Starting /dee2/code/volunteer_pipeline.sh SRR5031096
    current disk space = 160480116736
    free memory = 73947608 
SRR5031096 SRAfilesize
774d4bc5c408e4ef364b6299459363ff  SRR5031096.sra
SRR5031096.sra file validated
SRR5031096 is single end
SRR5031096 is conventional basespace
SRR5031096 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031096_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	31.85825	31.0	31.0	34.0	30.0	34.0
2	32.3535	33.0	31.0	34.0	31.0	34.0
3	32.31625	33.0	31.0	34.0	31.0	34.0
4	36.13125	37.0	35.0	37.0	35.0	37.0
5	36.082	37.0	35.0	37.0	35.0	37.0
6	35.84125	37.0	35.0	37.0	35.0	37.0
7	35.6365	37.0	35.0	37.0	35.0	37.0
8	35.51725	37.0	35.0	37.0	33.0	37.0
9	36.664	39.0	35.0	39.0	32.0	39.0
10	36.208	39.0	35.0	39.0	31.0	39.0
11	37.30925	39.0	37.0	39.0	34.0	39.0
12	37.533	39.0	37.0	39.0	35.0	39.0
13	37.42475	39.0	37.0	39.0	35.0	39.0
14	38.03825	40.0	37.0	41.0	33.0	41.0
15	36.6615	39.0	36.0	41.0	27.0	41.0
16	36.85725	38.0	36.0	40.0	32.0	41.0
17	36.495	39.0	36.0	40.0	30.0	41.0
18	38.125	39.0	37.0	41.0	34.0	41.0
19	38.5265	40.0	38.0	41.0	35.0	41.0
20	38.34575	40.0	38.0	41.0	34.0	41.0
21	38.3575	40.0	38.0	41.0	34.0	41.0
22	37.0455	39.0	36.0	40.0	31.0	41.0
23	37.6825	39.0	37.0	40.0	32.0	41.0
24	37.15325	39.0	36.0	40.0	31.0	41.0
25	38.02925	40.0	37.0	41.0	33.0	41.0
26	37.941	40.0	37.0	41.0	33.0	41.0
27	38.2515	40.0	38.0	41.0	34.0	41.0
28	38.383	40.0	38.0	41.0	34.0	41.0
29	38.333	40.0	38.0	41.0	34.0	41.0
30	38.73125	40.0	38.0	41.0	35.0	41.0
31	38.56175	40.0	38.0	41.0	35.0	41.0
32	38.6095	40.0	38.0	41.0	34.0	41.0
33	38.3855	40.0	38.0	41.0	34.0	41.0
34	37.86525	40.0	38.0	41.0	33.0	41.0
35	37.289	40.0	36.0	41.0	30.0	41.0
36	33.10625	35.0	30.0	39.0	23.0	41.0
37	34.95375	37.0	33.0	39.0	29.0	40.0
38	36.37225	38.0	35.0	40.0	30.0	40.0
39	36.5375	38.0	35.0	40.0	31.0	40.0
40	36.8675	39.0	36.0	40.0	31.0	41.0
41	37.34775	39.0	37.0	40.0	32.0	41.0
42	37.2695	40.0	37.0	41.0	31.0	41.0
43	37.55	40.0	37.0	41.0	33.0	41.0
44	36.779	39.0	36.0	40.0	31.0	41.0
45	36.93975	39.0	36.0	40.0	31.0	41.0
46	36.77825	39.0	36.0	40.0	31.0	41.0
47	35.585	38.0	34.0	40.0	27.0	41.0
48	36.5975	39.0	35.0	40.0	30.0	41.0
49	36.81325	39.0	36.0	41.0	31.0	41.0
50	34.5745	37.0	34.0	40.0	27.0	40.0
>>END_MODULE
>>Per tile sequence quality	pass
#Tile	Base	Mean
1101	1	0.0
1101	2	0.0
1101	3	0.0
1101	4	0.0
1101	5	0.0
1101	6	0.0
1101	7	0.0
1101	8	0.0
1101	9	0.0
1101	10	0.0
1101	11	0.0
1101	12	0.0
1101	13	0.0
1101	14	0.0
1101	15	0.0
1101	16	0.0
1101	17	0.0
1101	18	0.0
1101	19	0.0
1101	20	0.0
1101	21	0.0
1101	22	0.0
1101	23	0.0
1101	24	0.0
1101	25	0.0
1101	26	0.0
1101	27	0.0
1101	28	0.0
1101	29	0.0
1101	30	0.0
1101	31	0.0
1101	32	0.0
1101	33	0.0
1101	34	0.0
1101	35	0.0
1101	36	0.0
1101	37	0.0
1101	38	0.0
1101	39	0.0
1101	40	0.0
1101	41	0.0
1101	42	0.0
1101	43	0.0
1101	44	0.0
1101	45	0.0
1101	46	0.0
1101	47	0.0
1101	48	0.0
1101	49	0.0
1101	50	0.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
13	1.0
14	0.0
15	1.0
16	1.0
17	0.0
18	1.0
19	4.0
20	4.0
21	2.0
22	10.0
23	3.0
24	9.0
25	9.0
26	10.0
27	14.0
28	23.0
29	43.0
30	65.0
31	79.0
32	115.0
33	146.0
34	207.0
35	299.0
36	448.0
37	780.0
38	1067.0
39	659.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	7.5	27.05	51.2	14.249999999999998
2	27.33866933466733	28.73936968484242	16.50825412706353	27.41370685342671
3	23.5	22.0	17.45	37.05
4	35.675000000000004	29.025000000000002	12.9	22.400000000000002
5	27.05	35.425000000000004	28.000000000000004	9.525
6	31.45	13.15	39.775	15.625
