Starting /dee2/code/volunteer_pipeline.sh SRR5031020
    current disk space = 160547291136
    free memory = 73947276 
SRR5031020 SRAfilesize
98893c98fb87a791e930c7e67ffad1fc  SRR5031020.sra
SRR5031020.sra file validated
SRR5031020 is single end
SRR5031020 is conventional basespace
SRR5031020 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031020_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	32.29	33.0	31.0	34.0	31.0	34.0
2	32.5665	34.0	31.0	34.0	31.0	34.0
3	32.52775	34.0	31.0	34.0	31.0	34.0
4	36.15875	37.0	35.0	37.0	35.0	37.0
5	36.143	37.0	35.0	37.0	35.0	37.0
6	35.9285	37.0	35.0	37.0	35.0	37.0
7	35.89	37.0	35.0	37.0	35.0	37.0
8	35.948	37.0	35.0	37.0	35.0	37.0
9	37.61725	39.0	37.0	39.0	35.0	39.0
10	37.5425	39.0	37.0	39.0	35.0	39.0
11	37.34925	39.0	37.0	39.0	34.0	39.0
12	37.65275	39.0	37.0	39.0	35.0	39.0
13	37.58875	39.0	37.0	39.0	35.0	39.0
14	38.9535	40.0	38.0	41.0	35.0	41.0
15	38.772	40.0	38.0	41.0	35.0	41.0
16	38.91675	40.0	38.0	41.0	35.0	41.0
17	38.971	40.0	38.0	41.0	35.0	41.0
18	38.9015	40.0	38.0	41.0	35.0	41.0
19	38.81625	40.0	38.0	41.0	35.0	41.0
20	38.7545	40.0	38.0	41.0	34.0	41.0
21	38.8845	40.0	38.0	41.0	35.0	41.0
22	38.87425	40.0	38.0	41.0	35.0	41.0
23	38.5445	40.0	38.0	41.0	34.0	41.0
24	38.7315	40.0	38.0	41.0	34.0	41.0
25	38.811	40.0	38.0	41.0	34.0	41.0
26	38.726	40.0	38.0	41.0	35.0	41.0
27	38.793	40.0	38.0	41.0	35.0	41.0
28	38.68375	40.0	38.0	41.0	34.0	41.0
29	38.45975	40.0	38.0	41.0	34.0	41.0
30	38.33625	40.0	38.0	41.0	34.0	41.0
31	38.468	40.0	38.0	41.0	34.0	41.0
32	38.35825	40.0	38.0	41.0	34.0	41.0
33	38.04175	40.0	38.0	41.0	33.0	41.0
34	37.98675	40.0	38.0	41.0	33.0	41.0
35	37.7145	40.0	37.0	41.0	33.0	41.0
36	37.70175	40.0	37.0	41.0	33.0	41.0
37	37.2975	40.0	37.0	41.0	31.0	41.0
38	37.19175	39.0	36.0	41.0	31.0	41.0
39	37.6365	40.0	37.0	41.0	33.0	41.0
40	37.75425	40.0	37.0	41.0	33.0	41.0
41	37.9425	40.0	37.0	41.0	33.0	41.0
42	37.82475	40.0	37.0	41.0	33.0	41.0
43	37.784	40.0	37.0	41.0	33.0	41.0
44	37.74	40.0	37.0	41.0	33.0	41.0
45	37.6655	40.0	37.0	41.0	33.0	41.0
46	37.59575	40.0	37.0	41.0	33.0	41.0
47	37.25	40.0	36.0	41.0	31.0	41.0
48	37.0645	40.0	36.0	41.0	31.0	41.0
49	37.1395	40.0	36.0	41.0	32.0	41.0
50	36.64175	39.0	35.0	41.0	31.0	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
15	1.0
16	1.0
17	2.0
18	0.0
19	4.0
20	3.0
21	2.0
22	5.0
23	7.0
24	8.0
25	10.0
26	18.0
27	23.0
28	19.0
29	39.0
30	37.0
31	68.0
32	73.0
33	113.0
34	164.0
35	209.0
36	284.0
37	420.0
38	740.0
39	1750.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	8.225	25.0	52.300000000000004	14.475
2	24.28035043804756	27.659574468085108	18.3729662077597	29.687108886107634
3	24.55	21.8	22.15	31.5
4	33.550000000000004	28.425	13.4	24.625
5	21.75	42.025	26.85	9.375
6	34.699999999999996	16.625	34.300000000000004	14.374999999999998
7	15.299999999999999	19.725	23.599999999999998	41.375
8	24.575	29.9	15.6	29.925
9	20.724999999999998	34.4	28.4	16.475
10	21.55	23.125	28.199999999999996	27.125
11	31.6	8.9	18.425	41.075
12	15.299999999999999	18.15	31.874999999999996	34.675
13	33.125	18.825	31.35	16.7
14	34.325	30.049999999999997	19.650000000000002	15.975
15	34.325	25.174999999999997	27.950000000000003	12.55
16	19.025	18.775	23.025000000000002	39.175
17	24.099999999999998	21.9	40.25	13.750000000000002
18	27.150000000000002	17.75	28.575	26.525
19	36.325	13.875000000000002	33.300000000000004	16.5
20	43.325	16.175	27.450000000000003	13.05
21	20.674999999999997	21.8	29.4	28.125
22	30.3	12.475	46.650000000000006	10.575
23	27.175	12.55	44.4	15.875
24	51.675000000000004	13.8	26.775	7.75
