Starting /dee2/code/volunteer_pipeline.sh SRR5030926
    current disk space = 160626294784
    free memory = 56711944 
SRR5030926 SRAfilesize
10262a9fb9dea8d66f6b44c200687535  SRR5030926.sra
SRR5030926.sra file validated
SRR5030926 is single end
SRR5030926 is conventional basespace
SRR5030926 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030926_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	51
>>END_MODULE
>>Per base sequence quality	fail
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	32.3905	33.0	31.0	34.0	31.0	34.0
2	32.69925	34.0	31.0	34.0	31.0	34.0
3	32.69175	34.0	31.0	34.0	31.0	34.0
4	36.21675	37.0	37.0	37.0	35.0	37.0
5	36.23975	37.0	37.0	37.0	35.0	37.0
6	35.87625	37.0	35.0	37.0	35.0	37.0
7	36.06375	37.0	35.0	37.0	35.0	37.0
8	36.17375	37.0	36.0	37.0	35.0	37.0
9	37.8785	39.0	38.0	39.0	35.0	39.0
10	37.903	39.0	38.0	39.0	35.0	39.0
11	37.85575	39.0	38.0	39.0	35.0	39.0
12	37.86375	39.0	38.0	39.0	35.0	39.0
13	37.8405	39.0	38.0	39.0	35.0	39.0
14	39.3695	41.0	39.0	41.0	36.0	41.0
15	39.331	41.0	39.0	41.0	36.0	41.0
16	39.11825	40.0	39.0	41.0	36.0	41.0
17	39.194	40.0	39.0	41.0	36.0	41.0
18	39.28025	41.0	39.0	41.0	36.0	41.0
19	38.9635	40.0	38.0	41.0	35.0	41.0
20	39.10725	40.0	39.0	41.0	36.0	41.0
21	39.181	40.0	39.0	41.0	36.0	41.0
22	39.259	41.0	39.0	41.0	36.0	41.0
23	39.139	40.0	39.0	41.0	36.0	41.0
24	38.38025	40.0	38.0	41.0	34.0	41.0
25	38.7065	40.0	38.0	41.0	35.0	41.0
26	38.74175	40.0	38.0	41.0	34.0	41.0
27	38.81225	40.0	39.0	41.0	35.0	41.0
28	38.694	40.0	38.0	41.0	35.0	41.0
29	38.77375	40.0	38.0	41.0	34.0	41.0
30	38.441	40.0	38.0	41.0	34.0	41.0
31	38.763	40.0	38.0	41.0	35.0	41.0
32	38.95525	41.0	39.0	41.0	35.0	41.0
33	37.52475	40.0	38.0	41.0	32.0	41.0
34	37.23275	40.0	38.0	41.0	31.0	41.0
35	33.43	38.0	32.0	40.0	15.0	41.0
36	28.7535	37.0	15.0	40.0	8.0	41.0
37	29.48925	35.0	23.0	39.0	6.0	40.0
38	32.343	37.0	31.0	40.0	15.0	41.0
39	31.77575	37.0	30.0	40.0	7.0	41.0
40	32.631	38.0	31.0	40.0	6.0	41.0
41	30.48875	36.0	27.0	40.0	2.0	41.0
42	32.2535	38.0	31.0	40.0	2.0	41.0
43	30.62125	37.0	26.0	40.0	2.0	41.0
44	31.51075	38.0	31.0	40.0	2.0	41.0
45	29.0425	36.0	24.0	40.0	2.0	41.0
46	26.96775	34.0	9.0	39.0	2.0	41.0
47	27.28025	34.0	15.0	39.0	2.0	41.0
48	28.0485	35.0	18.0	40.0	2.0	41.0
49	25.94475	35.0	2.0	40.0	2.0	41.0
50	22.69	29.0	2.0	38.0	2.0	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
12	1.0
13	1.0
14	0.0
15	0.0
16	0.0
17	3.0
18	3.0
19	9.0
20	13.0
21	12.0
22	28.0
23	37.0
24	41.0
25	60.0
26	102.0
27	143.0
28	74.0
29	96.0
30	114.0
31	172.0
32	179.0
33	153.0
34	224.0
35	279.0
36	379.0
37	424.0
38	580.0
39	873.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	8.813219829744618	23.760640961442164	54.20630946419629	13.219829744616925
2	26.75	26.400000000000002	24.099999999999998	22.75
3	15.875	20.150000000000002	21.2	42.775
4	26.3	38.925	13.475000000000001	21.3
5	23.849999999999998	38.224999999999994	27.1	10.825
6	33.275	15.45	38.475	12.8
7	14.499999999999998	24.25	26.075	35.175
8	25.1	41.6	14.325	18.975
9	15.275	39.7	33.324999999999996	11.700000000000001
10	19.5	22.35	28.125	30.025000000000002
11	37.15	11.825	13.175	37.85
12	16.875	20.125	21.525	41.475
13	17.724999999999998	23.474999999999998	39.25	19.55
14	38.550000000000004	21.6	26.025	13.825000000000001
15	40.025	21.55	26.05	12.375
16	14.499999999999998	26.1	22.7	36.7
17	24.975	25.55	36.1	13.375
18	28.199999999999996	20.95	26.575	24.275
19	36.425000000000004	15.299999999999999	32.425	15.85
20	48.949999999999996	16.925	22.925	11.200000000000001
