Starting /dee2/code/volunteer_pipeline.sh SRR5031106
    current disk space = 160470810624
    free memory = 1020968536 
SRR5031106 SRAfilesize
7ce2f4ab851847bf3402814a42d7d755  SRR5031106.sra
SRR5031106.sra file validated
SRR5031106 is single end
SRR5031106 is conventional basespace
SRR5031106 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031106_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	31.86025	31.0	31.0	34.0	30.0	34.0
2	32.363	33.0	31.0	34.0	31.0	34.0
3	32.386	33.0	31.0	34.0	31.0	34.0
4	36.11775	37.0	35.0	37.0	35.0	37.0
5	36.02275	37.0	35.0	37.0	35.0	37.0
6	35.9905	37.0	35.0	37.0	35.0	37.0
7	35.63575	37.0	35.0	37.0	33.0	37.0
8	35.5295	37.0	35.0	37.0	33.0	37.0
9	36.816	39.0	37.0	39.0	33.0	39.0
10	36.461	39.0	35.0	39.0	32.0	39.0
11	37.3115	39.0	37.0	39.0	34.0	39.0
12	37.591	39.0	37.0	39.0	35.0	39.0
13	37.2845	39.0	37.0	39.0	34.0	39.0
14	38.188	40.0	37.0	41.0	33.0	41.0
15	36.87575	39.0	36.0	41.0	30.0	41.0
16	36.605	38.0	36.0	40.0	30.0	41.0
17	36.877	39.0	36.0	40.0	31.0	41.0
18	38.02075	39.0	37.0	41.0	34.0	41.0
19	38.7015	40.0	38.0	41.0	35.0	41.0
20	38.40975	40.0	38.0	41.0	34.0	41.0
21	38.66475	40.0	38.0	41.0	35.0	41.0
22	37.612	39.0	37.0	40.0	32.0	41.0
23	38.0755	39.0	38.0	40.0	34.0	41.0
24	37.37375	39.0	37.0	40.0	31.0	41.0
25	38.14075	40.0	37.0	41.0	33.0	41.0
26	38.06225	40.0	37.0	41.0	33.0	41.0
27	38.19475	40.0	38.0	41.0	34.0	41.0
28	38.361	40.0	38.0	41.0	34.0	41.0
29	38.3575	40.0	38.0	41.0	34.0	41.0
30	38.7155	40.0	38.0	41.0	34.0	41.0
31	38.72475	40.0	38.0	41.0	35.0	41.0
32	38.65225	40.0	38.0	41.0	35.0	41.0
33	38.66525	40.0	38.0	41.0	35.0	41.0
34	38.30725	40.0	38.0	41.0	34.0	41.0
35	37.577	40.0	37.0	41.0	31.0	41.0
36	33.23425	35.0	30.0	40.0	23.0	41.0
37	35.106	37.0	33.0	39.0	30.0	40.0
38	36.69475	38.0	36.0	40.0	31.0	40.0
39	36.85225	38.0	36.0	40.0	32.0	40.0
40	37.14375	39.0	37.0	40.0	32.0	41.0
41	37.4705	40.0	37.0	40.0	33.0	41.0
42	37.402	40.0	37.0	41.0	32.0	41.0
43	37.4785	40.0	37.0	41.0	33.0	41.0
44	36.59475	39.0	35.0	40.0	30.0	41.0
45	36.652	39.0	36.0	40.0	30.0	41.0
46	36.487	39.0	36.0	40.0	30.0	41.0
47	35.63525	38.0	34.0	40.0	28.0	41.0
48	36.8345	39.0	37.0	40.0	31.0	41.0
49	36.89725	40.0	37.0	41.0	31.0	41.0
50	35.073	38.0	34.0	40.0	29.0	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
15	2.0
16	1.0
17	2.0
18	1.0
19	4.0
20	4.0
21	7.0
22	7.0
23	7.0
24	12.0
25	12.0
26	12.0
27	20.0
28	24.0
29	43.0
30	46.0
31	66.0
32	90.0
33	131.0
34	181.0
35	272.0
36	448.0
37	724.0
38	1152.0
39	732.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	6.606606606606606	26.776776776776778	54.729729729729726	11.886886886886886
2	22.466850137603203	29.171878909181885	16.81260945709282	31.548661496122094
3	25.15	21.125	18.85	34.875
4	33.0	29.599999999999998	12.675	24.725
5	23.25	39.675	27.200000000000003	9.875
6	36.425000000000004	13.575000000000001	36.825	13.175
7	12.925	23.075000000000003	24.224999999999998	39.775
8	25.7	31.1	12.5	30.7
9	21.775	36.8	28.375	13.05
10	19.2	21.45	28.675	30.675
11	32.574999999999996	9.0	15.475	42.95
12	13.15	16.35	33.0	37.5
13	33.074999999999996	17.150000000000002	32.925	16.85
14	34.2	31.125000000000004	20.200000000000003	14.475
15	36.7	19.05	28.449999999999996	15.8
16	16.85	18.85	21.0	43.3
17	26.150000000000002	17.349999999999998	40.475	16.025
18	25.374999999999996	16.825000000000003	31.525	26.275
19	36.7	13.475000000000001	31.674999999999997	18.15
20	49.65	11.924999999999999	27.875	10.549999999999999
21	21.45	20.25	29.299999999999997	28.999999999999996
22	29.225	10.95	49.475	10.35
23	26.55	10.95	50.875	11.625
24	54.425000000000004	10.5	26.974999999999998	8.1
25	56.225	24.224999999999998	12.875	6.675000000000001
26	27.85	51.725	12.625	7.8
27	14.124999999999998	53.5	24.3	8.075000000000001
28	9.425	25.374999999999996	53.125	12.075
29	8.725	10.15	61.625	19.5
30	8.125	4.45	39.050000000000004	48.375
31	11.725	3.45	48.949999999999996	35.875
32	26.825	4.1000000000000005	22.275	46.800000000000004
33	59.675	5.825	11.5	23.0
34	69.72500000000001	5.325	12.675	12.275
35	70.625	5.7250000000000005	16.75	6.9
36	45.25	5.875	37.475	11.4
37	48.575	7.1	19.825	24.5
