.675	RNA PCR Primer, Index 1 (100% over 27bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	26	0.65	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	25	0.625	RNA PCR Primer, Index 1 (100% over 29bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	25	0.625	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	25	0.625	RNA PCR Primer, Index 1 (100% over 26bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 33bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (96% over 28bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGA	21	0.525	RNA PCR Primer, Index 7 (97% over 35bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	21	0.525	RNA PCR Primer, Index 1 (96% over 28bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	21	0.525	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	20	0.5	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	19	0.475	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	19	0.475	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	19	0.475	RNA PCR Primer, Index 1 (100% over 28bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGACGACATCTC	17	0.42500000000000004	RNA PCR Primer, Index 41 (100% over 44bp)
GCGGATGATGACACCTGGGTATGCTGCACACTCCCGACTGCGTCGTGGGG	17	0.42500000000000004	No Hit
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	16	0.4	No Hit
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	16	0.4	RNA PCR Primer, Index 1 (100% over 26bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGAAATCAAA	16	0.4	No Hit
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCG	15	0.375	RNA PCR Primer, Index 1 (96% over 27bp)
TGAACTGATGATATCATTTCTTTCCCCGTCAGATCGACCCTGTTGATCTC	15	0.375	No Hit
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
CGACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGC	14	0.35000000000000003	No Hit
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 30bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	13	0.325	No Hit
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
GACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGCT	13	0.325	No Hit
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	13	0.325	No Hit
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGC	13	0.325	RNA PCR Primer, Index 1 (96% over 29bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (96% over 28bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	13	0.325	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCGG	12	0.3	No Hit
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	11	0.27499999999999997	No Hit
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCG	10	0.25	RNA PCR Primer, Index 1 (96% over 27bp)
TGCTGTGATGAGATGACTAAGTAGGAAGTGCCGTCAGAGTCGATAACTGA	10	0.25	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGCTGGAATTCTCGGGTGCC	10	0.25	No Hit
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCG	10	0.25	RNA PCR Primer, Index 1 (96% over 27bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
GCATGTGATGACATTATTTAGCGACCAAAGTCTGATAAAGATGATTGTGA	9	0.22499999999999998	No Hit
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	9	0.22499999999999998	No Hit
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAC	9	0.22499999999999998	No Hit
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCG	9	0.22499999999999998	RNA PCR Primer, Index 1 (96% over 27bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	9	0.22499999999999998	No Hit
GTAAATGATGAGATTCCATTGGTCCGTGTTTCTGAACTACATGATTTTCC	9	0.22499999999999998	No Hit
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCG	9	0.22499999999999998	No Hit
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAA	8	0.2	No Hit
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (96% over 28bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCG	8	0.2	RNA PCR Primer, Index 1 (96% over 27bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCG	8	0.2	RNA PCR Primer, Index 1 (96% over 27bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
GTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAAT	8	0.2	No Hit
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
CACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCC	7	0.17500000000000002	No Hit
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (96% over 28bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
ATACATGATGATCTCACACAACTTGAACTCTCTCACTGATTACTTGATGA	7	0.17500000000000002	No Hit
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	7	0.17500000000000002	No Hit
TTGCATGATGACTTGAATTGTCGGATACCCCTTCACCCCGTTCATGGGTG	7	0.17500000000000002	No Hit
GTGAAATGATGGCAAATCATCTTTCGGGACTGACCTGAAATGAAGAGAAT	7	0.17500000000000002	No Hit
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGGGCCAAGGAACTCCG	6	0.15	RNA PCR Primer, Index 1 (96% over 27bp)
CGACACAAGGGTTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACG	6	0.15	RNA PCR Primer, Index 6 (100% over 34bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	6	0.15	RNA PCR Primer, Index 1 (100% over 25bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AGCCCATGATGGTATGAGAGTAGTGGACAGAAGGGATTTCTGAAAAACAC	6	0.15	No Hit
TTCAAGTAATCCAGGATAGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	6	0.15	No Hit
CTGCAGTGATGACTATCTTAGGACACCTTTGGATTTACCGTGAAAAGAAG	6	0.15	No Hit
