Starting /dee2/code/volunteer_pipeline.sh SRR5031104
    current disk space = 160472039424
    free memory = 73952548 
SRR5031104 SRAfilesize
b41bcdcf62f81fb90e0381cd6c65b7a2  SRR5031104.sra
SRR5031104.sra file validated
SRR5031104 is single end
SRR5031104 is conventional basespace
SRR5031104 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031104_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	32.09075	33.0	31.0	34.0	30.0	34.0
2	32.46275	34.0	31.0	34.0	31.0	34.0
3	32.4365	33.0	31.0	34.0	31.0	34.0
4	36.16575	37.0	35.0	37.0	35.0	37.0
5	36.10975	37.0	35.0	37.0	35.0	37.0
6	36.01875	37.0	35.0	37.0	35.0	37.0
7	35.87175	37.0	35.0	37.0	35.0	37.0
8	35.75625	37.0	35.0	37.0	35.0	37.0
9	37.10175	39.0	37.0	39.0	33.0	39.0
10	36.895	39.0	37.0	39.0	33.0	39.0
11	37.46275	39.0	37.0	39.0	35.0	39.0
12	37.752	39.0	37.0	39.0	35.0	39.0
13	37.47225	39.0	37.0	39.0	35.0	39.0
14	38.70475	40.0	38.0	41.0	34.0	41.0
15	37.0745	40.0	37.0	41.0	31.0	41.0
16	36.57225	39.0	36.0	40.0	30.0	41.0
17	36.8025	39.0	36.0	40.0	31.0	41.0
18	38.23575	40.0	37.0	41.0	34.0	41.0
19	38.8635	40.0	38.0	41.0	36.0	41.0
20	38.525	40.0	38.0	41.0	35.0	41.0
21	38.6715	40.0	38.0	41.0	35.0	41.0
22	37.715	40.0	37.0	41.0	32.0	41.0
23	38.186	39.0	38.0	40.0	34.0	41.0
24	37.51575	40.0	37.0	41.0	32.0	41.0
25	38.49925	40.0	38.0	41.0	34.0	41.0
26	38.46925	40.0	38.0	41.0	34.0	41.0
27	38.714	40.0	38.0	41.0	35.0	41.0
28	38.78925	40.0	38.0	41.0	35.0	41.0
29	38.7705	40.0	39.0	41.0	35.0	41.0
30	38.96425	40.0	39.0	41.0	35.0	41.0
31	38.8595	40.0	38.0	41.0	35.0	41.0
32	38.80275	40.0	38.0	41.0	35.0	41.0
33	38.96375	40.0	39.0	41.0	35.0	41.0
34	38.38375	40.0	38.0	41.0	34.0	41.0
35	37.86375	40.0	37.0	41.0	32.0	41.0
36	33.42025	35.0	30.0	40.0	23.0	41.0
37	35.267	37.0	34.0	39.0	30.0	40.0
38	36.72025	38.0	36.0	40.0	31.0	40.0
39	37.114	39.0	37.0	40.0	33.0	40.0
40	37.50475	39.0	37.0	40.0	33.0	41.0
41	37.93825	40.0	38.0	41.0	33.0	41.0
42	37.71175	40.0	38.0	41.0	33.0	41.0
43	37.7625	40.0	38.0	41.0	33.0	41.0
44	36.57725	39.0	36.0	40.0	30.0	41.0
45	36.99175	39.0	37.0	40.0	31.0	41.0
46	37.147	40.0	37.0	40.0	32.0	41.0
47	36.393	39.0	36.0	40.0	30.0	41.0
48	37.3255	40.0	37.0	40.0	33.0	41.0
49	37.572	40.0	38.0	41.0	33.0	41.0
50	35.6285	38.0	35.0	40.0	30.0	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
11	1.0
12	0.0
13	0.0
14	1.0
15	0.0
16	1.0
17	1.0
18	0.0
19	1.0
20	3.0
21	8.0
22	4.0
23	5.0
24	12.0
25	12.0
26	15.0
27	14.0
28	26.0
29	25.0
30	34.0
31	52.0
32	75.0
33	121.0
34	187.0
35	254.0
36	405.0
37	660.0
38	1211.0
39	872.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	4.97997997997998	23.34834834834835	59.80980980980981	11.861861861861863
2	23.38507761642464	28.567851777666498	21.031547320981474	27.01552328492739
3	17.4	17.25	17.575	47.775
4	25.8	39.65	10.549999999999999	24.0
5	20.424999999999997	38.4	30.4	10.775
6	36.675000000000004	14.05	38.175	11.1
7	9.8	26.5	24.125	39.574999999999996
8	23.549999999999997	43.625	11.899999999999999	20.925
9	19.35	41.825	28.625	10.2
10	16.175	17.849999999999998	27.450000000000003	38.525
11	31.075000000000003	9.2	12.825000000000001	46.9
12	14.124999999999998	13.125	25.35	47.4
13	19.075	19.45	39.925	21.55
14	41.225	22.7	25.124999999999996	10.95
15	38.4	19.525000000000002	29.175	12.9
16	11.85	26.55	19.3	42.3
17	25.900000000000002	20.474999999999998	38.6	15.024999999999999
18	29.875	16.925	28.4	24.8
19	41.625	12.075	28.425	17.875
20	53.449999999999996	14.85	22.35	9.35
21	21.675	26.025	23.275000000000002	29.025000000000002
22	33.675	9.375	50.675000000000004	6.275
23	25.874999999999996	10.174999999999999	53.6	10.35
24	56.825	10.100000000000001	26.900000000000002	6.175
25	59.25	23.7	12.1	4.95
26	27.85	54.55	10.875	6.7250000000000005
27	11.225	58.15	23.625	7.000000000000001
28	6.1	25.825	56.325	11.75
29	7.3	8.525	66.07499999999999	18.099999999999998
30	6.1	3.4250000000000003	39.6	50.875
31	11.825	2.475	51.0	34.699999999999996