21	21.4	25.174999999999997	24.575	28.849999999999998
22	32.6	11.774999999999999	46.875	8.75
23	23.525	14.45	48.65	13.375
24	51.175000000000004	11.600000000000001	29.5	7.725
25	55.525000000000006	21.025	14.45	9.0
26	30.675	45.85	12.15	11.325000000000001
27	13.15	54.1	21.025	11.725
28	9.35	28.299999999999997	49.45	12.9
29	11.375	11.799999999999999	59.52499999999999	17.299999999999997
30	9.425	6.125	39.324999999999996	45.125
31	12.3	5.525	47.3	34.875
32	24.349999999999998	5.575	26.200000000000003	43.875
33	52.300000000000004	8.15	13.65	25.900000000000002
34	67.7	4.425	11.95	15.925
35	65.275	6.5	18.3	9.925
36	65.925	7.049999999999999	16.5	10.525
37	42.525	10.575	23.95	22.95
38	27.85	11.975	12.4	47.775
39	16.0	21.5	9.8	52.7
40	13.275	49.05	9.3	28.375
41	23.65	52.900000000000006	8.200000000000001	15.25
42	50.55	31.974999999999998	9.275	8.200000000000001
43	54.125	29.075	8.075000000000001	8.725
44	32.800000000000004	49.025	6.75	11.425
45	16.3	52.575	8.1	23.025000000000002
46	11.0	31.85	22.7	34.449999999999996
47	9.049999999999999	14.6	34.449999999999996	41.9
48	9.925	9.65	24.65	55.775
49	10.875	22.725	12.325	54.074999999999996
50	27.506876719179797	29.15728932233058	8.077019254813704	35.25881470367592
>>END_MODULE
>>Per sequence GC content	fail
#GC Content	Count
0	0.0
1	0.0
2	0.0
3	0.0
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.0
10	0.0
11	0.0
12	0.0
13	1.0
14	2.0
15	1.5
16	1.0
17	0.5
18	0.0
19	0.5
20	1.0
21	0.5
22	0.0
23	0.0
24	0.0
25	0.5
26	1.0
27	1.5
28	2.0
29	2.0
30	2.0
31	3.0
32	4.0
33	12.0
34	20.0
35	29.0
36	38.0
37	42.5
38	47.0
39	47.5
40	48.0
41	57.5
42	67.0
43	86.0
44	105.0
45	193.5
46	282.0
47	362.5
48	443.0
49	505.5
50	568.0
51	759.5
52	951.0
53	695.5
54	440.0
55	375.5
56	311.0
57	292.5
58	274.0
59	199.5
60	125.0
61	95.5
62	66.0
63	87.0
64	108.0
65	67.5
66	27.0
67	18.0
68	9.0
69	13.5
70	18.0
71	23.0
72	28.0
73	17.5
74	7.0
75	3.5
76	0.0
77	1.5
78	3.0
79	2.5
80	2.0
81	1.0
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	0.15
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	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	0.025
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
50	4000.0
>>END_MODULE
>>Sequence Duplication Levels	fail
#Total Deduplicated Percentage	49.35
#Duplication Level	Percentage of deduplicated	Percentage of total
1	79.83789260385005	39.4
2	8.358662613981762	8.25
3	3.596757852077001	5.325
4	2.330293819655522	4.6
5	1.3171225937183384	3.25
6	0.911854103343465	2.7
7	0.5572441742654508	1.925
8	0.4052684903748734	1.6
9	0.3546099290780142	1.575
>10	2.178318135764944	22.7
>50	0.10131712259371835	3.875
>100	0.050658561296859174	4.8
>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	192	4.8	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	95	2.375	RNA PCR Primer, Index 1 (96% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	60	1.5	No Hit
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	49	1.225	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	40	1.0	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	38	0.95	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	35	0.8750000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	35	0.8750000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	33	0.8250000000000001	No Hit
