Starting /dee2/code/volunteer_pipeline.sh SRR5031028
    current disk space = 160544604160
    free memory = 73956108 
SRR5031028 SRAfilesize
baba5b4654837f7ef42ea7c84c6d9509  SRR5031028.sra
SRR5031028.sra file validated
SRR5031028 is single end
SRR5031028 is conventional basespace
SRR5031028 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031028_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	32.259	33.0	31.0	34.0	31.0	34.0
2	32.50925	34.0	31.0	34.0	31.0	34.0
3	32.5615	34.0	31.0	34.0	31.0	34.0
4	36.17025	37.0	35.0	37.0	35.0	37.0
5	36.0535	37.0	35.0	37.0	35.0	37.0
6	35.9645	37.0	35.0	37.0	35.0	37.0
7	35.8695	37.0	35.0	37.0	35.0	37.0
8	35.981	37.0	35.0	37.0	35.0	37.0
9	37.573	39.0	37.0	39.0	35.0	39.0
10	37.6045	39.0	37.0	39.0	35.0	39.0
11	37.1025	39.0	37.0	39.0	33.0	39.0
12	37.61425	39.0	37.0	39.0	35.0	39.0
13	37.6135	39.0	37.0	39.0	35.0	39.0
14	39.05175	40.0	38.0	41.0	36.0	41.0
15	39.03975	40.0	38.0	41.0	35.0	41.0
16	39.02975	40.0	38.0	41.0	36.0	41.0
17	39.17625	40.0	39.0	41.0	36.0	41.0
18	38.96475	41.0	38.0	41.0	35.0	41.0
19	38.75025	40.0	38.0	41.0	34.0	41.0
20	38.7565	40.0	38.0	41.0	34.0	41.0
21	38.86125	40.0	38.0	41.0	35.0	41.0
22	38.8585	40.0	38.0	41.0	35.0	41.0
23	38.5885	40.0	38.0	41.0	34.0	41.0
24	38.87775	40.0	38.0	41.0	35.0	41.0
25	38.98875	40.0	38.0	41.0	35.0	41.0
26	38.837	40.0	38.0	41.0	35.0	41.0
27	38.9675	40.0	38.0	41.0	35.0	41.0
28	38.72075	40.0	38.0	41.0	35.0	41.0
29	38.28825	40.0	38.0	41.0	33.0	41.0
30	38.051	40.0	38.0	41.0	33.0	41.0
31	38.40075	40.0	38.0	41.0	34.0	41.0
32	38.25825	40.0	38.0	41.0	33.0	41.0
33	37.7125	40.0	37.0	41.0	33.0	41.0
34	37.894	40.0	37.0	41.0	33.0	41.0
35	37.77825	40.0	37.0	41.0	33.0	41.0
36	37.64425	39.0	37.0	41.0	33.0	41.0
37	36.95275	39.0	36.0	40.0	30.0	41.0
38	36.902	39.0	36.0	40.0	31.0	41.0
39	37.35975	39.0	37.0	41.0	32.0	41.0
40	37.4835	40.0	37.0	41.0	32.0	41.0
41	37.73775	40.0	37.0	41.0	33.0	41.0
42	37.7545	40.0	37.0	41.0	33.0	41.0
43	37.87125	40.0	37.0	41.0	33.0	41.0
44	37.77325	40.0	37.0	41.0	33.0	41.0
45	37.6285	40.0	37.0	41.0	33.0	41.0
46	37.3505	40.0	36.0	41.0	33.0	41.0
47	36.50675	39.0	35.0	41.0	30.0	41.0
48	36.0575	39.0	35.0	41.0	29.0	41.0
49	36.201	39.0	35.0	41.0	30.0	41.0
50	35.5715	38.0	34.0	40.0	29.0	41.0
>>END_MODULE
>>Per tile sequence quality	pass
#Tile	Base	Mean
1101	1	0.0
1101	2	0.0
1101	3	0.0
1101	4	0.0
1101	5	0.0
1101	6	0.0
1101	7	0.0
1101	8	0.0
1101	9	0.0
1101	10	0.0
1101	11	0.0
1101	12	0.0
1101	13	0.0
1101	14	0.0
1101	15	0.0
1101	16	0.0
1101	17	0.0
1101	18	0.0
1101	19	0.0
1101	20	0.0
1101	21	0.0
1101	22	0.0
1101	23	0.0
1101	24	0.0
1101	25	0.0
1101	26	0.0
1101	27	0.0
1101	28	0.0
1101	29	0.0
1101	30	0.0
1101	31	0.0
1101	32	0.0
1101	33	0.0
1101	34	0.0
1101	35	0.0
1101	36	0.0
1101	37	0.0
1101	38	0.0
1101	39	0.0
1101	40	0.0
1101	41	0.0
1101	42	0.0
1101	43	0.0
1101	44	0.0
1101	45	0.0
1101	46	0.0
1101	47	0.0
1101	48	0.0
1101	49	0.0
1101	50	0.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
14	1.0
15	0.0
16	0.0
17	0.0
18	2.0
19	2.0
20	3.0
21	7.0
22	4.0
23	7.0
24	5.0
25	9.0
26	15.0
27	17.0
28	33.0
29	33.0
30	57.0
31	74.0
32	83.0
33	104.0
34	152.0
35	199.0
36	295.0
37	526.0
38	819.0
39	1553.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	12.174999999999999	24.775	42.9	20.150000000000002
2	23.520561685055167	25.877632898696092	19.50852557673019	31.093279839518555
3	23.3	16.35	26.0	34.35
4	35.975	27.224999999999998	16.35	20.45
5	21.45	35.725	27.35	15.475
6	28.325	16.3	36.775000000000006	18.6
7	19.975	20.075000000000003	19.675	40.275
8	21.5	26.35	20.225	31.924999999999997
9	25.25	28.349999999999998	24.975	21.425
10	23.075000000000003	21.0	28.299999999999997	27.625
11	33.625	12.950000000000001	16.825000000000003	36.6
12	18.425	19.975	31.075000000000003	30.525000000000002