32	25.775	3.675	21.6	48.949999999999996
33	62.275000000000006	4.75	10.625	22.35
34	73.275	4.075	11.924999999999999	10.725
35	74.375	4.375	15.775	5.475
36	44.725	4.375	40.675	10.225
37	50.125	6.75	20.349999999999998	22.775000000000002
38	22.175	12.875	9.55	55.400000000000006
39	12.2	22.85	5.8999999999999995	59.050000000000004
40	11.725	55.15	5.55	27.575
41	23.35	59.599999999999994	4.6	12.45
42	55.625	33.25	5.7	5.425
43	60.25	29.275000000000002	4.0	6.4750000000000005
44	29.675	55.775	3.5749999999999997	10.975
45	13.675	59.8	9.25	17.275
46	6.625	27.750000000000004	16.1	49.525000000000006
47	3.975	12.225	43.85	39.95
48	6.375	10.95	20.225	62.45
49	10.25	17.974999999999998	9.65	62.125
50	16.25	43.25	9.725	30.775000000000002
>>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	1.0
28	2.0
29	1.5
30	1.0
31	1.5
32	2.0
33	2.5
34	3.0
35	7.0
36	11.0
37	8.5
38	6.0
39	9.0
40	12.0
41	14.5
42	17.0
43	45.5
44	74.0
45	124.5
46	175.0
47	369.5
48	564.0
49	599.0
50	634.0
51	895.0
52	1156.0
53	794.0
54	432.0
55	412.5
56	393.0
57	335.5
58	278.0
59	183.0
60	88.0
61	66.0
62	44.0
63	47.0
64	50.0
65	40.5
66	31.0
67	19.5
68	8.0
69	5.5
70	3.0
71	8.5
72	14.0
73	7.0
74	0.0
75	0.5
76	1.0
77	1.0
78	1.0
79	0.5
80	0.0
81	0.0
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	0.15
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	37.1
#Duplication Level	Percentage of deduplicated	Percentage of total
1	75.67385444743935	28.075
2	9.231805929919137	6.8500000000000005
3	4.919137466307277	5.475
4	2.897574123989218	4.3
5	1.1455525606469004	2.125
6	0.6738544474393532	1.5
7	0.8086253369272237	2.1
8	0.8086253369272237	2.4
9	0.4716981132075472	1.575
>10	2.964959568733154	22.825
>50	0.13477088948787064	3.025
>100	0.2695417789757413	19.75
>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
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	252	6.3	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	184	4.6	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	182	4.55	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	172	4.3	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	69	1.725	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	52	1.3	RNA PCR Primer, Index 1 (100% over 30bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	40	1.0	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	37	0.9249999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	36	0.8999999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	36	0.8999999999999999	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	35	0.8750000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	34	0.8500000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	33	0.8250000000000001	No Hit
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	30	0.75	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	30	0.75	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	27	0.675	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	26	0.65	RNA PCR Primer, Index 1 (100% over 29bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	26	0.65	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	24	0.6	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	23	0.575	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	21	0.525	RNA PCR Primer, Index 1 (100% over 30bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	21	0.525	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	19	0.475	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (96% over 28bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 29bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTACCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TCCTGTACTGAGCTGCCCCGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	15	0.375	RNA PCR Primer, Index 1 (100% over 26bp)
TTCCCTTTGTCATCCTATGCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
TCCTGTACTGAGCTGCCCCGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
TCCTGTACTGAGCTGCCCCGATGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAAAAGATCTCGTATGC	12	0.3	RNA PCR Primer, Index 28 (100% over 50bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	10	0.25	RNA PCR Primer, Index 1 (100% over 30bp)
TCCCTGAGACCCTTTAACCTGTATGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	10	0.25	RNA PCR Primer, Index 1 (100% over 30bp)
AAGCTGCCAGTTGAAGCACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGCATTCTCGGGTGCCAAGGAACTCCAGT	9	0.22499999999999998	RNA PCR Primer, Index 1 (96% over 30bp)
TCCTGTACTGAGCTGCCCCGAGATGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAAATGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	8	0.2	RNA PCR Primer, Index 1 (100% over 33bp)
TGTAAACATCCTACACTCAGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCA	8	0.2	RNA PCR Primer, Index 7 (100% over 35bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
CACCCGTAGAACCGACCTTGCGATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATCGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCAACGCTGTCGGTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
CTATACGACCTGCTGCCTTTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATTCAGGATAGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAAAAGATCTC	7	0.17500000000000002	RNA PCR Primer, Index 28 (100% over 44bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTTGGAATTCTCGGGTGCC	7	0.17500000000000002	No Hit
TGTAAACATCCCCGACTGGAAGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
AGAGGTAGTAGGTTGCATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCCGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCCGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	7	0.17500000000000002	No Hit
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGTTTGTACAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (96% over 28bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGTGGAATTCTCGGGTGCC	6	0.15	No Hit
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
CGCGACCTCAGATCAGCCGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	6	0.15	No Hit
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGATGGCATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (96% over 30bp)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
AAGCTGCCAGTTGAAGACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TAAGGCACGCGGTGAATGAAATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGCCTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
CATTATTACTTTTGGTACGCGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AAGCCCTTACCCCAAAAAGCATTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAGCTTGGACTTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (96% over 26bp)
AACATTCAACCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	5	0.125	No Hit
TCTCCCAACCCTTGTACCAGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTCACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGCCCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AAGCTGCCAGTTGACGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
>>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	0.4	0.0	0.0	0.0
2	0.0	0.4	0.0	0.0	0.0
3	0.0	0.525	0.0	0.0	0.0
4	0.0	0.55	0.0	0.0	0.0
5	0.0	0.6	0.0	0.0	0.0
6	0.0	0.7	0.0	0.0	0.0
7	0.0	1.05	0.0	0.0	0.0
8	0.0	1.25	0.0	0.0	0.0
9	0.0	1.35	0.0	0.0	0.0
10	0.0	1.55	0.0	0.0	0.0
11	0.0	1.65	0.0	0.0	0.0
12	0.0	1.8	0.0	0.0	0.0
13	0.0	1.825	0.0	0.0	0.0
14	0.0	2.05	0.0	0.0	0.0
15	0.0	2.35	0.0	0.0	0.0
16	0.0	2.825	0.0	0.0	0.0
17	0.0	3.325	0.0	0.0	0.0
18	0.0	3.95	0.0	0.0	0.0
19	0.0	4.225	0.0	0.0	0.0
20	0.0	5.075	0.0	0.0	0.0
21	0.0	10.475	0.0	0.0	0.0
22	0.0	23.325	0.0	0.0	0.0
23	0.0	62.0	0.0	0.0	0.0
24	0.0	78.95	0.0	0.0	0.0
25	0.0	84.5	0.0	0.0	0.0
26	0.0	85.325	0.0	0.0	0.0
27	0.0	85.725	0.0	0.0	0.0
28	0.0	86.2	0.0	0.0	0.0
29	0.0	86.725	0.0	0.0	0.0
30	0.0	87.175	0.0	0.0	0.0
31	0.0	87.9	0.0	0.0	0.0
32	0.0	88.4	0.0	0.0	0.0