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	27	0.675	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	27	0.675	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	27	0.675	RNA PCR Primer, Index 1 (96% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	25	0.625	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	25	0.625	RNA PCR Primer, Index 1 (96% over 28bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	23	0.575	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	20	0.5	RNA PCR Primer, Index 1 (100% over 29bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	19	0.475	RNA PCR Primer, Index 1 (96% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCG	18	0.44999999999999996	RNA PCR Primer, Index 1 (96% over 27bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 29bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 29bp)
TCCTGTACTGAGCTGCCCCGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	16	0.4	RNA PCR Primer, Index 1 (100% over 27bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	16	0.4	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	15	0.375	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (96% over 28bp)
TCCTGTACTGAGCTGCCCCGATGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (96% over 28bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 30bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
GCGGATGATGACACCTGGGTATGCTGCACACTCCCGACTGCGTCGTGGGG	12	0.3	No Hit
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCACGATATCTCGTATGC	12	0.3	RNA PCR Primer, Index 31 (100% over 50bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 33bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGTTTGTGCTGTTATGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (96% over 28bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	9	0.22499999999999998	No Hit
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCG	9	0.22499999999999998	RNA PCR Primer, Index 1 (96% over 27bp)
CACCCTGATGAACTGAATACCGCCCCAGTCTGATAGCTGTGGAGAAAGGT	9	0.22499999999999998	No Hit
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGGGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (96% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (96% over 28bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	8	0.2	No Hit
GCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCA	8	0.2	RNA PCR Primer, Index 1 (100% over 32bp)
GACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGCT	8	0.2	No Hit
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TCCTGTACTGAGCTGCCCCGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCA	7	0.17500000000000002	RNA PCR Primer, Index 7 (100% over 35bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACCCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (95% over 24bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	7	0.17500000000000002	No Hit
TCCTGTACTGAGCTGCCCCGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (96% over 28bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGGGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (96% over 28bp)
AACATTCAACGCTGTCGGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAATTCCG	6	0.15	RNA PCR Primer, Index 1 (95% over 23bp)
GCATGTGATGACATTATTTAGCGACCAAAGTCTGATAAAGATGATTGTGA	6	0.15	No Hit
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCG	6	0.15	RNA PCR Primer, Index 1 (96% over 27bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGGGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (96% over 28bp)
GTGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCA	6	0.15	No Hit
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGGAATTCTCGGGTGCCA	6	0.15	No Hit
TTCAAGTAATCCAGGATAGGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTACACTCAGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGAAATCAAA	6	0.15	No Hit
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCCTGTACTGAGCTGCCCCGAGATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
CGACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGC	5	0.125	No Hit
TGCTGTGATGAGATGACTAAGTAGGAAGTGCCGTCAGAGTCGATAACTGA	5	0.125	No Hit
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGTGGAATTCTCGGGTGC	5	0.125	No Hit
CTGACCTATGAATTGACAGCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCATTGCTGTCGGTGGGATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TTAAGGCACGCGGTGAATTGGAATTCTCGGGTGCCAAGGAACTCCAGTCA	5	0.125	RNA PCR Primer, Index 1 (100% over 32bp)
AGCCCATGATGGTATGAGAGTAGTGGACAGAAGGGATTTCTGAAAAACAC	5	0.125	No Hit
TTAAGGCACGCGGTGAATGCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGGGCCAAGGAACTCCG	5	0.125	RNA PCR Primer, Index 1 (96% over 27bp)
CTGCAGTGATGACTATCTTAGGACACCTTTGGATTTACCGTGAAAAGAAG	5	0.125	No Hit
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACCCCG	5	0.125	RNA PCR Primer, Index 1 (95% over 24bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	5	0.125	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGGAATTCTCGGGTGCCAA	5	0.125	No Hit
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCGG	5	0.125	No Hit
TGAGGTAGTAGGTTGTATAGTTATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAAT	5	0.125	No Hit
CTGACTTGATGAAAGTACTTTTGAACCCTTTTCCATCTGATGTGGAATTC	5	0.125	No Hit
TGTAAACATCCTCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
AGCAGCATTGTACAGGGCTATGTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
GTGAAATGATGGCAAATCATCTTTCGGGACTGACCTGAAATGAAGAGAAT	5	0.125	No Hit
>>END_MODULE
>>Adapter Content	fail
#Position	Illumina Universal Adapter	Illumina Small RNA 3' Adapter	Illumina Small RNA 5' Adapter	Nextera Transposase Sequence	SOLID Small RNA Adapter
1	0.0	0.35	0.0	0.0	0.0
2	0.0	0.35	0.0	0.0	0.0
3	0.0	0.375	0.0	0.0	0.0
4	0.0	0.4	0.0	0.0	0.0
5	0.0	0.45	0.0	0.0	0.0
6	0.0	0.55	0.0	0.0	0.0
7	0.0	0.7	0.0	0.0	0.0
8	0.0	0.725	0.0	0.0	0.0
9	0.0	0.8	0.0	0.0	0.0
10	0.0	1.0	0.0	0.0	0.0
11	0.0	1.15	0.0	0.0	0.0
12	0.0	1.325	0.0	0.0	0.0
13	0.0	1.475	0.0	0.0	0.0
14	0.0	1.825	0.0	0.0	0.0
15	0.0	2.05	0.0	0.0	0.0
16	0.0	2.5	0.0	0.0	0.0
17	0.0	2.825	0.0	0.0	0.0
18	0.0	3.625	0.0	0.0	0.0
19	0.0	4.325	0.0	0.0	0.0
20	0.0	5.6	0.0	0.0	0.0
21	0.0	9.075	0.0	0.0	0.0
22	0.0	19.35	0.0	0.0	0.0
23	0.0	50.675	0.0	0.0	0.0
24	0.0	67.9	0.0	0.0	0.0
25	0.0	73.925	0.0	0.0	0.0
26	0.0	75.075	0.0	0.0	0.0
27	0.0	75.475	0.0	0.0	0.0
28	0.0	76.025	0.0	0.0	0.0
29	0.0	76.15	0.0	0.0	0.0
30	0.0	76.55	0.0	0.0	0.0
31	0.0	77.15	0.0	0.0	0.0
32	0.0	77.85	0.0	0.0	0.0
33	0.0	78.725	0.0	0.0	0.0
34	0.0	81.225	0.0	0.0	0.0
35	0.0	81.9	0.0	0.0	0.0
36	0.0	82.275	0.0	0.0	0.0
37	0.0	82.85	0.0	0.0	0.0
38	0.0	83.3	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
AACGCTG	45	2.728484E-10	44.000004	8
ACGCTGT	45	2.728484E-10	44.000004	9
TTGTATA	20	6.952051E-4	44.000004	13
TTCAACG	45	2.728484E-10	44.000004	5
TAGTTTG	20	6.952051E-4	44.000004	18
TCAACGC	45	2.728484E-10	44.000004	6
GTATAGT	20	6.952051E-4	44.000004	15
ATAGTTT	20	6.952051E-4	44.000004	17
GCTGTCG	45	2.728484E-10	44.000004	11
AGGCTTG	20	6.952051E-4	44.000004	18
GCTTGGC	20	6.952051E-4	44.000004	15
TGTATAG	20	6.952051E-4	44.000004	14
AGTTTGG	20	6.952051E-4	44.000004	19
TATAGTT	20	6.952051E-4	44.000004	16
CAACGCT	45	2.728484E-10	44.000004	7
CGCTGTC	45	2.728484E-10	44.000004	10
GAGGTAG	30	1.9515464E-6	44.0	2