38	24.4	13.075000000000001	10.625	51.9
39	13.05	24.125	6.8500000000000005	55.974999999999994
40	13.3	53.125	7.074999999999999	26.5
41	23.95	54.574999999999996	6.05	15.425
42	53.175	31.374999999999996	6.550000000000001	8.9
43	56.25	30.599999999999998	4.9750000000000005	8.175
44	30.2	53.025	4.125	12.65
45	15.575	55.525000000000006	10.825	18.075
46	9.2	26.900000000000002	17.1	46.800000000000004
47	5.8999999999999995	13.675	40.375	40.050000000000004
48	6.550000000000001	11.55	19.675	62.224999999999994
49	11.05	19.7	10.45	58.8
50	17.375	41.275	10.4	30.95
>>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	0.0
26	0.0
27	0.0
28	0.0
29	0.0
30	0.0
31	2.0
32	4.0
33	3.5
34	3.0
35	7.5
36	12.0
37	10.0
38	8.0
39	12.5
40	17.0
41	17.5
42	18.0
43	52.0
44	86.0
45	125.5
46	165.0
47	299.0
48	433.0
49	527.5
50	622.0
51	817.0
52	1012.0
53	737.0
54	462.0
55	493.5
56	525.0
57	413.5
58	302.0
59	204.0
60	106.0
61	78.0
62	50.0
63	70.5
64	91.0
65	62.0
66	33.0
67	24.5
68	16.0
69	11.0
70	6.0
71	15.0
72	24.0
73	14.0
74	4.0
75	2.0
76	0.0
77	0.0
78	0.0
79	0.5
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	0.1
2	0.075
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	40.125
#Duplication Level	Percentage of deduplicated	Percentage of total
1	77.38317757009345	31.05
2	9.221183800623054	7.3999999999999995
3	3.7383177570093453	4.5
4	2.1183800623052957	3.4000000000000004
5	1.61993769470405	3.25
6	1.0591900311526479	2.55
7	0.6853582554517134	1.925
8	0.6230529595015576	2.0
9	0.4984423676012461	1.7999999999999998
>10	2.4922118380062304	19.375
>50	0.24922118380062305	6.775
>100	0.3115264797507788	15.975
>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	148	3.6999999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	146	3.65	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	126	3.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	110	2.75	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	109	2.725	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	87	2.175	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	74	1.8499999999999999	RNA PCR Primer, Index 1 (100% over 30bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	56	1.4000000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	54	1.35	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	38	0.95	RNA PCR Primer, Index 1 (100% over 29bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	36	0.8999999999999999	No Hit
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	35	0.8750000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	31	0.775	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	31	0.775	RNA PCR Primer, Index 1 (100% over 27bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	30	0.75	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	26	0.65	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	24	0.6	RNA PCR Primer, Index 1 (100% over 26bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	24	0.6	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	23	0.575	RNA PCR Primer, Index 1 (100% over 28bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCA	21	0.525	RNA PCR Primer, Index 7 (100% over 35bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	21	0.525	RNA PCR Primer, Index 1 (100% over 28bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	20	0.5	RNA PCR Primer, Index 1 (100% over 33bp)
GGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	20	0.5	No Hit
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	19	0.475	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	19	0.475	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	19	0.475	RNA PCR Primer, Index 1 (100% over 28bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 26bp)
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	16	0.4	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	15	0.375	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGTGGCATTCTCGGGTGCCAAGGAACTCCAGT	14	0.35000000000000003	RNA PCR Primer, Index 1 (96% over 30bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCACCGGATCTCGTATGC	13	0.325	RNA PCR Primer, Index 30 (100% over 50bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	12	0.3	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 30bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 30bp)
AAGCTGCCAGTTGAAGCACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (96% over 28bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	10	0.25	No Hit
AAGCTGCCAGTTGAAGACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGAACCATCACTCGCCTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATCGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGACGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGATTGTCTAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTTGTCCCGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGACCCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTACCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCACCGGATCTC	8	0.2	RNA PCR Primer, Index 30 (100% over 44bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGTTTGTGCTGTTATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
AGCTGGTGTTGTGACTCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	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)
TCCCTGAGACCCTTTAACCTGTGCTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (96% over 28bp)
TGAGGTAGGAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGGCAATGGTAGAACTCACATGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
AACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	6	0.15	No Hit
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCAATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCATTGTTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (96% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGGCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (96% over 30bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TAAGGCACGCGGTGAATGCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
CGCGACCTCAGATCCGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	6	0.15	No Hit
ACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCA	5	0.125	RNA PCR Primer, Index 7 (100% over 35bp)
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
CGACACAAGGGTTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC	5	0.125	RNA PCR Primer, Index 2 (100% over 34bp)
TGAGGTAGTAGTTTGTACAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	5	0.125	No Hit
TCGGATCCGTCTGAGCTTGGCTTTTTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
TAGCACCATCTGAAATCGGTTATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ACTAATCCTAGCCCTAGCCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
AAGGGATTCTGATGTTGGTCACATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGCCTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
AGAGGTAGTAGGTTGCATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGT	5	0.125	No Hit
TATGCAAGGGCAAGCTCTCTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	5	0.125	RNA PCR Primer, Index 1 (100% over 31bp)
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CGCACGGGGTCGGCGGCGATGTCGGCTGGAATTCTCGGGTGCCAAGGAAC	5	0.125	RNA PCR Primer, Index 1 (100% over 24bp)
AAGCTGCCAGTTGACGCACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTAATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGGAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AACCCGTAGATCCGAACTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTATTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
CAACGGAATCCCAACAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
AAGGGATTCTGATGTTGGTCATGGAATTCTCGGGTGCCAAGGAACTCCAG	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	0.45	0.0	0.0	0.0
2	0.0	0.45	0.0	0.0	0.0
3	0.0	0.5	0.0	0.0	0.0
4	0.0	0.55	0.0	0.0	0.0
5	0.0	0.65	0.0	0.0	0.0
6	0.0	0.7	0.0	0.0	0.0
7	0.0	1.275	0.0	0.0	0.0
8	0.0	1.35	0.0	0.0	0.0
9	0.0	1.4	0.0	0.0	0.0
10	0.0	1.55	0.0	0.0	0.0
11	0.0	1.675	0.0	0.0	0.0
12	0.0	1.85	0.0	0.0	0.0
13	0.0	2.05	0.0	0.0	0.0
14	0.0	2.15	0.0	0.0	0.0
15	0.0	2.5	0.0	0.0	0.0
16	0.0	3.675	0.0	0.0	0.0
17	0.0	4.275	0.0	0.0	0.0
18	0.0	5.55	0.0	0.0	0.0
19	0.0	5.9	0.0	0.0	0.0
20	0.0	6.6	0.0	0.0	0.0
21	0.0	11.725	0.0	0.0	0.0