33	0.0	88.975	0.0	0.0	0.0
34	0.0	91.05	0.0	0.0	0.0
35	0.0	91.55	0.0	0.0	0.0
36	0.0	91.9	0.0	0.0	0.0
37	0.0	92.35	0.0	0.0	0.0
38	0.0	92.625	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
AACGCTG	65	0.0	44.000004	8
GAGGTAG	20	6.952051E-4	44.000004	2
GTTTGGA	20	6.952051E-4	44.000004	20
AAGTAAT	65	0.0	44.000004	4
TCAAGTA	65	0.0	44.000004	2
ACGCTGT	65	0.0	44.000004	9
CCTGTTG	20	6.952051E-4	44.000004	18
TTCAAGT	65	0.0	44.000004	1
TTCAACG	65	0.0	44.000004	5
TCAACGC	65	0.0	44.000004	6
GTGAGTG	45	2.728484E-10	44.000004	18
ACCTGTT	20	6.952051E-4	44.000004	17
CTTGGTG	20	6.952051E-4	44.000004	16
GGATAGG	65	0.0	44.000004	14
AGGCTTG	40	5.315087E-9	44.000004	18
GGTAGTA	20	6.952051E-4	44.000004	4
TGAGGTA	20	6.952051E-4	44.000004	1
ACCTTGC	20	6.952051E-4	44.000004	15
AGGTAGT	20	6.952051E-4	44.000004	3
TGAGTGG	45	2.728484E-10	44.000004	19
>>END_MODULE
Read 241111 spots for SRR5031104.sra
Written 241111 spots for SRR5031104.sra
Read 241111 spots for SRR5031104.sra
Written 241111 spots for SRR5031104.sra
Read 241111 spots for SRR5031104.sra
Written 241111 spots for SRR5031104.sra
Read 241111 spots for SRR5031104.sra
Written 241111 spots for SRR5031104.sra
Read 241111 spots for SRR5031104.sra
Written 241111 spots for SRR5031104.sra
Read 241111 spots for SRR5031104.sra
Written 241111 spots for SRR5031104.sra
Read 241111 spots for SRR5031104.sra
Written 241111 spots for SRR5031104.sra
Read 241111 spots for SRR5031104.sra
Written 241111 spots for SRR5031104.sra
Read 241111 spots for SRR5031104.sra
Written 241111 spots for SRR5031104.sra
Read 241111 spots for SRR5031104.sra
Written 241111 spots for SRR5031104.sra
Read 241112 spots for SRR5031104.sra
Written 241112 spots for SRR5031104.sra
Read 241111 spots for SRR5031104.sra
Written 241111 spots for SRR5031104.sra
SRR ids: ['SRR5031104.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_sqqx0lx8
SRR5031104.sra spots: 2893333
blocks: [[1, 241111], [241112, 482222], [482223, 723333], [723334, 964444], [964445, 1205555], [1205556, 1446666], [1446667, 1687777], [1687778, 1928888], [1928889, 2169999], [2170000, 2411110], [2411111, 2652221], [2652222, 2893333]]
SRR5031104 file size 500416
SRR5031104 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031104 SRR5031104_1.fastq
Input file:	SRR5031104_1.fastq
trimmed:	SRR5031104-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 07:24:39 2020 >> started

Wed Mar  4 07:24:41 2020 >> done (1.832s)
2893333 reads processed; of these:
    142 ( 0.00%) short reads filtered out after trimming by size control
      5 ( 0.00%) empty reads filtered out after trimming by size control
2893186 (99.99%) reads available; of these:
 204114 ( 7.05%) trimmed reads available after processing
2689072 (92.95%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     54	  0.00%
 19	     88	  0.00%
 20	    166	  0.01%
 21	    261	  0.01%
 22	    489	  0.02%
 23	    519	  0.02%
 24	    523	  0.02%
 25	    649	  0.02%
 26	    444	  0.02%
 27	    629	  0.02%
 28	    854	  0.03%
 29	   2021	  0.07%
 30	    782	  0.03%
 31	    834	  0.03%
 32	   1041	  0.04%
 33	   2084	  0.07%
 34	   2933	  0.10%
 35	   8689	  0.30%
 36	   4851	  0.17%
 37	   3909	  0.14%
 38	   3423	  0.12%
 39	   3763	  0.13%
 40	   4323	  0.15%
 41	   5389	  0.19%
 42	   6515	  0.23%
 43	  10483	  0.36%
 44	  10539	  0.36%
 45	  13747	  0.48%
 46	  14638	  0.51%
 47	  13780	  0.48%
 48	  42046	  1.45%
 49	  43648	  1.51%
 50	2689072	 92.95%
2893186 reads passed initial QC


criterion=sequence-density
sequence-density=93.37
sequence-density-rank=1
fanout-score=16.98
fanout-score-rank=2
prefix-density=94.20
prefix-fanout=16.8
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAAAAGATCTCGTATGCC


criterion=fanout-score
sequence-density=3.74
sequence-density-rank=4
fanout-score=71.72
fanout-score-rank=1
prefix-density=94.44
