Starting /dee2/code/volunteer_pipeline.sh SRR5031063
    current disk space = 160494911488
    free memory = 73947444 
SRR5031063 SRAfilesize
3cdef8982861ab5be8fdd887815fbedd  SRR5031063.sra
SRR5031063.sra file validated
SRR5031063 is single end
SRR5031063 is conventional basespace
SRR5031063 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031063_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	32.2875	33.0	31.0	34.0	30.0	34.0
2	32.519	34.0	31.0	34.0	31.0	34.0
3	32.57275	34.0	31.0	34.0	31.0	34.0
4	36.147	37.0	35.0	37.0	35.0	37.0
5	35.787	37.0	35.0	37.0	35.0	37.0
6	35.80475	37.0	35.0	37.0	35.0	37.0
7	35.8955	37.0	35.0	37.0	35.0	37.0
8	35.71275	37.0	35.0	37.0	33.0	37.0
9	37.541	39.0	37.0	39.0	35.0	39.0
10	37.74325	39.0	37.0	39.0	35.0	39.0
11	37.468	39.0	37.0	39.0	35.0	39.0
12	37.51325	39.0	37.0	39.0	35.0	39.0
13	37.611	39.0	37.0	39.0	35.0	39.0
14	38.95725	40.0	38.0	41.0	35.0	41.0
15	38.8145	40.0	38.0	41.0	34.0	41.0
16	38.83775	40.0	38.0	41.0	35.0	41.0
17	38.743	40.0	38.0	41.0	34.0	41.0
18	38.8345	40.0	38.0	41.0	34.0	41.0
19	38.42425	40.0	38.0	41.0	34.0	41.0
20	38.6485	40.0	38.0	41.0	34.0	41.0
21	38.6335	40.0	38.0	41.0	34.0	41.0
22	38.761	40.0	38.0	41.0	34.0	41.0
23	38.582	40.0	38.0	41.0	34.0	41.0
24	38.60075	40.0	38.0	41.0	34.0	41.0
25	38.87225	40.0	38.0	41.0	34.0	41.0
26	38.49925	40.0	38.0	41.0	34.0	41.0
27	38.5595	40.0	38.0	41.0	34.0	41.0
28	38.39175	40.0	38.0	41.0	34.0	41.0
29	37.90025	40.0	37.0	41.0	32.0	41.0
30	37.97025	40.0	38.0	41.0	33.0	41.0
31	38.142	40.0	38.0	41.0	33.0	41.0
32	38.01275	40.0	38.0	41.0	33.0	41.0
33	38.05875	40.0	38.0	41.0	33.0	41.0
34	38.268	40.0	38.0	41.0	34.0	41.0
35	38.127	40.0	38.0	41.0	34.0	41.0
36	37.74725	40.0	37.0	41.0	33.0	41.0
37	37.16725	40.0	37.0	41.0	31.0	41.0
38	36.604	39.0	35.0	41.0	30.0	41.0
39	37.07775	39.0	36.0	41.0	31.0	41.0
40	37.3325	39.0	37.0	41.0	32.0	41.0
41	37.51425	40.0	37.0	41.0	32.0	41.0
42	37.743	40.0	37.0	41.0	33.0	41.0
43	37.8505	40.0	38.0	41.0	33.0	41.0
44	37.58475	40.0	37.0	41.0	33.0	41.0
45	37.5555	40.0	37.0	41.0	33.0	41.0
46	37.445	40.0	37.0	41.0	33.0	41.0
47	36.9135	40.0	36.0	41.0	31.0	41.0
48	36.6015	39.0	36.0	41.0	30.0	41.0
49	36.7765	40.0	36.0	41.0	31.0	41.0
50	36.186	39.0	35.0	41.0	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
14	1.0
15	1.0
16	1.0
17	0.0
18	2.0
19	5.0
20	10.0
21	6.0
22	7.0
23	4.0
24	5.0
25	10.0
26	17.0
27	18.0
28	38.0
29	36.0
30	51.0
31	75.0
32	90.0
33	112.0
34	174.0
35	217.0
36	268.0
37	401.0
38	756.0
39	1695.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	11.25	25.974999999999998	45.425	17.349999999999998
2	20.77596996245307	28.961201501877348	19.749687108886107	30.51314142678348
3	23.35	17.1	22.15	37.4
4	33.025	28.199999999999996	15.950000000000001	22.825
5	21.975	35.675000000000004	27.85	14.499999999999998
6	30.65	15.45	36.125	17.775
7	17.875	21.0	21.65	39.475
8	21.475	29.2	18.925	30.4
9	24.925	33.175	24.775	17.125
10	23.375	19.8	29.2	27.625
11	31.95	12.425	17.849999999999998	37.775
12	15.5	18.85	31.75	33.900000000000006
13	27.375	17.299999999999997	34.0	21.325
14	29.975	31.775	18.45	19.8
15	36.05	23.125	26.450000000000003	14.374999999999998
16	19.725	20.974999999999998	22.85	36.449999999999996
17	28.225	21.775	35.175	14.825
18	27.3	16.475	31.1	25.124999999999996
19	36.225	13.625000000000002	32.775	17.375
20	44.25	15.275	26.650000000000002	13.825000000000001
21	25.5	23.25	22.175	29.075
22	29.65	13.750000000000002	45.675	10.925
23	24.9	14.374999999999998	43.6	17.125
24	49.4	15.299999999999999	26.700000000000003	8.6
25	47.875	22.825	16.875	12.425
26	28.625	43.075	14.899999999999999	13.4