7	13.725000000000001	26.575	21.5	38.2
8	28.175	27.875	15.775	28.175
9	19.6	34.925	29.25	16.225
10	17.8	22.35	27.3	32.550000000000004
11	40.675	8.55	13.675	37.1
12	16.925	19.650000000000002	27.775	35.65
13	28.749999999999996	13.900000000000002	40.625	16.725
14	31.85	26.325	26.375	15.45
15	37.824999999999996	16.2	27.450000000000003	18.525
16	18.975	15.775	23.125	42.125
17	27.900000000000002	23.025000000000002	34.4	14.674999999999999
18	26.724999999999998	16.35	29.925	27.0
19	33.75	16.975	32.525	16.75
20	50.4	10.95	27.250000000000004	11.4
21	24.575	20.825	28.775000000000002	25.825
22	28.599999999999998	10.65	48.8	11.95
23	25.1	12.1	49.875	12.925
24	52.675000000000004	10.625	26.825	9.875
25	54.449999999999996	23.0	15.299999999999999	7.249999999999999
26	28.499999999999996	48.775	12.35	10.375
27	15.65	51.0	22.0	11.35
28	11.1	26.400000000000002	49.675000000000004	12.825000000000001
29	11.55	10.375	58.35	19.725
30	8.125	4.65	38.775	48.449999999999996
31	12.475	4.1000000000000005	48.975	34.449999999999996
32	26.200000000000003	5.45	22.25	46.1
33	56.85	7.875	12.55	22.725
34	67.575	4.9750000000000005	13.8	13.65
35	69.19999999999999	6.425	17.5	6.875000000000001
36	46.675	6.550000000000001	35.8	10.975
37	48.675000000000004	9.35	20.125	21.85
38	23.5	14.025000000000002	12.225	50.24999999999999
39	13.900000000000002	22.55	8.875	54.675
40	12.65	51.025	9.5	26.825
41	21.825	52.7	7.9	17.575
42	51.275000000000006	30.75	9.375	8.6
43	55.25	28.025	7.074999999999999	9.65
44	32.125	49.2	5.4	13.275
45	18.375	53.175	10.875	17.575
46	12.125	26.825	17.150000000000002	43.9
47	7.725	14.05	40.525	37.7
48	9.85	10.35	21.125	58.675
49	12.975	17.424999999999997	12.25	57.35
50	18.025	38.525	10.674999999999999	32.775
>>END_MODULE
>>Per sequence GC content	warn
#GC Content	Count
0	0.0
1	0.0
2	0.0
3	0.0
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.0
10	0.0
11	0.0
12	0.0
13	0.0
14	0.0
15	0.0
16	0.0
17	0.0
18	0.0
19	0.0
20	0.0
21	0.0
22	0.0
23	0.0
24	0.0
25	0.5
26	1.0
27	1.0
28	1.0
29	2.0
30	3.0
31	2.5
32	2.0
33	2.0
34	2.0
35	3.5
36	5.0
37	7.5
38	10.0
39	18.0
40	26.0
41	29.0
42	32.0
43	86.0
44	140.0
45	154.5
46	169.0
47	261.5
48	354.0
49	459.5
50	565.0
51	749.5
52	934.0
53	699.0
54	464.0
55	493.5
56	523.0
57	416.5
58	310.0
59	223.0
60	136.0
61	103.0
62	70.0
63	111.0
64	152.0
65	97.0
66	42.0
67	31.0
68	20.0
69	13.0
70	6.0
71	15.0
72	24.0
73	14.5
74	5.0
75	3.5
76	2.0
77	1.5
78	1.0
79	1.0
80	1.0
81	0.5
82	0.0
83	0.0
84	0.0
85	0.0
86	0.0
87	0.0
88	0.0
89	0.0
90	0.0
91	0.0
92	0.0
93	0.0
94	0.0
95	0.0
96	0.0
97	0.0
98	0.0
99	0.0
100	0.0
>>END_MODULE
>>Per base N content	pass
#Base	N-Count
1	0.0
2	0.05
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	40.525
#Duplication Level	Percentage of deduplicated	Percentage of total
1	77.60641579272054	31.45
2	9.623689080814312	7.8
3	3.824799506477483	4.65
4	2.2208513263417644	3.5999999999999996
5	0.987045033929673	2.0
6	0.7402837754472548	1.7999999999999998
7	0.7402837754472548	2.1
8	0.8019740900678594	2.6
9	0.30845157310302285	1.125
>10	2.4676125848241828	18.975
>50	0.5552128315854411	16.85
>100	0.12338062924120913	7.049999999999999
>500	0.0	0.0
>1k	0.0	0.0
>5k	0.0	0.0
>10k+	0.0	0.0
>>END_MODULE
>>Overrepresented sequences	fail
#Sequence	Count	Percentage	Possible Source