GTTTGGA	25	3.6958358E-5	44.0	20
AAGTAAT	30	1.9515464E-6	44.0	4
AATCCAG	30	1.9515464E-6	44.0	8
>>END_MODULE
Read 279340 spots for SRR5030926.sra
Written 279340 spots for SRR5030926.sra
Read 279340 spots for SRR5030926.sra
Written 279340 spots for SRR5030926.sra
Read 279340 spots for SRR5030926.sra
Written 279340 spots for SRR5030926.sra
Read 279340 spots for SRR5030926.sra
Written 279340 spots for SRR5030926.sra
Read 279340 spots for SRR5030926.sra
Written 279340 spots for SRR5030926.sra
Read 279340 spots for SRR5030926.sra
Written 279340 spots for SRR5030926.sra
Read 279340 spots for SRR5030926.sra
Written 279340 spots for SRR5030926.sra
Read 279340 spots for SRR5030926.sra
Written 279340 spots for SRR5030926.sra
Read 279340 spots for SRR5030926.sra
Written 279340 spots for SRR5030926.sra
Read 279344 spots for SRR5030926.sra
Written 279344 spots for SRR5030926.sra
Read 279340 spots for SRR5030926.sra
Written 279340 spots for SRR5030926.sra
Read 279340 spots for SRR5030926.sra
Written 279340 spots for SRR5030926.sra
SRR ids: ['SRR5030926.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_pf_uq80h
SRR5030926.sra spots: 3352084
blocks: [[1, 279340], [279341, 558680], [558681, 838020], [838021, 1117360], [1117361, 1396700], [1396701, 1676040], [1676041, 1955380], [1955381, 2234720], [2234721, 2514060], [2514061, 2793400], [2793401, 3072740], [3072741, 3352084]]
SRR5030926 file size 579915
SRR5030926 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030926 SRR5030926_1.fastq
Input file:	SRR5030926_1.fastq
trimmed:	SRR5030926-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 06:46:14 2020 >> started

Wed Mar  4 06:46:16 2020 >> done (2.031s)
3352084 reads processed; of these:
    131 ( 0.00%) short reads filtered out after trimming by size control
     10 ( 0.00%) empty reads filtered out after trimming by size control
3351943 (100.00%) reads available; of these:
 388935 (11.60%) trimmed reads available after processing
2963008 (88.40%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     35	  0.00%
 19	     65	  0.00%
 20	    121	  0.00%
 21	    194	  0.01%
 22	    330	  0.01%
 23	    384	  0.01%
 24	    382	  0.01%
 25	    454	  0.01%
 26	    457	  0.01%
 27	    560	  0.02%
 28	    921	  0.03%
 29	   1492	  0.04%
 30	    878	  0.03%
 31	   1197	  0.04%
 32	   3111	  0.09%
 33	   9837	  0.29%
 34	  29688	  0.89%
 35	   7153	  0.21%
 36	   8477	  0.25%
 37	   3942	  0.12%
 38	   8116	  0.24%
 39	   6294	  0.19%
 40	  14317	  0.43%
 41	   7863	  0.23%
 42	  20256	  0.60%
 43	   8322	  0.25%
 44	  43090	  1.29%
 45	  22944	  0.68%
 46	  19559	  0.58%
 47	  21060	  0.63%
 48	  75969	  2.27%
 49	  71467	  2.13%
 50	2963008	 88.40%
3351943 reads passed initial QC


criterion=sequence-density
sequence-density=82.45
sequence-density-rank=1
fanout-score=18.94
fanout-score-rank=2
prefix-density=84.75
prefix-fanout=18.4
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCACGATATCTCGTATGCC


criterion=fanout-score
sequence-density=4.33
sequence-density-rank=2
fanout-score=55.48
fanout-score-rank=1
prefix-density=84.53
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCACGATATCTCGTATGCC -o SRR5030926 -
Input file:	STDIN
trimmed:	SRR5030926-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCACGATATCTCGTATGCC
-- 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 06:46:33 2020 >> started

Wed Mar  4 06:46:38 2020 >> done (5.190s)
3271173 reads processed; of these:
 115293 ( 3.52%) short reads filtered out after trimming by size control