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
AGCTACATCTGGCTACTGGGTCTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TTGCAATGATGACTTATATATCTGTCAATCCCCTGAGAGATCACTGACGA	6	0.15	No Hit
GGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	6	0.15	No Hit
AAGGGATTCTGATGTTGGTCATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
GGTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCG	5	0.125	No Hit
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAATTCCG	5	0.125	RNA PCR Primer, Index 1 (95% over 23bp)
TACCATGATGATAACATAGTTCAGCAGACTTAACTCTGATGAACAATCAT	5	0.125	No Hit
GTCTGATGATGAGCCCATTGCCCTGAGCTCTTGTGATGCTGGCTTCAAAG	5	0.125	No Hit
CACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACG	5	0.125	RNA PCR Primer, Index 6 (100% over 34bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CACCCTGATGAACTGAATACCGCCCCAGTCTGATAGCTGTGGAGAAAGGT	5	0.125	No Hit
TGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	5	0.125	No Hit
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCGGG	5	0.125	No Hit
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGGGCCAAGGAACTCCG	5	0.125	RNA PCR Primer, Index 1 (96% over 27bp)
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	5	0.125	No Hit
TCTTTGGTTATCTAGCTGTATGTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CTGCATGATGACGAACAAATACTGACTACCTGAAGATCTTATTAGCTCTA	5	0.125	No Hit
ACGCACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTC	5	0.125	No Hit
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
CACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAAT	5	0.125	No Hit
TCCCTGAGACCCTAACTTGTGAAATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGTTTGTGCTGTTATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
GTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATACT	5	0.125	No Hit
CCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGAC	5	0.125	RNA PCR Primer, Index 6 (97% over 36bp)
GAGCAATGATGACCCCAACATGCCATCTGAGTGGCTTTGCTGAAATCCAG	5	0.125	No Hit
TGTAAACATCCTCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	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	0.8	0.0	0.0	0.0
2	0.0	0.85	0.0	0.0	0.0
3	0.0	0.925	0.0	0.0	0.0
4	0.0	0.95	0.0	0.0	0.0
5	0.0	1.0	0.0	0.0	0.0
6	0.0	1.125	0.0	0.0	0.0
7	0.0	1.625	0.0	0.0	0.0
8	0.0	1.675	0.0	0.0	0.0
9	0.0	1.8	0.0	0.0	0.0
10	0.0	2.05	0.0	0.0	0.0
11	0.0	2.325	0.0	0.0	0.0
12	0.0	2.7	0.0	0.0	0.0
13	0.0	2.975	0.0	0.0	0.0
14	0.0	3.25	0.0	0.0	0.0
15	0.0	3.825	0.0	0.0	0.0
16	0.0	4.825	0.0	0.0	0.0
17	0.0	5.55	0.0	0.0	0.0
18	0.0	6.9	0.0	0.0	0.0
19	0.0	7.475	0.0	0.0	0.0
20	0.0	8.5	0.0	0.0	0.0
21	0.0	12.025	0.0	0.0	0.0
22	0.0	20.775	0.0	0.0	0.0
23	0.0	44.125	0.0	0.0	0.0
24	0.0	55.9	0.0	0.0	0.0
25	0.0	61.075	0.0	0.0	0.0
26	0.0	62.5	0.0	0.0	0.0
27	0.0	63.35	0.0	0.0	0.0
28	0.0	64.0	0.0	0.0	0.0
29	0.0	64.325	0.0	0.0	0.0
30	0.0	64.875	0.0	0.0	0.0
31	0.0	65.675	0.0	0.0	0.0
32	0.0	66.65	0.0	0.0	0.0
33	0.0	67.525	0.0	0.0	0.0
34	0.0	71.325	0.0	0.0	0.0
35	0.0	72.275	0.0	0.0	0.0
36	0.0	72.925	0.0	0.0	0.0
37	0.0	73.675	0.0	0.0	0.0
38	0.0	73.975	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TTCAAGT	20	6.54202E-4	44.531643	1
AAGCTGC	20	6.54202E-4	44.531643	1
TCCCTGA	20	6.54202E-4	44.531643	1
TGAGACC	20	6.971556E-4	43.975	5
ACTGTTG	20	6.971556E-4	43.975	18
GTTGAAG	20	6.971556E-4	43.975	10
AAGTAAT	20	6.971556E-4	43.975	4
TCAAGTA	20	6.971556E-4	43.975	2
AATCCAG	20	6.971556E-4	43.975	8
CAGTTGA	20	6.971556E-4	43.975	8
CTGAGAC	20	6.971556E-4	43.975	4
ATCCAGG	20	6.971556E-4	43.975	9
CCAGTTG	20	6.971556E-4	43.975	7
AACTGTT	20	6.971556E-4	43.975	17
AGGATAG	20	6.971556E-4	43.975	13
ATAGGCT	20	6.971556E-4	43.975	16
AGGAATT	20	6.971556E-4	43.975	41
CCTGAGA	20	6.971556E-4	43.975	3
AGAACTG	20	6.971556E-4	43.975	15
GGATAGG	20	6.971556E-4	43.975	14
>>END_MODULE
Read 230836 spots for SRR5030880.sra
Written 230836 spots for SRR5030880.sra
Read 230836 spots for SRR5030880.sra
Written 230836 spots for SRR5030880.sra
Read 230836 spots for SRR5030880.sra
Written 230836 spots for SRR5030880.sra
Read 230836 spots for SRR5030880.sra
Written 230836 spots for SRR5030880.sra
Read 230836 spots for SRR5030880.sra
Written 230836 spots for SRR5030880.sra
Read 230836 spots for SRR5030880.sra
Written 230836 spots for SRR5030880.sra
Read 230836 spots for SRR5030880.sra
Written 230836 spots for SRR5030880.sra
Read 230836 spots for SRR5030880.sra
Written 230836 spots for SRR5030880.sra
Read 230836 spots for SRR5030880.sra
Written 230836 spots for SRR5030880.sra
Read 230836 spots for SRR5030880.sra
Written 230836 spots for SRR5030880.sra
Read 230836 spots for SRR5030880.sra
Written 230836 spots for SRR5030880.sra
Read 230843 spots for SRR5030880.sra
Written 230843 spots for SRR5030880.sra
SRR ids: ['SRR5030880.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_ll1dqcj9
SRR5030880.sra spots: 2770039
blocks: [[1, 230836], [230837, 461672], [461673, 692508], [692509, 923344], [923345, 1154180], [1154181, 1385016], [1385017, 1615852], [1615853, 1846688], [1846689, 2077524], [2077525, 2308360], [2308361, 2539196], [2539197, 2770039]]
SRR5030880 file size 479030
SRR5030880 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030880 SRR5030880_1.fastq
Input file:	SRR5030880_1.fastq
trimmed:	SRR5030880-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 06:34:39 2020 >> started