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	173	4.324999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	109	2.725	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	97	2.4250000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	95	2.375	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	90	2.25	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	81	2.025	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	78	1.95	No Hit
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	61	1.525	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	59	1.4749999999999999	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	59	1.4749999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	54	1.35	RNA PCR Primer, Index 1 (100% over 30bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	48	1.2	RNA PCR Primer, Index 1 (100% over 29bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGGCCATCTCGTATGC	36	0.8999999999999999	RNA PCR Primer, Index 20 (100% over 50bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	35	0.8750000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	35	0.8750000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
GGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	29	0.7250000000000001	No Hit
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	27	0.675	RNA PCR Primer, Index 1 (100% over 27bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	26	0.65	RNA PCR Primer, Index 1 (100% over 27bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	24	0.6	RNA PCR Primer, Index 1 (100% over 33bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	24	0.6	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	23	0.575	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	23	0.575	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTCGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	21	0.525	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	21	0.525	RNA PCR Primer, Index 1 (100% over 26bp)
AAGCTGCCAGTTGACGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	19	0.475	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	19	0.475	RNA PCR Primer, Index 1 (100% over 26bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 29bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 26bp)
AAGCTGCCAGTTGAAGCACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGT	15	0.375	RNA PCR Primer, Index 1 (97% over 35bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (96% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGTTTGTGCTGTTATGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
CGCGACCTCAGATCCGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	11	0.27499999999999997	No Hit
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGGCCATCTC	10	0.25	RNA PCR Primer, Index 20 (100% over 44bp)
TTTGAACCATCACTCGCCTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TGCGGGGCTAGGGCTAACAGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
CAACGGAATCCCAACAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	9	0.22499999999999998	No Hit
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
ACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGT	9	0.22499999999999998	RNA PCR Primer, Index 1 (97% over 35bp)
CACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACG	9	0.22499999999999998	RNA PCR Primer, Index 6 (100% over 34bp)
AGCTACATCTGGCTCCTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (100% over 30bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	8	0.2	No Hit
TGAGGTAGTAGATTGTCTAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
CACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGG	8	0.2	RNA PCR Primer, Index 17 (97% over 37bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
TCACAGTGACCCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGTGGCATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (96% over 30bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
CCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTG	7	0.17500000000000002	RNA PCR Primer, Index 15 (97% over 36bp)
TATTGCACTTGTCCCGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
TGTAAACATCCTCGCCTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
AAGGGATTCTGATGTTGGTCACTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGCTAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTTGCCTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTACCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (96% over 28bp)
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTACCCTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (96% over 28bp)
CTAGACTGAGGCTCCTTGAGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
GAATGTTGCTCGGTGAACCCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	5	0.125	No Hit
AACATTCATTGCTGTCGGTGGGTTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
AAGGGATTCTGATGTTGGTCACATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGGCCATCTCGTATGCC	5	0.125	RNA PCR Primer, Index 20 (98% over 50bp)
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTCTTGGAATTCTCGGGTG	5	0.125	No Hit
CTTTCAGTCGGATGTTTACAGCTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	5	0.125	No Hit
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TATTGCACTCGTCCCGGCCTCATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GCCGCCTGGATACCGCAGCTAGGAATAATGGAATTCTCGGGTGCCAAGGA	5	0.125	RNA PCR Primer, Index 1 (100% over 22bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGATTGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AAGGGATTCTGATGTTGGTCACACTGGAATTCTCGGGTGCCAAGGAACTC	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	1.2	0.0	0.0	0.0
2	0.0	1.225	0.0	0.0	0.0
3	0.0	1.3	0.0	0.0	0.0
4	0.0	1.325	0.0	0.0	0.0
5	0.0	1.375	0.0	0.0	0.0
6	0.0	1.5	0.0	0.0	0.0
7	0.0	1.9	0.0	0.0	0.0
8	0.0	2.0	0.0	0.0	0.0
9	0.0	2.05	0.0	0.0	0.0
10	0.0	2.125	0.0	0.0	0.0
11	0.0	2.275	0.0	0.0	0.0
12	0.0	2.35	0.0	0.0	0.0
13	0.0	2.475	0.0	0.0	0.0
14	0.0	2.925	0.0	0.0	0.0
15	0.0	3.375	0.0	0.0	0.0
16	0.0	4.325	0.0	0.0	0.0
17	0.0	5.025	0.0	0.0	0.0
18	0.0	6.0	0.0	0.0	0.0
19	0.0	6.525	0.0	0.0	0.0
20	0.0	7.25	0.0	0.0	0.0
21	0.0	11.65	0.0	0.0	0.0
22	0.0	23.375	0.0	0.0	0.0
23	0.0	55.975	0.0	0.0	0.0
24	0.0	71.05	0.0	0.0	0.0
25	0.0	77.075	0.0	0.0	0.0
26	0.0	78.175	0.0	0.0	0.0
27	0.0	78.775	0.0	0.0	0.0
28	0.0	79.3	0.0	0.0	0.0
29	0.0	79.875	0.0	0.0	0.0
30	0.0	80.3	0.0	0.0	0.0
31	0.0	80.8	0.0	0.0	0.0
32	0.0	82.325	0.0	0.0	0.0
33	0.0	83.05	0.0	0.0	0.0
34	0.0	86.475	0.0	0.0	0.0
35	0.0	87.425	0.0	0.0	0.0
36	0.0	88.275	0.0	0.0	0.0
37	0.0	89.2	0.0	0.0	0.0
38	0.0	89.65	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
ACAGTGA	20	6.952051E-4	44.000004	3
ACCGGTC	20	6.952051E-4	44.000004	10
TGTTGGA	20	6.952051E-4	44.000004	20
AACCGGT	20	6.952051E-4	44.000004	9
TTGTATA	20	6.952051E-4	44.000004	13
GAGCTTG	40	5.315087E-9	44.000004	13
GGATCCG	40	5.315087E-9	44.000004	3
CCGTCTG	40	5.315087E-9	44.000004	7
TCGGATC	40	5.315087E-9	44.000004	1
GATTGTA	20	6.952051E-4	44.000004	11
ACATTCA	45	2.728484E-10	44.000004	2
GTATAGT	20	6.952051E-4	44.000004	15
ATAGTTT	20	6.952051E-4	44.000004	17
GCTGTCG	45	2.728484E-10	44.000004	11
GAACCGG	20	6.952051E-4	44.000004	8
ATTGTAT	20	6.952051E-4	44.000004	12
GATCCGT	40	5.315087E-9	44.000004	4