25	50.425	25.4	15.125	9.049999999999999
26	28.675	46.75	13.925	10.65
27	16.05	47.225	24.2	12.525
28	10.8	24.7	49.425000000000004	15.075
29	11.700000000000001	13.025	56.75	18.525
30	10.025	6.375	37.724999999999994	45.875
31	14.674999999999999	5.050000000000001	46.175	34.1
32	28.625	6.25	20.925	44.2
33	54.85	8.425	13.075000000000001	23.65
34	61.675000000000004	6.9750000000000005	16.175	15.174999999999999
35	65.77499999999999	6.25	19.0	8.975
36	43.0	7.2749999999999995	36.125	13.600000000000001
37	44.75	10.274999999999999	20.349999999999998	24.625
38	23.799999999999997	15.8	12.275	48.125
39	16.325	24.75	10.174999999999999	48.75
40	15.325	48.5	9.950000000000001	26.224999999999998
41	25.900000000000002	48.35	8.25	17.5
42	48.449999999999996	30.599999999999998	11.450000000000001	9.5
43	51.55	31.05	7.124999999999999	10.274999999999999
44	31.474999999999998	47.8	7.124999999999999	13.600000000000001
45	18.675	49.175000000000004	12.675	19.475
46	12.625	26.75	18.075	42.55
47	7.75	15.425	38.275	38.550000000000004
48	10.05	12.75	20.4	56.8
49	12.975	18.8	14.424999999999999	53.800000000000004
50	18.275	35.775	14.2	31.75
>>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	1.0
10	2.0
11	1.0
12	0.0
13	0.0
14	0.0
15	0.0
16	0.0
17	0.0
18	0.0
19	0.0
20	0.0
21	0.5
22	1.0
23	0.5
24	0.0
25	0.0
26	0.0
27	2.0
28	4.0
29	3.5
30	3.0
31	5.0
32	7.0
33	8.5
34	10.0
35	21.5
36	33.0
37	26.5
38	20.0
39	29.5
40	39.0
41	43.5
42	48.0
43	78.5
44	109.0
45	150.0
46	191.0
47	335.5
48	480.0
49	609.0
50	738.0
51	802.5
52	867.0
53	610.0
54	353.0
55	431.5
56	510.0
57	353.5
58	197.0
59	134.5
60	72.0
61	59.0
62	46.0
63	88.5
64	131.0
65	79.5
66	28.0
67	23.5
68	19.0
69	21.5
70	24.0
71	44.0
72	64.0
73	33.5
74	3.0
75	1.5
76	0.0
77	0.0
78	0.0
79	0.0
80	0.0
81	0.5
82	1.0
83	0.5
84	0.0
85	0.0
86	0.0
87	0.0
88	0.0
89	0.0
90	0.0
91	0.0
92	0.0
93	0.0
94	0.0
95	0.0
96	0.0
97	0.0
98	0.0
99	0.0
100	0.0
>>END_MODULE
>>Per base N content	pass
#Base	N-Count
1	0.0
2	0.125
3	0.0
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.0
10	0.0
11	0.0
12	0.0
13	0.0
14	0.0
15	0.0
16	0.0
17	0.0
18	0.0
19	0.0
20	0.0
21	0.0
22	0.0
23	0.0
24	0.0
25	0.0
26	0.0
27	0.0
28	0.0
29	0.0
30	0.0
31	0.0
32	0.0
33	0.0
34	0.0
35	0.0
36	0.0
37	0.0
38	0.0
39	0.0
40	0.0
41	0.0
42	0.0
43	0.0
44	0.0
45	0.0
46	0.0
47	0.0
48	0.0
49	0.0
50	0.0
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
50	4000.0
>>END_MODULE
>>Sequence Duplication Levels	fail
#Total Deduplicated Percentage	36.4
#Duplication Level	Percentage of deduplicated	Percentage of total
1	76.92307692307693	28.000000000000004
2	8.447802197802199	6.15
3	4.1208791208791204	4.5
4	2.541208791208791	3.6999999999999997
5	1.2362637362637363	2.25
6	1.0302197802197801	2.25
7	0.6868131868131868	1.7500000000000002
8	0.5494505494505495	1.6
9	0.4120879120879121	1.35
>10	3.4340659340659343	24.45
>50	0.27472527472527475	8.425
>100	0.3434065934065934	15.575
>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
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	162	4.05	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	131	3.2750000000000004	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	121	3.025	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	105	2.625	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	104	2.6	RNA PCR Primer, Index 1 (100% over 30bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	96	2.4	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	93	2.325	RNA PCR Primer, Index 1 (100% over 29bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	82	2.0500000000000003	No Hit