27	17.424999999999997	44.9	24.05	13.625000000000002
28	13.5	24.325	45.775	16.400000000000002
29	13.975000000000001	14.799999999999999	52.1	19.125
30	11.65	8.0	35.225	45.125
31	14.399999999999999	6.15	45.824999999999996	33.625
32	27.175	6.375	23.1	43.35
33	51.05	9.275	15.625	24.05
34	58.425000000000004	8.125	17.175	16.275000000000002
35	62.375	8.674999999999999	18.65	10.299999999999999
36	42.525	9.35	35.05	13.075000000000001
37	45.324999999999996	12.225	20.225	22.225
38	24.875	17.7	13.100000000000001	44.324999999999996
39	16.35	23.425	12.775	47.449999999999996
40	15.024999999999999	45.574999999999996	13.750000000000002	25.650000000000002
41	22.75	46.875	10.8	19.575
42	45.5	27.650000000000002	15.325	11.525
43	48.949999999999996	27.950000000000003	10.025	13.075000000000001
44	32.025	45.375	8.7	13.900000000000002
45	21.099999999999998	47.4	13.600000000000001	17.9
46	16.725	25.650000000000002	18.325	39.300000000000004
47	10.975	14.975	39.6	34.449999999999996
48	12.950000000000001	12.125	21.475	53.449999999999996
49	12.725	18.425	15.475	53.37499999999999
50	17.175	35.8	14.424999999999999	32.6
>>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	0.5
10	1.0
11	0.5
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	0.5
24	0.0
25	0.5
26	1.0
27	2.5
28	4.0
29	3.5
30	3.0
31	5.0
32	7.0
33	9.5
34	12.0
35	22.0
36	32.0
37	33.0
38	34.0
39	40.5
40	47.0
41	51.5
42	56.0
43	78.0
44	100.0
45	130.0
46	160.0
47	301.5
48	443.0
49	525.0
50	607.0
51	728.0
52	849.0
53	634.0
54	419.0
55	475.5
56	532.0
57	402.0
58	272.0
59	181.5
60	91.0
61	71.5
62	52.0
63	99.5
64	147.0
65	90.5
66	34.0
67	24.5
68	15.0
69	16.0
70	17.0
71	36.5
72	56.0
73	28.5
74	1.0
75	1.0
76	1.0
77	1.5
78	2.0
79	2.0
80	2.0
81	2.0
82	2.0
83	1.0
84	0.0
85	0.0
86	0.0
87	0.0
88	0.0
89	0.0
90	0.0
91	0.0
92	0.0
93	0.0
94	0.0
95	0.0
96	0.0
97	0.0
98	0.0
99	0.0
100	0.0
>>END_MODULE
>>Per base N content	pass
#Base	N-Count
1	0.0
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	40.275
#Duplication Level	Percentage of deduplicated	Percentage of total
1	76.1018001241465	30.65
2	9.186840471756673	7.3999999999999995
3	4.531346989447548	5.475
4	2.5450031036623217	4.1000000000000005
5	1.7380509000620732	3.5000000000000004
6	0.8690254500310366	2.1
7	0.6828057107386716	1.925
8	0.4965859714463066	1.6
9	0.5586592178770949	2.025
>10	2.793296089385475	20.25
>50	0.2482929857231533	8.674999999999999
>100	0.2482929857231533	12.3
>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
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	142	3.55	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	123	3.075	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	117	2.9250000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	110	2.75	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	97	2.4250000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	94	2.35	No Hit
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	92	2.3	RNA PCR Primer, Index 1 (100% over 30bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	64	1.6	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	44	1.0999999999999999	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	39	0.975	RNA PCR Primer, Index 1 (100% over 28bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	31	0.775	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	31	0.775	RNA PCR Primer, Index 1 (100% over 26bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	27	0.675	RNA PCR Primer, Index 1 (100% over 33bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	25	0.625	RNA PCR Primer, Index 1 (100% over 28bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCA	24	0.6	RNA PCR Primer, Index 7 (100% over 35bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	23	0.575	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	23	0.575	RNA PCR Primer, Index 1 (100% over 26bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 29bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	21	0.525	No Hit