AGTGAAC	20	6.952051E-4	44.000004	5
TCTCTTT	20	6.952051E-4	44.000004	15
TCCGTCT	40	5.315087E-9	44.000004	6
>>END_MODULE
Read 45376 spots for SRR5031096.sra
Written 45376 spots for SRR5031096.sra
Read 45376 spots for SRR5031096.sra
Written 45376 spots for SRR5031096.sra
Read 45376 spots for SRR5031096.sra
Written 45376 spots for SRR5031096.sra
Read 45376 spots for SRR5031096.sra
Written 45376 spots for SRR5031096.sra
Read 45376 spots for SRR5031096.sra
Written 45376 spots for SRR5031096.sra
Read 45376 spots for SRR5031096.sra
Written 45376 spots for SRR5031096.sra
Read 45376 spots for SRR5031096.sra
Written 45376 spots for SRR5031096.sra
Read 45376 spots for SRR5031096.sra
Written 45376 spots for SRR5031096.sra
Read 45376 spots for SRR5031096.sra
Written 45376 spots for SRR5031096.sra
Read 45376 spots for SRR5031096.sra
Written 45376 spots for SRR5031096.sra
Read 45380 spots for SRR5031096.sra
Written 45380 spots for SRR5031096.sra
Read 45376 spots for SRR5031096.sra
Written 45376 spots for SRR5031096.sra
SRR ids: ['SRR5031096.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_sz_zeakq
SRR5031096.sra spots: 544516
blocks: [[1, 45376], [45377, 90752], [90753, 136128], [136129, 181504], [181505, 226880], [226881, 272256], [272257, 317632], [317633, 363008], [363009, 408384], [408385, 453760], [453761, 499136], [499137, 544516]]
SRR5031096 file size 93741
SRR5031096 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031096 SRR5031096_1.fastq
Input file:	SRR5031096_1.fastq
trimmed:	SRR5031096-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 07:22:49 2020 >> started

Wed Mar  4 07:22:49 2020 >> done (0.543s)
544516 reads processed; of these:
    49 ( 0.01%) short reads filtered out after trimming by size control
     1 ( 0.00%) empty reads filtered out after trimming by size control
544466 (99.99%) reads available; of these:
 49692 ( 9.13%) trimmed reads available after processing
494774 (90.87%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	    13	  0.00%
 19	    28	  0.01%
 20	    42	  0.01%
 21	    54	  0.01%
 22	   108	  0.02%
 23	   109	  0.02%
 24	   111	  0.02%
 25	   155	  0.03%
 26	   110	  0.02%
 27	   143	  0.03%
 28	   165	  0.03%
 29	   332	  0.06%
 30	   189	  0.03%
 31	   226	  0.04%
 32	   286	  0.05%
 33	   426	  0.08%
 34	   659	  0.12%
 35	  1366	  0.25%
 36	   933	  0.17%
 37	   886	  0.16%
 38	   890	  0.16%
 39	  1002	  0.18%
 40	  1311	  0.24%
 41	  1124	  0.21%
 42	  1335	  0.25%
 43	  2357	  0.43%
 44	  2663	  0.49%
 45	  3789	  0.70%
 46	  4525	  0.83%
 47	  3631	  0.67%
 48	  9858	  1.81%
 49	 10866	  2.00%
 50	494774	 90.87%
544466 reads passed initial QC


criterion=sequence-density
sequence-density=89.99
sequence-density-rank=1
fanout-score=20.61
fanout-score-rank=2
prefix-density=90.58
prefix-fanout=20.5
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGGCCATCTCGTATGCC


criterion=fanout-score
sequence-density=4.19
sequence-density-rank=2
fanout-score=61.91
fanout-score-rank=1
prefix-density=90.23
prefix-fanout=2.9
sequence=GAATTCTCGGGGGCCAAGGAACT
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGGCCATCTCGTATGCC -o SRR5031096 -
Input file:	STDIN
trimmed:	SRR5031096-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGGCCATCTCGTATGCC
-- 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 07:22:56 2020 >> started

Wed Mar  4 07:22:57 2020 >> done (0.706s)
532367 reads processed; of these:
 29903 ( 5.62%) short reads filtered out after trimming by size control