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	66	1.6500000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	50	1.25	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	41	1.0250000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	40	1.0	RNA PCR Primer, Index 1 (100% over 27bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	40	1.0	RNA PCR Primer, Index 1 (100% over 27bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	39	0.975	No Hit
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	38	0.95	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	38	0.95	RNA PCR Primer, Index 1 (100% over 26bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	37	0.9249999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	35	0.8750000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	32	0.8	RNA PCR Primer, Index 1 (100% over 26bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	27	0.675	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	27	0.675	RNA PCR Primer, Index 1 (100% over 27bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	25	0.625	RNA PCR Primer, Index 1 (100% over 27bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCT	24	0.6	RNA PCR Primer, Index 1 (97% over 35bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	21	0.525	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	19	0.475	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	19	0.475	RNA PCR Primer, Index 1 (100% over 29bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	16	0.4	RNA PCR Primer, Index 1 (100% over 33bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	16	0.4	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTCAGAATCTCGTATGC	16	0.4	RNA PCR Primer, Index 40 (100% over 50bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	15	0.375	No Hit
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	13	0.325	RNA PCR Primer, Index 1 (100% over 25bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTCAGAATCTC	13	0.325	RNA PCR Primer, Index 40 (100% over 44bp)
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	12	0.3	RNA PCR Primer, Index 1 (100% over 30bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGGCAATGGTAGAACTCACATGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTATGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	11	0.27499999999999997	No Hit
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	10	0.25	RNA PCR Primer, Index 1 (100% over 30bp)
TGTAAACATCCTACACTCAGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGATGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	10	0.25	RNA PCR Primer, Index 1 (100% over 33bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	10	0.25	No Hit
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	10	0.25	No Hit
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	9	0.22499999999999998	No Hit
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	9	0.22499999999999998	No Hit
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	8	0.2	RNA PCR Primer, Index 1 (100% over 31bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTC	8	0.2	No Hit
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	8	0.2	No Hit
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
CCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (97% over 36bp)
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	7	0.17500000000000002	No Hit
TGAGGTAGTAGTTTGTACAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGTGGAATTCTCGGGTGCC	7	0.17500000000000002	No Hit