13	29.349999999999998	16.125	33.300000000000004	21.224999999999998
14	29.325000000000003	28.9	18.425	23.35
15	34.1	23.525	27.725	14.649999999999999
16	20.1	18.35	25.174999999999997	36.375
17	28.549999999999997	22.15	32.45	16.85
18	26.875	14.499999999999998	30.825000000000003	27.800000000000004
19	35.65	15.049999999999999	31.65	17.65
20	40.375	17.275	25.775	16.575
21	26.674999999999997	20.974999999999998	23.849999999999998	28.499999999999996
22	32.9	14.7	39.125	13.275
23	26.450000000000003	15.225	37.35	20.974999999999998
24	48.025	17.150000000000002	25.45	9.375
25	44.6	24.575	16.8	14.025000000000002
26	29.9	38.35	15.875	15.875
27	18.6	40.325	22.7	18.375
28	14.45	23.225	42.4	19.925
29	17.5	14.524999999999999	50.349999999999994	17.625
30	14.249999999999998	8.875	31.125000000000004	45.75
31	17.0	7.449999999999999	42.449999999999996	33.1
32	30.25	8.0	21.15	40.6
33	47.05	13.3	15.35	24.3
34	51.349999999999994	10.174999999999999	21.85	16.625
35	61.0	8.225	17.724999999999998	13.05
36	40.725	9.975000000000001	33.775	15.525
37	39.65	16.3	20.775	23.275000000000002
38	24.575	21.525	13.8	40.1
39	18.35	22.825	15.024999999999999	43.8
40	17.8	41.725	16.325	24.15
41	24.425	42.3	11.924999999999999	21.349999999999998
42	41.675000000000004	27.474999999999998	16.55	14.299999999999999
43	47.15	27.375	10.25	15.225
44	32.75	39.15	11.375	16.725
45	21.725	42.675000000000004	16.5	19.1
46	19.0	24.575	17.25	39.175
47	13.775	15.525	36.6	34.1
48	16.625	12.825000000000001	21.475	49.075
49	15.525	17.2	18.95	48.325
50	19.025	31.874999999999996	15.275	33.825
>>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	0.5
18	1.0
19	2.0
20	3.0
21	2.0
22	1.0
23	0.5
24	0.0
25	0.5
26	1.0
27	1.0
28	1.0
29	3.5
30	6.0
31	14.5
32	23.0
33	22.0
34	21.0
35	22.0
36	23.0
37	29.5
38	36.0
39	42.0
40	48.0
41	58.0
42	68.0
43	86.5
44	105.0
45	126.0
46	147.0
47	231.5
48	316.0
49	417.0
50	518.0
51	629.0
52	740.0
53	574.0
54	408.0
55	520.0
56	632.0
57	475.0
58	318.0
59	213.5
60	109.0
61	77.5
62	46.0
63	106.5
64	167.0
65	104.5
66	42.0
67	32.5
68	23.0
69	31.0
70	39.0
71	91.5
72	144.0
73	75.0
74	6.0
75	4.0
76	2.0
77	1.0
78	0.0
79	2.5
80	5.0
81	2.5
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	0.3
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	39.900000000000006
#Duplication Level	Percentage of deduplicated	Percentage of total
1	74.81203007518798	29.849999999999998
2	10.401002506265664	8.3
3	4.260651629072681	5.1
4	2.6942355889724308	4.3
5	1.6917293233082706	3.375
6	1.3157894736842104	3.15
7	1.0651629072681703	2.9749999999999996
8	0.5012531328320802	1.6
9	0.43859649122807015	1.575
>10	2.1303258145363406	15.325
>50	0.43859649122807015	12.1
>100	0.2506265664160401	12.35
>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	138	3.45	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	131	3.2750000000000004	No Hit
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	117	2.9250000000000003	RNA PCR Primer, Index 1 (100% over 30bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	108	2.7	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	96	2.4	RNA PCR Primer, Index 1 (100% over 28bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	77	1.925	No Hit
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	67	1.675	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	65	1.625	RNA PCR Primer, Index 1 (100% over 28bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTC	64	1.6	RNA PCR Primer, Index 5 (97% over 35bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	59	1.4749999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	56	1.4000000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	36	0.8999999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	32	0.8	RNA PCR Primer, Index 1 (100% over 33bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	31	0.775	No Hit