  8023 ( 1.51%) empty reads filtered out after trimming by size control
494441 (92.88%) reads available; of these:
478681 (96.81%) trimmed reads available after processing
 15760 ( 3.19%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  3080	  0.62%
 19	  5576	  1.13%
 20	 25032	  5.06%
 21	 64207	 12.99%
 22	175531	 35.50%
 23	 84066	 17.00%
 24	 33208	  6.72%
 25	  8692	  1.76%
 26	  4278	  0.87%
 27	  3341	  0.68%
 28	  3497	  0.71%
 29	  3172	  0.64%
 30	  3956	  0.80%
 31	  7505	  1.52%
 32	  4769	  0.96%
 33	 17892	  3.62%
 34	  4643	  0.94%
 35	  3692	  0.75%
 36	  4852	  0.98%
 37	  1775	  0.36%
 38	  1922	  0.39%
 39	  1663	  0.34%
 40	  2359	  0.48%
 41	  2783	  0.56%
 42	  2961	  0.60%
 43	  2009	  0.41%
 44	  1299	  0.26%
 45	  1622	  0.33%
 46	  1145	  0.23%
 47	  1003	  0.20%
 48	   184	  0.04%
 49	   253	  0.05%
 50	 12474	  2.52%


criterion=sequence-density
sequence-density=10.20
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=7
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTT


criterion=fanout-score
sequence-density=2.26
sequence-density-rank=8
fanout-score=14.82
fanout-score-rank=1
prefix-density=1.97
prefix-fanout=14.8
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGGCCATCTCGTATGC
                                 Started job on |	Mar 04 07:23:18
                             Started mapping on |	Mar 04 07:23:18
                                    Finished on |	Mar 04 07:23:48
       Mapping speed, Million of reads per hour |	60.78

                          Number of input reads |	506540
                      Average input read length |	25
                                    UNIQUE READS:
                   Uniquely mapped reads number |	249351
                        Uniquely mapped reads % |	49.23%
                          Average mapped length |	23.66
                       Number of splices: Total |	1050
            Number of splices: Annotated (sjdb) |	276
                       Number of splices: GT/AG |	1031
                       Number of splices: GC/AG |	10
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	9
                      Mismatch rate per base, % |	0.38%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.84
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.00
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	203079
             % of reads mapped to multiple loci |	40.09%
        Number of reads mapped to too many loci |	7345
             % of reads mapped to too many loci |	1.45%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	8.73%
                     % of reads unmapped: other |	0.50%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	54110	54110	54110
N_multimapping	203079	203079	203079
N_noFeature	19621	21960	174132
N_ambiguous	136439	70385	1624
UnstrandedReadsAssigned:93291 PositiveStrandReadsAssigned:157006 NegativeStrandReadsAssigned:73595
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=22 echo kmer=19
SRR5031096 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: SRR5031096-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 506,540 reads, 116,995 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 947 rounds

 109283 SRR5031096.ke.tsv
  52636 SRR5031096.se.tsv
 161919 total
==> SRR5031096.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

==> SRR5031096.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031096 completed mapping pipeline successfully