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	20	0.5	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	20	0.5	RNA PCR Primer, Index 1 (100% over 27bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	20	0.5	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	19	0.475	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 26bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 29bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCATTTTATCTC	17	0.42500000000000004	RNA PCR Primer, Index 35 (100% over 44bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	16	0.4	RNA PCR Primer, Index 1 (100% over 27bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
TACCCTGTAGAACCGAATTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
AACCCGTAGATCCGAACTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	13	0.325	No Hit
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	13	0.325	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	12	0.3	No Hit
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	12	0.3	No Hit
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	12	0.3	No Hit
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCATTTTATCTCGTATGC	12	0.3	RNA PCR Primer, Index 35 (100% over 50bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	12	0.3	No Hit
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 25bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGACTGGAATTCTCGGGT	11	0.27499999999999997	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGT	11	0.27499999999999997	No Hit
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTTGGAATTCTCGGGTGCC	10	0.25	No Hit
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
CATTATTACTTTTGGTACGCGTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCTGGAATTCTCGGGTG	9	0.22499999999999998	No Hit
CACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC	9	0.22499999999999998	RNA PCR Primer, Index 2 (100% over 34bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGGAATTCTCGGGTGCCAA	9	0.22499999999999998	No Hit
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TCTCCCAACCCTTGTACCAGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTTGGAATTCTCGGGTGCCA	8	0.2	No Hit
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	8	0.2	No Hit
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	8	0.2	No Hit
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
CCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAT	8	0.2	RNA PCR Primer, Index 9 (97% over 36bp)
TCCTGTACTGAGCTGCCCCGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TACCCTGTAGATCCGAATTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGCTGGAATTCTCGGGTGCC	7	0.17500000000000002	No Hit
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
GGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	7	0.17500000000000002	No Hit
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTC	7	0.17500000000000002	No Hit
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	7	0.17500000000000002	No Hit
TCCCTGTGGTCTAGTGGTTAGGATTCGGCGCTCTTGGAATTCTCGGGTGC	7	0.17500000000000002	No Hit
AACCCGTAGATCCGAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTTTTTGGAATTCTCGGGTGCCAAGGAACT	6	0.15	RNA PCR Primer, Index 1 (100% over 25bp)
TCCTGTACTGAGCTGCCCCGATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATGGAATTCTCGGGTGCCAAG	6	0.15	No Hit
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	6	0.15	RNA PCR Primer, Index 1 (100% over 31bp)
TGCGGGGCTAGGGCTAACAGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCTGGAATTCTCGGGTGC	6	0.15	No Hit
GCACGGGGTCGGCGGCGATGTCGGTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TATTGCACTCGTCCCGGCCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CGGCTTTGGTGACTCTAGATAACCTCGGGCCGATCGCACGCCCTGGAATT	5	0.125	No Hit
TATTGCACTTGTCCCGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAATTC	5	0.125	No Hit
TCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCC	5	0.125	No Hit
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTCACTGGAATTCTCGGGT	5	0.125	No Hit
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCCAGCATCAGTGATTTTGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	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
GGCTTTGGTGACTCTAGATAACCTCGGGCCGATCGCACGTGGAATTCTCG	5	0.125	No Hit
ATCATGATGGGCTCCTCGGTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGGAATTCTCGGGTGCCA	5	0.125	No Hit
TCCCTGGTCTAGTGGTTAGGATTCGGCGCTCTCTGGAATTCTCGGGTGCC	5	0.125	No Hit
CACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCATT	5	0.125	RNA PCR Primer, Index 32 (97% over 37bp)
ACTAATCCTAGCCCTAGCCCTATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTAACTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGAAATCAAA	5	0.125	No Hit
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TTCCCTTTGTCATCCTATGCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATGGAATTCTCGGGTGC	5	0.125	No Hit
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TAGCTTATCAGACTGATGTTGATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CTAGACTGAGGCTCCTTGAGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
>>END_MODULE
>>Adapter Content	fail
#Position	Illumina Universal Adapter	Illumina Small RNA 3' Adapter	Illumina Small RNA 5' Adapter	Nextera Transposase Sequence	SOLID Small RNA Adapter
1	0.0	0.3	0.0	0.0	0.0
2	0.0	0.35	0.0	0.0	0.0
3	0.0	0.375	0.0	0.0	0.0
4	0.0	0.4	0.0	0.0	0.0
5	0.0	0.475	0.0	0.0	0.0
6	0.0	0.55	0.0	0.0	0.0
7	0.0	1.15	0.0	0.0	0.0
8	0.0	1.325	0.0	0.0	0.0
9	0.0	1.375	0.0	0.0	0.0
10	0.0	1.525	0.0	0.0	0.0
11	0.0	1.825	0.0	0.0	0.0
12	0.0	2.225	0.0	0.0	0.0
13	0.0	2.45	0.0	0.0	0.0
14	0.0	2.775	0.0	0.0	0.0
15	0.0	3.225	0.0	0.0	0.0
16	0.0	4.3	0.0	0.0	0.0
17	0.0	5.1	0.0	0.0	0.0
18	0.0	6.45	0.0	0.0	0.0
19	0.0	6.875	0.0	0.0	0.0
20	0.0	7.8	0.0	0.0	0.0
21	0.0	12.275	0.0	0.0	0.0
22	0.0	22.575	0.0	0.0	0.0
23	0.0	49.825	0.0	0.0	0.0
24	0.0	62.0	0.0	0.0	0.0
25	0.0	68.0	0.0	0.0	0.0
26	0.0	69.95	0.0	0.0	0.0
27	0.0	70.85	0.0	0.0	0.0
28	0.0	71.3	0.0	0.0	0.0
29	0.0	71.9	0.0	0.0	0.0
30	0.0	72.25	0.0	0.0	0.0
31	0.0	73.075	0.0	0.0	0.0
32	0.0	74.425	0.0	0.0	0.0
33	0.0	75.75	0.0	0.0	0.0
34	0.0	80.175	0.0	0.0	0.0
35	0.0	81.95	0.0	0.0	0.0
36	0.0	83.275	0.0	0.0	0.0
37	0.0	84.85	0.0	0.0	0.0
38	0.0	85.5	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TGAGACC	20	6.952051E-4	44.000004	5
AAGTAAT	20	6.952051E-4	44.000004	4
TCAAGTA	20	6.952051E-4	44.000004	2
CTGAGCT	45	2.728484E-10	44.000004	11
CTGAGAC	20	6.952051E-4	44.000004	4
AGCTTGG	45	2.728484E-10	44.000004	14
TTCAAGT	20	6.952051E-4	44.000004	1
AGGATAG	20	6.952051E-4	44.000004	13
ATAGGCT	20	6.952051E-4	44.000004	16
GAGCTTG	45	2.728484E-10	44.000004	13
GGATCCG	45	2.728484E-10	44.000004	3
CCGTCTG	45	2.728484E-10	44.000004	7
CCTGAGA	20	6.952051E-4	44.000004	3
TCGGATC	45	2.728484E-10	44.000004	1
CGGATCC	45	2.728484E-10	44.000004	2