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	27	0.675	RNA PCR Primer, Index 1 (100% over 26bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	27	0.675	RNA PCR Primer, Index 1 (100% over 27bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCGGCAATCTC	24	0.6	RNA PCR Primer, Index 48 (100% over 44bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	24	0.6	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	23	0.575	RNA PCR Primer, Index 1 (100% over 28bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	21	0.525	No Hit
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	21	0.525	RNA PCR Primer, Index 1 (100% over 29bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 29bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 27bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	17	0.42500000000000004	No Hit
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	17	0.42500000000000004	No Hit
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	17	0.42500000000000004	No Hit
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	16	0.4	RNA PCR Primer, Index 1 (100% over 31bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	16	0.4	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	15	0.375	RNA PCR Primer, Index 1 (100% over 26bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	15	0.375	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	14	0.35000000000000003	No Hit
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 27bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCGGCAATCTCGTATGC	13	0.325	RNA PCR Primer, Index 48 (100% over 50bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGCTGGAATTCTCGGGTGCC	11	0.27499999999999997	No Hit
TCCTGTACTGAGCTGCCCCGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGT	10	0.25	No Hit
TACCCTGTAGAACCGAATTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTTGGAATTCTCGGGTGCCA	9	0.22499999999999998	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTATGG	9	0.22499999999999998	No Hit
TGCGGGGCTAGGGCTAACAGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TTCCCTTTGTCATCCTATGCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (100% over 30bp)
CTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACT	8	0.2	RNA PCR Primer, Index 3 (100% over 34bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGACTGGAATTCTCGGGT	8	0.2	No Hit
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTC	8	0.2	No Hit
TCTCCCAACCCTTGTACCAGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
GTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCG	7	0.17500000000000002	RNA PCR Primer, Index 10 (97% over 36bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TCCAGCATCAGTGATTTTGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
ACTAATCCTAGCCCTAGCCCTACACAAATATAATTATACTATTATATGGA	7	0.17500000000000002	No Hit
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
ACTAATCCTAGCCCTAGCCCTATGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATTCAGGATAGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TTTAGCTGTTAACTAAATTTTCGTAGGTTTAATTCCTGCCAATCTAGCCA	7	0.17500000000000002	No Hit
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
CGCACGGGGTCGGCGGCGATGTCGGCTGGAATTCTCGGGTGCCAAGGAAC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 24bp)
TACCCTGTAGAACCGAATTTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
AACCCGTAGATCCGAACTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	7	0.17500000000000002	No Hit
TACCCTGTAGATCCGAATTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCATTGCTGTCGGTGGGTTTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	6	0.15	RNA PCR Primer, Index 1 (100% over 25bp)
ATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAATTCTCGGGTGCCA	6	0.15	No Hit
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCCTGTACTGAGCTGCCCCGATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCTGGCTCCGTGTCTTCACTCCCTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	6	0.15	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTTGGAATTCTCGGGTGCCA	6	0.15	No Hit
TCCCTGTGGTCTAGTGGTTAGGATTCGGCGCTCTCTGGAATTCTCGGGTG	6	0.15	No Hit
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	6	0.15	No Hit
TCCCTGAGACCCTAACTTGTGAAATGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
CCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCG	6	0.15	RNA PCR Primer, Index 10 (97% over 36bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCTGGAATT	6	0.15	No Hit
TGTAAACATCCTCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCTGGAATTCTCGGGTGC	6	0.15	No Hit
CACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCT	5	0.125	No Hit
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
GCATTGGTAGTTCAATGGTAGAATTCTCGCCTCCCTGGAATTCTCGGGTG	5	0.125	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGTGGAATTCTCGGGTGCC	5	0.125	No Hit
AGAAATGCGGATATGGGACTGAGATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGATGAAGCACTGTAGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGGCAATGGTAGAACTCACACCTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	5	0.125	No Hit
TGACTTGATGAAAGTACTTTTGAACCCTTTTCCATCTGATGTGGAATTCT	5	0.125	No Hit
TATTGCACTCGTCCCGGCCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AGAATTGTGGCTGGACATCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GCCCGGCTAGCTCAGTCGGTAGAGCATGAGACTCTGGAATTCTCGGGTGC	5	0.125	No Hit
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTCTCTGGAATTCTCGGGT	5	0.125	No Hit
AAGAAAGATTGCAAGAACTGCTAATTCTGGAATTCTCGGGTGCCAAGGAA	5	0.125	RNA PCR Primer, Index 1 (100% over 23bp)
AATATAACACAGATGGCCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TACGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CTAGACTGAGGCTCCTTGAGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GCACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGC	5	0.125	No Hit
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
>>END_MODULE
>>Adapter Content	fail
#Position	Illumina Universal Adapter	Illumina Small RNA 3' Adapter	Illumina Small RNA 5' Adapter	Nextera Transposase Sequence	SOLID Small RNA Adapter
1	0.0	0.35	0.0	0.0	0.0
2	0.0	0.375	0.0	0.0	0.0
3	0.0	0.45	0.0	0.0	0.0
4	0.0	0.475	0.0	0.0	0.0
5	0.0	0.6	0.0	0.0	0.0
6	0.0	0.725	0.0	0.0	0.0
7	0.0	1.475	0.0	0.0	0.0
8	0.0	1.625	0.0	0.0	0.0
9	0.0	1.75	0.0	0.0	0.0
10	0.0	2.05	0.0	0.0	0.0
11	0.0	2.225	0.0	0.0	0.0
12	0.0	2.625	0.0	0.0	0.0
13	0.0	3.1	0.0	0.0	0.0
14	0.0	3.425	0.0	0.0	0.0
15	0.0	4.15	0.0	0.0	0.0
16	0.0	6.6	0.0	0.0	0.0
17	0.0	7.3	0.0	0.0	0.0
18	0.0	8.625	0.0	0.0	0.0
19	0.0	9.3	0.0	0.0	0.0
20	0.0	10.45	0.0	0.0	0.0
21	0.0	15.85	0.0	0.0	0.0
22	0.0	24.225	0.0	0.0	0.0
23	0.0	47.225	0.0	0.0	0.0
24	0.0	57.95	0.0	0.0	0.0
25	0.0	63.025	0.0	0.0	0.0
26	0.0	64.3	0.0	0.0	0.0
27	0.0	65.1	0.0	0.0	0.0
28	0.0	65.9	0.0	0.0	0.0
29	0.0	66.6	0.0	0.0	0.0
30	0.0	67.0	0.0	0.0	0.0
31	0.0	67.95	0.0	0.0	0.0
32	0.0	68.975	0.0	0.0	0.0
33	0.0	70.6	0.0	0.0	0.0
34	0.0	75.75	0.0	0.0	0.0
35	0.0	77.2	0.0	0.0	0.0
36	0.0	78.625	0.0	0.0	0.0
37	0.0	80.3	0.0	0.0	0.0
38	0.0	81.025	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
AACGCTG	40	5.315087E-9	44.000004	8
ACGCTGT	40	5.315087E-9	44.000004	9
TTCAACG	40	5.315087E-9	44.000004	5
TCGGTGA	40	5.315087E-9	44.000004	15
CATTCAA	40	5.315087E-9	44.000004	3
TCAACGC	40	5.315087E-9	44.000004	6
ACATTCA	45	2.728484E-10	44.000004	2
GCTGTCG	45	2.728484E-10	44.000004	11
GGCTTGG	20	6.952051E-4	44.000004	19