Wed Mar  4 06:34:40 2020 >> done (1.870s)
2770039 reads processed; of these:
    174 ( 0.01%) short reads filtered out after trimming by size control
      6 ( 0.00%) empty reads filtered out after trimming by size control
2769859 (99.99%) reads available; of these:
 336281 (12.14%) trimmed reads available after processing
2433578 (87.86%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     42	  0.00%
 19	     65	  0.00%
 20	    105	  0.00%
 21	    155	  0.01%
 22	    262	  0.01%
 23	    373	  0.01%
 24	    367	  0.01%
 25	    544	  0.02%
 26	    478	  0.02%
 27	    578	  0.02%
 28	    759	  0.03%
 29	   1168	  0.04%
 30	    914	  0.03%
 31	   1327	  0.05%
 32	   3399	  0.12%
 33	   9529	  0.34%
 34	  20214	  0.73%
 35	   4782	  0.17%
 36	   5140	  0.19%
 37	   3196	  0.12%
 38	   5952	  0.21%
 39	   6460	  0.23%
 40	  11639	  0.42%
 41	   7280	  0.26%
 42	  18043	  0.65%
 43	   7781	  0.28%
 44	  30503	  1.10%
 45	  21585	  0.78%
 46	  20795	  0.75%
 47	  22064	  0.80%
 48	  58132	  2.10%
 49	  72650	  2.62%
 50	2433578	 87.86%
2769859 reads passed initial QC