22	0.0	24.975	0.0	0.0	0.0
23	0.0	59.75	0.0	0.0	0.0
24	0.0	75.4	0.0	0.0	0.0
25	0.0	81.1	0.0	0.0	0.0
26	0.0	82.575	0.0	0.0	0.0
27	0.0	83.125	0.0	0.0	0.0
28	0.0	83.9	0.0	0.0	0.0
29	0.0	84.4	0.0	0.0	0.0
30	0.0	84.825	0.0	0.0	0.0
31	0.0	85.3	0.0	0.0	0.0
32	0.0	86.35	0.0	0.0	0.0
33	0.0	87.325	0.0	0.0	0.0
34	0.0	89.075	0.0	0.0	0.0
35	0.0	89.725	0.0	0.0	0.0
36	0.0	90.175	0.0	0.0	0.0
37	0.0	90.75	0.0	0.0	0.0
38	0.0	91.025	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
GAGGTAG	40	5.315087E-9	44.000004	2
CTGAGAC	20	6.952051E-4	44.000004	4
CCTGAGA	20	6.952051E-4	44.000004	3
CTTGGTG	20	6.952051E-4	44.000004	16
CTTGGCT	20	6.952051E-4	44.000004	16
GGCTTGG	40	5.315087E-9	44.000004	19
CCCTGAG	20	6.952051E-4	44.000004	2
GGTAGTA	40	5.315087E-9	44.000004	4
TTGGCTT	20	6.952051E-4	44.000004	17
TTGGTGG	20	6.952051E-4	44.000004	17
GGTGGAA	20	6.952051E-4	44.000004	19
AGGTAGT	40	5.315087E-9	44.000004	3
TGGTGGA	20	6.952051E-4	44.000004	18
GTAGTAG	40	5.315087E-9	44.000004	5
GAGACCC	20	6.952051E-4	44.000004	6
TGTAAAC	20	6.952051E-4	44.000004	1
TCCCTGA	20	6.952051E-4	44.000004	1
GTAGATT	25	3.6958358E-5	44.0	8
ACAGTGA	30	1.9515464E-6	44.0	3
>>END_MODULE
Read 50947 spots for SRR5031106.sra
Written 50947 spots for SRR5031106.sra
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Read 50983 spots for SRR5031106.sra
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Read 50947 spots for SRR5031106.sra
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SRR ids: ['SRR5031106.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_wcgaxw08
SRR5031106.sra spots: 2445492
blocks: [[1, 50947], [50948, 101894], [101895, 152841], [152842, 203788], [203789, 254735], [254736, 305682], [305683, 356629], [356630, 407576], [407577, 458523], [458524, 509470], [509471, 560417], [560418, 611364], [611365, 662311], [662312, 713258], [713259, 764205], [764206, 815152], [815153, 866099], [866100, 917046], [917047, 967993], [967994, 1018940], [1018941, 1069887], [1069888, 1120834], [1120835, 1171781], [1171782, 1222728], [1222729, 1273675], [1273676, 1324622], [1324623, 1375569], [1375570, 1426516], [1426517, 1477463], [1477464, 1528410], [1528411, 1579357], [1579358, 1630304], [1630305, 1681251], [1681252, 1732198], [1732199, 1783145], [1783146, 1834092], [1834093, 1885039], [1885040, 1935986], [1935987, 1986933], [1986934, 2037880], [2037881, 2088827], [2088828, 2139774], [2139775, 2190721], [2190722, 2241668], [2241669, 2292615], [2292616, 2343562], [2343563, 2394509], [2394510, 2445492]]
SRR5031106 file size 422793
SRR5031106 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 48 -o SRR5031106 SRR5031106_1.fastq
Input file:	SRR5031106_1.fastq
trimmed:	SRR5031106-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):	32
Wed Mar  4 07:25:07 2020 >> started

Wed Mar  4 07:25:08 2020 >> done (1.483s)
2445492 reads processed; of these:
    247 ( 0.01%) short reads filtered out after trimming by size control
      8 ( 0.00%) empty reads filtered out after trimming by size control
2445237 (99.99%) reads available; of these:
 211870 ( 8.66%) trimmed reads available after processing
2233367 (91.34%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     66	  0.00%
 19	    152	  0.01%
 20	    192	  0.01%
 21	    243	  0.01%
 22	    429	  0.02%
 23	    533	  0.02%
 24	    520	  0.02%
 25	    728	  0.03%
 26	    495	  0.02%
 27	    667	  0.03%
 28	    756	  0.03%
 29	   1412	  0.06%
 30	    700	  0.03%
 31	    800	  0.03%
 32	    948	  0.04%
 33	   1739	  0.07%
 34	   2773	  0.11%
 35	   6776	  0.28%
 36	   3944	  0.16%
 37	   3504	  0.14%
 38	   3636	  0.15%
 39	   4178	  0.17%
 40	   4992	  0.20%
 41	   5436	  0.22%
 42	   6489	  0.27%
 43	  10761	  0.44%
 44	  11812	  0.48%
 45	  16803	  0.69%
 46	  17173	  0.70%
 47	  15940	  0.65%
 48	  46847	  1.92%
 49	  40426	  1.65%
 50	2233367	 91.34%
2445237 reads passed initial QC


criterion=sequence-density
sequence-density=91.83
sequence-density-rank=1
fanout-score=20.00
fanout-score-rank=2
prefix-density=92.73
prefix-fanout=19.8
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCACCGGATCTCGTATGCC


criterion=fanout-score
sequence-density=3.67
sequence-density-rank=3
fanout-score=71.39
fanout-score-rank=1
prefix-density=92.79
prefix-fanout=2.8
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 48 -x TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCACCGGATCTCGTATGCC -o SRR5031106 -
Input file:	STDIN
trimmed:	SRR5031106-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCACCGGATCTCGTATGCC
-- 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):	32
Wed Mar  4 07:25:26 2020 >> started

Wed Mar  4 07:25:30 2020 >> done (3.756s)
2392080 reads processed; of these:
 123644 ( 5.17%) short reads filtered out after trimming by size control
  13581 ( 0.57%) empty reads filtered out after trimming by size control
2254855 (94.26%) reads available; of these:
2197577 (97.46%) trimmed reads available after processing
  57278 ( 2.54%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  12465	  0.55%
 19	  26281	  1.17%
 20	 138371	  6.14%
 21	 325869	 14.45%
 22	 835108	 37.04%
 23	 373033	 16.54%
 24	 159768	  7.09%
 25	  41096	  1.82%
 26	  18551	  0.82%
 27	  13992	  0.62%
 28	  14185	  0.63%
 29	  10720	  0.48%
 30	  17474	  0.77%
 31	  29499	  1.31%
 32	  20821	  0.92%
 33	  52236	  2.32%
 34	  14778	  0.66%
 35	  10785	  0.48%
 36	  12172	  0.54%
 37	   6324	  0.28%
 38	   6787	  0.30%
 39	   6079	  0.27%
 40	   9254	  0.41%
 41	  11202	  0.50%
 42	  12395	  0.55%
 43	   7627	  0.34%
 44	   5334	  0.24%
 45	   7611	  0.34%
 46	   5130	  0.23%
 47	   3819	  0.17%
 48	    694	  0.03%
 49	   1166	  0.05%
 50	  44229	  1.96%


criterion=sequence-density
sequence-density=8.82
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=16
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.50
sequence-density-rank=31
fanout-score=21.44
fanout-score-rank=1
prefix-density=10.62
prefix-fanout=1.0
sequence=CTGAGCTTGGCA
                                 Started job on |	Mar 04 07:26:09
                             Started mapping on |	Mar 04 07:26:10
                                    Finished on |	Mar 04 07:26:41
       Mapping speed, Million of reads per hour |	268.03

                          Number of input reads |	2308012
                      Average input read length |	24
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1242944
                        Uniquely mapped reads % |	53.85%
                          Average mapped length |	23.27
                       Number of splices: Total |	5494
            Number of splices: Annotated (sjdb) |	1455
                       Number of splices: GT/AG |	5422
                       Number of splices: GC/AG |	43
                       Number of splices: AT/AC |	1
               Number of splices: Non-canonical |	28
                      Mismatch rate per base, % |	0.39%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.87
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.07
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	865857
             % of reads mapped to multiple loci |	37.52%
        Number of reads mapped to too many loci |	30723
             % of reads mapped to too many loci |	1.33%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	6.92%
                     % of reads unmapped: other |	0.38%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	199211	199211	199211
N_multimapping	865857	865857	865857
N_noFeature	82809	92278	861781
N_ambiguous	681851	348134	7313
UnstrandedReadsAssigned:478284 PositiveStrandReadsAssigned:802532 NegativeStrandReadsAssigned:373850
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=21 echo kmer=19
SRR5031106 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: SRR5031106-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,308,012 reads, 575,078 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 654 rounds

 109283 SRR5031106.ke.tsv
  52636 SRR5031106.se.tsv
 161919 total
==> SRR5031106.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

==> SRR5031106.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031106 completed mapping pipeline successfully