CTGTCGG	45	2.728484E-10	44.000004	12
ATTCAAC	40	5.315087E-9	44.000004	4
GTCGGTG	45	2.728484E-10	44.000004	14
AACATTC	45	2.728484E-10	44.000004	1
TGTCGGT	45	2.728484E-10	44.000004	13
CAACGCT	40	5.315087E-9	44.000004	7
CGCTGTC	40	5.315087E-9	44.000004	10
CGCGACC	30	1.9515464E-6	44.0	1
CGCTGAT	25	3.6958358E-5	44.0	28
GGTGAGT	35	1.02281774E-7	44.0	17
CTGAGCT	35	1.02281774E-7	44.0	11
>>END_MODULE
Read 159436 spots for SRR5031028.sra
Written 159436 spots for SRR5031028.sra
Read 159436 spots for SRR5031028.sra
Written 159436 spots for SRR5031028.sra
Read 159436 spots for SRR5031028.sra
Written 159436 spots for SRR5031028.sra
Read 159436 spots for SRR5031028.sra
Written 159436 spots for SRR5031028.sra
Read 159436 spots for SRR5031028.sra
Written 159436 spots for SRR5031028.sra
Read 159436 spots for SRR5031028.sra
Written 159436 spots for SRR5031028.sra
Read 159436 spots for SRR5031028.sra
Written 159436 spots for SRR5031028.sra
Read 159436 spots for SRR5031028.sra
Written 159436 spots for SRR5031028.sra
Read 159436 spots for SRR5031028.sra
Written 159436 spots for SRR5031028.sra
Read 159436 spots for SRR5031028.sra
Written 159436 spots for SRR5031028.sra
Read 159441 spots for SRR5031028.sra
Written 159441 spots for SRR5031028.sra
Read 159436 spots for SRR5031028.sra
Written 159436 spots for SRR5031028.sra
SRR ids: ['SRR5031028.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_v17_cpee
SRR5031028.sra spots: 1913237
blocks: [[1, 159436], [159437, 318872], [318873, 478308], [478309, 637744], [637745, 797180], [797181, 956616], [956617, 1116052], [1116053, 1275488], [1275489, 1434924], [1434925, 1594360], [1594361, 1753796], [1753797, 1913237]]
SRR5031028 file size 330532
SRR5031028 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031028 SRR5031028_1.fastq
Input file:	SRR5031028_1.fastq
trimmed:	SRR5031028-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 07:09:13 2020 >> started

Wed Mar  4 07:09:14 2020 >> done (1.217s)
1913237 reads processed; of these:
    138 ( 0.01%) short reads filtered out after trimming by size control
      3 ( 0.00%) empty reads filtered out after trimming by size control
1913096 (99.99%) reads available; of these:
 127761 ( 6.68%) trimmed reads available after processing
1785335 (93.32%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     43	  0.00%
 19	     62	  0.00%
 20	    115	  0.01%
 21	    140	  0.01%
 22	    217	  0.01%
 23	    286	  0.01%
 24	    327	  0.02%
 25	    406	  0.02%
 26	    363	  0.02%
 27	    439	  0.02%
 28	    587	  0.03%
 29	    869	  0.05%
 30	    621	  0.03%
 31	    632	  0.03%
 32	    846	  0.04%
 33	    898	  0.05%
 34	   1022	  0.05%
 35	   1762	  0.09%
 36	   1743	  0.09%
 37	   1909	  0.10%
 38	   2071	  0.11%
 39	   2321	  0.12%
 40	   2501	  0.13%
 41	   2684	  0.14%
 42	   3359	  0.18%
 43	   5043	  0.26%
 44	   7163	  0.37%
 45	   9479	  0.50%
 46	  14206	  0.74%
 47	  15542	  0.81%
 48	  21180	  1.11%
 49	  28925	  1.51%
 50	1785335	 93.32%
1913096 reads passed initial QC


criterion=sequence-density
sequence-density=79.87
sequence-density-rank=1
fanout-score=21.48
fanout-score-rank=1
prefix-density=83.05
prefix-fanout=20.7
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCGGCAATCTCGTATGCC


criterion=fanout-score
sequence-density=79.87
sequence-density-rank=1
fanout-score=21.48
fanout-score-rank=1
prefix-density=83.05
prefix-fanout=20.7
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCGGCAATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCGGCAATCTCGTATGCC -o SRR5031028 -
Input file:	STDIN
trimmed:	SRR5031028-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCGGCAATCTCGTATGCC
-- 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 07:09:27 2020 >> started