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTCTCTGGAATTCTCGGGT	7	0.17500000000000002	No Hit
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TGACTTGATGAAAGTACTTTTGAACCCTTTTCCATCTGATGTGGAATTCT	7	0.17500000000000002	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGT	7	0.17500000000000002	No Hit
TAACAGTCTACAGCCATGGTCGTTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
GGAAAGGATGAACGAACTTGGCCTGACCTGGAATTCTCGGGTGCCAAGGA	6	0.15	RNA PCR Primer, Index 1 (100% over 22bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTTGGAATTCTCGGGTGCCA	6	0.15	No Hit
TATTGCACTCGTCCCGGCCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
AGCTACATTGTCTGCTGGGTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGGCAATGGTAGAACTCACACTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
GTGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCA	6	0.15	No Hit
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	6	0.15	No Hit
TCACAGTGAACCGGTCTCTTTATTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
AAGGGATTCTGATGTTGGTCATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
CGTGGGGGGCCCAAGTCCTTCTGATCGAGGCCTGGAATTCTCGGGTGCCA	5	0.125	No Hit
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CATCATCGTCTCAAATGAGTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	5	0.125	No Hit
CACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCT	5	0.125	No Hit
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TAGCACCATCTGAAATCGGTTATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TTAAGGCACGCGGTGAATGCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GAAGGATCATTATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTCAG	5	0.125	RNA PCR Primer, Index 40 (100% over 38bp)
TCACAGTGAACCGGTCTCTTTCTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TTTGGCAATGGTAGAACTCACACCGTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
CAAAGAATTCTCCTTTTGGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
>>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	0.425	0.0	0.0	0.0
2	0.0	0.5	0.0	0.0	0.0
3	0.0	0.575	0.0	0.0	0.0
4	0.0	0.65	0.0	0.0	0.0
5	0.0	0.725	0.0	0.0	0.0
6	0.0	0.775	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	1.35	0.0	0.0	0.0
10	0.0	1.475	0.0	0.0	0.0
11	0.0	1.575	0.0	0.0	0.0
12	0.0	1.725	0.0	0.0	0.0
13	0.0	1.95	0.0	0.0	0.0
14	0.0	2.3	0.0	0.0	0.0
15	0.0	2.875	0.0	0.0	0.0
16	0.0	4.225	0.0	0.0	0.0
17	0.0	4.775	0.0	0.0	0.0
18	0.0	5.9	0.0	0.0	0.0
19	0.0	6.35	0.0	0.0	0.0
20	0.0	7.25	0.0	0.0	0.0
21	0.0	13.1	0.0	0.0	0.0
22	0.0	25.4	0.0	0.0	0.0
23	0.0	54.825	0.0	0.0	0.0
24	0.0	68.325	0.0	0.0	0.0
25	0.0	75.1	0.0	0.0	0.0
26	0.0	76.675	0.0	0.0	0.0
27	0.0	77.375	0.0	0.0	0.0
28	0.0	77.95	0.0	0.0	0.0
29	0.0	78.8	0.0	0.0	0.0
30	0.0	79.275	0.0	0.0	0.0
31	0.0	80.2	0.0	0.0	0.0
32	0.0	80.95	0.0	0.0	0.0
33	0.0	81.95	0.0	0.0	0.0
34	0.0	85.2	0.0	0.0	0.0
35	0.0	86.0	0.0	0.0	0.0
36	0.0	86.625	0.0	0.0	0.0
37	0.0	87.7	0.0	0.0	0.0
38	0.0	88.125	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
ACTGTTG	20	6.952051E-4	44.000004	18
ACAGTGA	20	6.952051E-4	44.000004	3
ACCGGTC	20	6.952051E-4	44.000004	10
AACGCTG	20	6.952051E-4	44.000004	8
GGTTGTA	20	6.952051E-4	44.000004	11
GGTGAGT	20	6.952051E-4	44.000004	17
GTTTGGA	20	6.952051E-4	44.000004	20
GTTGAAG	20	6.952051E-4	44.000004	10
ACGCTGT	20	6.952051E-4	44.000004	9
AACCGGT	20	6.952051E-4	44.000004	9
CAGTTGA	20	6.952051E-4	44.000004	8
TAAACAT	20	6.952051E-4	44.000004	3
TTGTATA	20	6.952051E-4	44.000004	13
AAACATC	20	6.952051E-4	44.000004	4
AACTGTT	20	6.952051E-4	44.000004	17
TTCAACG	20	6.952051E-4	44.000004	5
GGTCTCT	20	6.952051E-4	44.000004	13