criterion=sequence-density
sequence-density=74.11
sequence-density-rank=1
fanout-score=22.12
fanout-score-rank=3
prefix-density=76.96
prefix-fanout=21.3
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGACGACATCTCGTATGCC


criterion=fanout-score
sequence-density=1.61
sequence-density-rank=6
fanout-score=459.51
fanout-score-rank=1
prefix-density=75.97
prefix-fanout=9.7
sequence=GGAATTCTCGGTGCCAAGGA
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGACGACATCTCGTATGCC -o SRR5030880 -
Input file:	STDIN
trimmed:	SRR5030880-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGACGACATCTCGTATGCC
-- 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 06:34:55 2020 >> started

Wed Mar  4 06:34:59 2020 >> done (4.353s)
2695996 reads processed; of these:
 161497 ( 5.99%) short reads filtered out after trimming by size control
  21913 ( 0.81%) empty reads filtered out after trimming by size control
2512586 (93.20%) reads available; of these:
2089819 (83.17%) trimmed reads available after processing
 422767 (16.83%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  18675	  0.74%
 19	  26644	  1.06%
 20	 102766	  4.09%
 21	 245683	  9.78%
 22	 631861	 25.15%
 23	 314788	 12.53%
 24	 142958	  5.69%
 25	  41284	  1.64%
 26	  23368	  0.93%
 27	  20432	  0.81%
 28	  21199	  0.84%
 29	  18695	  0.74%
 30	  23797	  0.95%
 31	  28642	  1.14%
 32	  28112	  1.12%
 33	 100610	  4.00%
 34	  31802	  1.27%
 35	  24846	  0.99%
 36	  32678	  1.30%
 37	  16222	  0.65%
 38	  18483	  0.74%
 39	  18369	  0.73%
 40	  25229	  1.00%
 41	  28520	  1.14%
 42	  34776	  1.38%
 43	  25587	  1.02%
 44	  26000	  1.03%
 45	  26238	  1.04%
 46	  23499	  0.94%
 47	  20416	  0.81%
 48	   6442	  0.26%
 49	  11675	  0.46%
 50	 352290	 14.02%


criterion=sequence-density
sequence-density=6.43
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=0.47
sequence-density-rank=26
fanout-score=11.40
fanout-score-rank=1
prefix-density=5.40
prefix-fanout=1.0
sequence=TGAGCTTGGCTATT
                                 Started job on |	Mar 04 06:35:23
                             Started mapping on |	Mar 04 06:35:23
                                    Finished on |	Mar 04 06:35:48
       Mapping speed, Million of reads per hour |	372.45

                          Number of input reads |	2586449
                      Average input read length |	30
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1291123
                        Uniquely mapped reads % |	49.92%
                          Average mapped length |	28.91
                       Number of splices: Total |	1858
            Number of splices: Annotated (sjdb) |	332
                       Number of splices: GT/AG |	1708
                       Number of splices: GC/AG |	29
                       Number of splices: AT/AC |	1
               Number of splices: Non-canonical |	120
                      Mismatch rate per base, % |	0.28%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.26
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.11
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	822500
             % of reads mapped to multiple loci |	31.80%
        Number of reads mapped to too many loci |	85725
             % of reads mapped to too many loci |	3.31%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	13.84%
                     % of reads unmapped: other |	1.13%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	472826	472826	472826
N_multimapping	822500	822500	822500
N_noFeature	84363	102404	960811
N_ambiguous	686962	405769	22198
UnstrandedReadsAssigned:519798 PositiveStrandReadsAssigned:782950 NegativeStrandReadsAssigned:308114
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5030880 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: SRR5030880-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,586,449 reads, 597,607 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,099 rounds

 109283 SRR5030880.ke.tsv
  52636 SRR5030880.se.tsv
 161919 total
==> SRR5030880.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

==> SRR5030880.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030880 completed mapping pipeline successfully