Wed Mar  4 07:09:29 2020 >> done (2.362s)
1865269 reads processed; of these:
 155404 ( 8.33%) short reads filtered out after trimming by size control
   9909 ( 0.53%) empty reads filtered out after trimming by size control
1699956 (91.14%) reads available; of these:
1565667 (92.10%) trimmed reads available after processing
 134289 ( 7.90%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  10231	  0.60%
 19	  20733	  1.22%
 20	  90141	  5.30%
 21	 163542	  9.62%
 22	 429756	 25.28%
 23	 205986	 12.12%
 24	  97049	  5.71%
 25	  30063	  1.77%
 26	  17314	  1.02%
 27	  14104	  0.83%
 28	  15696	  0.92%
 29	  12787	  0.75%
 30	  16867	  0.99%
 31	  22181	  1.30%
 32	  24695	  1.45%
 33	  95223	  5.60%
 34	  30071	  1.77%
 35	  26438	  1.56%
 36	  31723	  1.87%
 37	  15055	  0.89%
 38	  17767	  1.05%
 39	  14920	  0.88%
 40	  22857	  1.34%
 41	  26576	  1.56%
 42	  30656	  1.80%
 43	  22536	  1.33%
 44	  16788	  0.99%
 45	  25081	  1.48%
 46	  19331	  1.14%
 47	  14478	  0.85%
 48	   1385	  0.08%
 49	   2375	  0.14%
 50	 115551	  6.80%


criterion=sequence-density
sequence-density=7.73
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=13
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTT


criterion=fanout-score
sequence-density=2.25
sequence-density-rank=3
fanout-score=21.16
fanout-score-rank=1
prefix-density=2.38
prefix-fanout=20.0
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCGGCAATCTCGTATGC
                                 Started job on |	Mar 04 07:10:04
                             Started mapping on |	Mar 04 07:10:04
                                    Finished on |	Mar 04 07:10:27
       Mapping speed, Million of reads per hour |	273.57

                          Number of input reads |	1747783
                      Average input read length |	29
                                    UNIQUE READS:
                   Uniquely mapped reads number |	869871
                        Uniquely mapped reads % |	49.77%
                          Average mapped length |	25.75
                       Number of splices: Total |	1269
            Number of splices: Annotated (sjdb) |	207
                       Number of splices: GT/AG |	1182
                       Number of splices: GC/AG |	14
                       Number of splices: AT/AC |	1
               Number of splices: Non-canonical |	72
                      Mismatch rate per base, % |	0.24%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.83
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.12
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	526139
             % of reads mapped to multiple loci |	30.10%
        Number of reads mapped to too many loci |	54232
             % of reads mapped to too many loci |	3.10%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	15.62%
                     % of reads unmapped: other |	1.41%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	351773	351773	351773
N_multimapping	526139	526139	526139
N_noFeature	47948	63707	566091
N_ambiguous	474275	206439	10672
UnstrandedReadsAssigned:347648 PositiveStrandReadsAssigned:599725 NegativeStrandReadsAssigned:293108
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5031028 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: SRR5031028-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 1,747,783 reads, 415,843 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,128 rounds

 109283 SRR5031028.ke.tsv
  52636 SRR5031028.se.tsv
 161919 total
==> SRR5031028.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

==> SRR5031028.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031028 completed mapping pipeline successfully