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 12 -x TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAAAAGATCTCGTATGCC -o SRR5031104 -
Input file:	STDIN
trimmed:	SRR5031104-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAAAAGATCTCGTATGCC
-- 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 07:24:59 2020 >> started

Wed Mar  4 07:25:03 2020 >> done (3.784s)
2831629 reads processed; of these:
 103931 ( 3.67%) short reads filtered out after trimming by size control
  12317 ( 0.43%) empty reads filtered out after trimming by size control
2715381 (95.89%) reads available; of these:
2664305 (98.12%) trimmed reads available after processing
  51076 ( 1.88%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  13321	  0.49%
 19	  32542	  1.20%
 20	 160723	  5.92%
 21	 356175	 13.12%
 22	1112541	 40.97%
 23	 519060	 19.12%
 24	 174712	  6.43%
 25	  28600	  1.05%
 26	  13287	  0.49%
 27	  12251	  0.45%
 28	  13419	  0.49%
 29	  10141	  0.37%
 30	  17030	  0.63%
 31	  21044	  0.77%
 32	  23400	  0.86%
 33	  51061	  1.88%
 34	  17554	  0.65%
 35	  10460	  0.39%
 36	  11332	  0.42%
 37	   6482	  0.24%
 38	   7400	  0.27%
 39	   6195	  0.23%
 40	   8256	  0.30%
 41	  10380	  0.38%
 42	  10366	  0.38%
 43	   7106	  0.26%
 44	   5545	  0.20%
 45	   6341	  0.23%
 46	   4375	  0.16%
 47	   3302	  0.12%
 48	    651	  0.02%
 49	   1255	  0.05%
 50	  39074	  1.44%


criterion=sequence-density
sequence-density=12.58
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=17
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.51
sequence-density-rank=29
fanout-score=16.36
fanout-score-rank=1
prefix-density=8.25
prefix-fanout=1.0
sequence=CTGAGCTTGGCATT
                                 Started job on |	Mar 04 07:25:26
                             Started mapping on |	Mar 04 07:25:27
                                    Finished on |	Mar 04 07:25:57
       Mapping speed, Million of reads per hour |	333.23

                          Number of input reads |	2776938
                      Average input read length |	24
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1333951
                        Uniquely mapped reads % |	48.04%
                          Average mapped length |	22.98
                       Number of splices: Total |	6644
            Number of splices: Annotated (sjdb) |	2765
                       Number of splices: GT/AG |	6557
                       Number of splices: GC/AG |	46
                       Number of splices: AT/AC |	2
               Number of splices: Non-canonical |	39
                      Mismatch rate per base, % |	0.28%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.51
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.00
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1243484
             % of reads mapped to multiple loci |	44.78%
        Number of reads mapped to too many loci |	38897
             % of reads mapped to too many loci |	1.40%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	5.39%
                     % of reads unmapped: other |	0.40%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	199503	199503	199503
N_multimapping	1243484	1243484	1243484
N_noFeature	62306	72711	979407
N_ambiguous	748876	441655	6177
UnstrandedReadsAssigned:522769 PositiveStrandReadsAssigned:819585 NegativeStrandReadsAssigned:348367
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=21 echo kmer=19
SRR5031104 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: SRR5031104-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,776,938 reads, 578,956 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,090 rounds

 109283 SRR5031104.ke.tsv
  52636 SRR5031104.se.tsv
 161919 total
==> SRR5031104.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

==> SRR5031104.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031104 completed mapping pipeline successfully