GGATAGG	20	6.952051E-4	44.000004	14
AGTAATC	20	6.952051E-4	44.000004	5
GATCCGT	45	2.728484E-10	44.000004	4
CCCTGAG	20	6.952051E-4	44.000004	2
TTGGCTT	20	6.952051E-4	44.000004	17
>>END_MODULE
Read 221891 spots for SRR5031063.sra
Written 221891 spots for SRR5031063.sra
Read 221891 spots for SRR5031063.sra
Written 221891 spots for SRR5031063.sra
Read 221891 spots for SRR5031063.sra
Written 221891 spots for SRR5031063.sra
Read 221891 spots for SRR5031063.sra
Written 221891 spots for SRR5031063.sra
Read 221891 spots for SRR5031063.sra
Written 221891 spots for SRR5031063.sra
Read 221891 spots for SRR5031063.sra
Written 221891 spots for SRR5031063.sra
Read 221898 spots for SRR5031063.sra
Written 221898 spots for SRR5031063.sra
Read 221891 spots for SRR5031063.sra
Written 221891 spots for SRR5031063.sra
Read 221891 spots for SRR5031063.sra
Written 221891 spots for SRR5031063.sra
Read 221891 spots for SRR5031063.sra
Written 221891 spots for SRR5031063.sra
Read 221891 spots for SRR5031063.sra
Written 221891 spots for SRR5031063.sra
Read 221891 spots for SRR5031063.sra
Written 221891 spots for SRR5031063.sra
SRR ids: ['SRR5031063.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_aaj_pscg
SRR5031063.sra spots: 2662699
blocks: [[1, 221891], [221892, 443782], [443783, 665673], [665674, 887564], [887565, 1109455], [1109456, 1331346], [1331347, 1553237], [1553238, 1775128], [1775129, 1997019], [1997020, 2218910], [2218911, 2440801], [2440802, 2662699]]
SRR5031063 file size 460438
SRR5031063 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031063 SRR5031063_1.fastq
Input file:	SRR5031063_1.fastq
trimmed:	SRR5031063-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 07:16:27 2020 >> started

Wed Mar  4 07:16:30 2020 >> done (3.122s)
2662699 reads processed; of these:
    211 ( 0.01%) short reads filtered out after trimming by size control
      9 ( 0.00%) empty reads filtered out after trimming by size control
2662479 (99.99%) reads available; of these:
 135255 ( 5.08%) trimmed reads available after processing
2527224 (94.92%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     60	  0.00%
 19	     81	  0.00%
 20	    214	  0.01%
 21	    229	  0.01%
 22	    428	  0.02%
 23	    430	  0.02%
 24	    546	  0.02%
 25	    673	  0.03%
 26	    549	  0.02%
 27	    647	  0.02%
 28	    777	  0.03%
 29	   1274	  0.05%
 30	    822	  0.03%
 31	    837	  0.03%
 32	    933	  0.04%
 33	   1148	  0.04%
 34	   1323	  0.05%
 35	   2532	  0.10%
 36	   2461	  0.09%
 37	   2402	  0.09%
 38	   2378	  0.09%
 39	   2639	  0.10%
 40	   2917	  0.11%
 41	   3101	  0.12%
 42	   3968	  0.15%
 43	   5687	  0.21%
 44	   7449	  0.28%
 45	   8726	  0.33%
 46	  13009	  0.49%
 47	  16430	  0.62%
 48	  24415	  0.92%
 49	  26170	  0.98%
 50	2527224	 94.92%
2662479 reads passed initial QC


criterion=sequence-density
sequence-density=85.25
sequence-density-rank=1
fanout-score=22.37
fanout-score-rank=2
prefix-density=87.73
prefix-fanout=21.7
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCATTTTATCTCGTATGCC


criterion=fanout-score
sequence-density=0.01
sequence-density-rank=11
fanout-score=100.10
fanout-score-rank=1
prefix-density=0.53
prefix-fanout=1.0
sequence=TTCCCGTGGACTAATCCTAGCCCTAGCCCTACACAAATATAATTATACTATTAT
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCATTTTATCTCGTATGCC -o SRR5031063 -
Input file:	STDIN
trimmed:	SRR5031063-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCATTTTATCTCGTATGCC
-- 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 07:16:52 2020 >> started