  16004 ( 0.49%) empty reads filtered out after trimming by size control
3139876 (95.99%) reads available; of these:
2793699 (88.97%) trimmed reads available after processing
 346177 (11.03%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  20579	  0.66%
 19	  34596	  1.10%
 20	 122662	  3.91%
 21	 356537	 11.36%
 22	1008128	 32.11%
 23	 556704	 17.73%
 24	 198487	  6.32%
 25	  31507	  1.00%
 26	  17567	  0.56%
 27	  17573	  0.56%
 28	  19118	  0.61%
 29	  16062	  0.51%
 30	  23251	  0.74%
 31	  28154	  0.90%
 32	  30692	  0.98%
 33	  81739	  2.60%
 34	  27766	  0.88%
 35	  17839	  0.57%
 36	  25497	  0.81%
 37	  12841	  0.41%
 38	  16013	  0.51%
 39	  14903	  0.47%
 40	  21281	  0.68%
 41	  23673	  0.75%
 42	  29148	  0.93%
 43	  19963	  0.64%
 44	  21658	  0.69%
 45	  19697	  0.63%
 46	  16531	  0.53%
 47	  13934	  0.44%
 48	   5981	  0.19%
 49	   9594	  0.31%
 50	 280201	  8.92%


criterion=sequence-density
sequence-density=4.93
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=20
prefix-density=0.00
prefix-fanout=1.0
sequence=TCCCTGAGACCCTTTAACCTGTGAA


criterion=fanout-score
sequence-density=0.43
sequence-density-rank=30
fanout-score=9.06
fanout-score-rank=1
prefix-density=0.75
prefix-fanout=5.2
sequence=GGAATTCTCGGGGCCCAGG
                                 Started job on |	Mar 04 06:47:00
                             Started mapping on |	Mar 04 06:47:00
                                    Finished on |	Mar 04 06:47:25
       Mapping speed, Million of reads per hour |	463.77

                          Number of input reads |	3220646
                      Average input read length |	27
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1499087
                        Uniquely mapped reads % |	46.55%
                          Average mapped length |	26.78
                       Number of splices: Total |	1584
            Number of splices: Annotated (sjdb) |	234
                       Number of splices: GT/AG |	1431
                       Number of splices: GC/AG |	18
                       Number of splices: AT/AC |	2
               Number of splices: Non-canonical |	133
                      Mismatch rate per base, % |	0.18%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.25
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.11
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1332629
             % of reads mapped to multiple loci |	41.38%
        Number of reads mapped to too many loci |	77370
             % of reads mapped to too many loci |	2.40%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	9.15%
                     % of reads unmapped: other |	0.53%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	388930	388930	388930
N_multimapping	1332629	1332629	1332629
N_noFeature	73827	88091	1197620
N_ambiguous	781285	524627	13063
UnstrandedReadsAssigned:643975 PositiveStrandReadsAssigned:886369 NegativeStrandReadsAssigned:288404
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5030926 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: SRR5030926-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,220,646 reads, 601,534 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,094 rounds

 109283 SRR5030926.ke.tsv
  52636 SRR5030926.se.tsv
 161919 total
==> SRR5030926.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

==> SRR5030926.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030926 completed mapping pipeline successfully