CATTCAA	20	6.952051E-4	44.000004	3
TCAACGC	20	6.952051E-4	44.000004	6
GAAGAAC	20	6.952051E-4	44.000004	13
>>END_MODULE
Read 186771 spots for SRR5031020.sra
Written 186771 spots for SRR5031020.sra
Read 186771 spots for SRR5031020.sra
Written 186771 spots for SRR5031020.sra
Read 186771 spots for SRR5031020.sra
Written 186771 spots for SRR5031020.sra
Read 186771 spots for SRR5031020.sra
Written 186771 spots for SRR5031020.sra
Read 186771 spots for SRR5031020.sra
Written 186771 spots for SRR5031020.sra
Read 186771 spots for SRR5031020.sra
Written 186771 spots for SRR5031020.sra
Read 186771 spots for SRR5031020.sra
Written 186771 spots for SRR5031020.sra
Read 186771 spots for SRR5031020.sra
Written 186771 spots for SRR5031020.sra
Read 186771 spots for SRR5031020.sra
Written 186771 spots for SRR5031020.sra
Read 186771 spots for SRR5031020.sra
Written 186771 spots for SRR5031020.sra
Read 186771 spots for SRR5031020.sra
Written 186771 spots for SRR5031020.sra
Read 186771 spots for SRR5031020.sra
Written 186771 spots for SRR5031020.sra
SRR ids: ['SRR5031020.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_u_m1m6wa
SRR5031020.sra spots: 2241252
blocks: [[1, 186771], [186772, 373542], [373543, 560313], [560314, 747084], [747085, 933855], [933856, 1120626], [1120627, 1307397], [1307398, 1494168], [1494169, 1680939], [1680940, 1867710], [1867711, 2054481], [2054482, 2241252]]
SRR5031020 file size 387385
SRR5031020 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031020 SRR5031020_1.fastq
Input file:	SRR5031020_1.fastq
trimmed:	SRR5031020-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 07:07:42 2020 >> started

Wed Mar  4 07:07:44 2020 >> done (1.944s)
2241252 reads processed; of these:
    177 ( 0.01%) short reads filtered out after trimming by size control
      5 ( 0.00%) empty reads filtered out after trimming by size control
2241070 (99.99%) reads available; of these:
 123401 ( 5.51%) trimmed reads available after processing
2117669 (94.49%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     53	  0.00%
 19	     70	  0.00%
 20	    162	  0.01%
 21	    169	  0.01%
 22	    332	  0.01%
 23	    375	  0.02%
 24	    421	  0.02%
 25	    537	  0.02%
 26	    458	  0.02%
 27	    595	  0.03%
 28	    654	  0.03%
 29	   1062	  0.05%
 30	    705	  0.03%
 31	    748	  0.03%
 32	    865	  0.04%
 33	   1054	  0.05%
 34	   1197	  0.05%
 35	   2126	  0.09%
 36	   1865	  0.08%
 37	   2304	  0.10%
 38	   2140	  0.10%
 39	   2379	  0.11%
 40	   2526	  0.11%
 41	   2737	  0.12%
 42	   3657	  0.16%
 43	   5224	  0.23%
 44	   6835	  0.30%
 45	   7984	  0.36%
 46	  11569	  0.52%
 47	  14055	  0.63%
 48	  21930	  0.98%
 49	  26613	  1.19%
 50	2117669	 94.49%
2241070 reads passed initial QC


criterion=sequence-density
sequence-density=87.66
sequence-density-rank=1
fanout-score=21.42
fanout-score-rank=1
prefix-density=89.60
prefix-fanout=21.0
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTCAGAATCTCGTATGCC


criterion=fanout-score
sequence-density=87.66
sequence-density-rank=1
fanout-score=21.42
fanout-score-rank=1
prefix-density=89.60
prefix-fanout=21.0
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTCAGAATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTCAGAATCTCGTATGCC -o SRR5031020 -
Input file:	STDIN
trimmed:	SRR5031020-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTCAGAATCTCGTATGCC
-- 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 07:08:03 2020 >> started

Wed Mar  4 07:08:08 2020 >> done (5.043s)
2190137 reads processed; of these:
 127778 ( 5.83%) short reads filtered out after trimming by size control
   8324 ( 0.38%) empty reads filtered out after trimming by size control
2054035 (93.79%) reads available; of these:
1966649 (95.75%) trimmed reads available after processing
  87386 ( 4.25%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  11922	  0.58%
 19	  23848	  1.16%
 20	 120359	  5.86%
 21	 278922	 13.58%
 22	 651365	 31.71%
 23	 313668	 15.27%
 24	 142763	  6.95%
 25	  38354	  1.87%
 26	  18596	  0.91%
 27	  14050	  0.68%
 28	  14593	  0.71%
 29	  11275	  0.55%
 30	  16152	  0.79%
 31	  20974	  1.02%
 32	  23782	  1.16%
 33	  62869	  3.06%
 34	  21945	  1.07%
 35	  16512	  0.80%
 36	  20185	  0.98%
 37	  10117	  0.49%
 38	  10569	  0.51%
 39	  10111	  0.49%
 40	  15922	  0.78%
 41	  20465	  1.00%
 42	  24082	  1.17%
 43	  17083	  0.83%
 44	  12358	  0.60%
 45	  16522	  0.80%
 46	  12493	  0.61%
 47	   9079	  0.44%
 48	    984	  0.05%
 49	   1667	  0.08%
 50	  70449	  3.43%


criterion=sequence-density
sequence-density=7.60
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=18
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.02
sequence-density-rank=39
fanout-score=114.86
fanout-score-rank=1
prefix-density=2.17
prefix-fanout=1.0
sequence=ATTGTATAGTTTAACAGTCTACAGCCATGGTCGT
                                 Started job on |	Mar 04 07:08:40
                             Started mapping on |	Mar 04 07:08:41
                                    Finished on |	Mar 04 07:09:07
       Mapping speed, Million of reads per hour |	291.46

                          Number of input reads |	2104968
                      Average input read length |	26
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1108541
                        Uniquely mapped reads % |	52.66%
                          Average mapped length |	24.17
                       Number of splices: Total |	1226
            Number of splices: Annotated (sjdb) |	446
                       Number of splices: GT/AG |	1151
                       Number of splices: GC/AG |	16
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	59
                      Mismatch rate per base, % |	0.18%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.85
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.10
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	737197
             % of reads mapped to multiple loci |	35.02%
        Number of reads mapped to too many loci |	42242
             % of reads mapped to too many loci |	2.01%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	9.66%
                     % of reads unmapped: other |	0.65%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	259230	259230	259230
N_multimapping	737197	737197	737197
N_noFeature	48966	61333	773885
N_ambiguous	601428	310562	10485
UnstrandedReadsAssigned:458147 PositiveStrandReadsAssigned:736646 NegativeStrandReadsAssigned:324171
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=21 echo kmer=19
SRR5031020 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: SRR5031020-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,104,968 reads, 529,385 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,109 rounds

 109283 SRR5031020.ke.tsv
  52636 SRR5031020.se.tsv
 161919 total
==> SRR5031020.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

==> SRR5031020.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	1
ENSMUSG00000051951	1
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031020 completed mapping pipeline successfully