Wed Mar  4 07:16:58 2020 >> done (6.191s)
2600561 reads processed; of these:
 154263 ( 5.93%) short reads filtered out after trimming by size control
  14339 ( 0.55%) empty reads filtered out after trimming by size control
2431959 (93.52%) reads available; of these:
2311199 (95.03%) trimmed reads available after processing
 120760 ( 4.97%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  14775	  0.61%
 19	  23731	  0.98%
 20	 127573	  5.25%
 21	 259044	 10.65%
 22	 720246	 29.62%
 23	 325982	 13.40%
 24	 155511	  6.39%
 25	  46764	  1.92%
 26	  24363	  1.00%
 27	  19984	  0.82%
 28	  22059	  0.91%
 29	  18821	  0.77%
 30	  27889	  1.15%
 31	  35176	  1.45%
 32	  39042	  1.61%
 33	 106639	  4.38%
 34	  44174	  1.82%
 35	  34758	  1.43%
 36	  42180	  1.73%
 37	  17934	  0.74%
 38	  20151	  0.83%
 39	  17406	  0.72%
 40	  25829	  1.06%
 41	  29958	  1.23%
 42	  33098	  1.36%
 43	  22700	  0.93%
 44	  17667	  0.73%
 45	  23565	  0.97%
 46	  17319	  0.71%
 47	  13050	  0.54%
 48	   1209	  0.05%
 49	   1574	  0.06%
 50	 101788	  4.19%


criterion=sequence-density
sequence-density=3.39
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=16
prefix-density=0.00
prefix-fanout=1.0
sequence=TCCCTGAGACCCT


criterion=fanout-score
sequence-density=0.51
sequence-density-rank=31
fanout-score=16.81
fanout-score-rank=1
prefix-density=8.48
prefix-fanout=1.0
sequence=TGAGCTTGGCTTTT
                                 Started job on |	Mar 04 07:17:27
                             Started mapping on |	Mar 04 07:17:28
                                    Finished on |	Mar 04 07:17:52
       Mapping speed, Million of reads per hour |	374.08

                          Number of input reads |	2493877
                      Average input read length |	27
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1328099
                        Uniquely mapped reads % |	53.25%
                          Average mapped length |	25.06
                       Number of splices: Total |	1873
            Number of splices: Annotated (sjdb) |	387
                       Number of splices: GT/AG |	1762
                       Number of splices: GC/AG |	30
                       Number of splices: AT/AC |	2
               Number of splices: Non-canonical |	79
                      Mismatch rate per base, % |	0.21%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.75
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.01
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	803687
             % of reads mapped to multiple loci |	32.23%
        Number of reads mapped to too many loci |	68920
             % of reads mapped to too many loci |	2.76%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	10.72%
                     % of reads unmapped: other |	1.04%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	362091	362091	362091
N_multimapping	803687	803687	803687
N_noFeature	65891	86176	893565
N_ambiguous	721171	341669	11718
UnstrandedReadsAssigned:541037 PositiveStrandReadsAssigned:900254 NegativeStrandReadsAssigned:422816
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5031063 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: SRR5031063-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,493,877 reads, 626,288 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 713 rounds

 109283 SRR5031063.ke.tsv
  52636 SRR5031063.se.tsv
 161919 total
==> SRR5031063.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

==> SRR5031063.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031063 completed mapping pipeline successfully
