Starting /dee2/code/volunteer_pipeline.sh SRR5031025
    current disk space = 286678303044
    free memory = 120891908 
SRR5031025 SRAfilesize
d257f403cbdde9748bbcf2bb5392a4b0  SRR5031025.sra
SRR5031025.sra file validated
SRR5031025 is single end
SRR5031025 is conventional basespace
SRR5031025 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031025_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	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	32.37775	33.0	31.0	34.0	31.0	34.0
2	32.62575	34.0	31.0	34.0	31.0	34.0
3	32.5375	34.0	31.0	34.0	31.0	34.0
4	36.21025	37.0	37.0	37.0	35.0	37.0
5	36.189	37.0	37.0	37.0	35.0	37.0
6	35.746	37.0	35.0	37.0	33.0	37.0
7	35.838	37.0	35.0	37.0	35.0	37.0
8	35.99725	37.0	35.0	37.0	35.0	37.0
9	37.5845	39.0	37.0	39.0	35.0	39.0
10	37.59475	39.0	37.0	39.0	35.0	39.0
11	37.42175	39.0	37.0	39.0	34.0	39.0
12	37.68375	39.0	37.0	39.0	35.0	39.0
13	37.684	39.0	37.0	39.0	35.0	39.0
14	39.15325	40.0	39.0	41.0	36.0	41.0
15	39.098	40.0	38.0	41.0	36.0	41.0
16	38.93225	40.0	38.0	41.0	35.0	41.0
17	39.14425	40.0	38.0	41.0	36.0	41.0
18	39.09975	41.0	39.0	41.0	36.0	41.0
19	38.99625	40.0	39.0	41.0	36.0	41.0
20	38.9495	40.0	39.0	41.0	35.0	41.0
21	38.98525	40.0	38.0	41.0	35.0	41.0
22	38.993	40.0	39.0	41.0	36.0	41.0
23	38.63075	40.0	38.0	41.0	34.0	41.0
24	38.905	40.0	39.0	41.0	35.0	41.0
25	39.08875	41.0	39.0	41.0	36.0	41.0
26	38.90525	40.0	38.0	41.0	35.0	41.0
27	39.00175	40.0	39.0	41.0	35.0	41.0
28	38.876	40.0	38.0	41.0	35.0	41.0
29	38.6445	40.0	38.0	41.0	34.0	41.0
30	38.67125	40.0	38.0	41.0	35.0	41.0
31	38.87925	40.0	38.0	41.0	35.0	41.0
32	38.91875	40.0	39.0	41.0	35.0	41.0
33	38.634	40.0	38.0	41.0	34.0	41.0
34	38.5825	40.0	38.0	41.0	34.0	41.0
35	38.3385	40.0	38.0	41.0	34.0	41.0
36	38.25	40.0	38.0	41.0	34.0	41.0
37	37.63125	40.0	37.0	41.0	32.0	41.0
38	37.5585	40.0	37.0	41.0	32.0	41.0
39	37.981	40.0	38.0	41.0	33.0	41.0
40	38.11825	40.0	38.0	41.0	33.0	41.0
41	38.408	40.0	38.0	41.0	34.0	41.0
42	38.173	40.0	38.0	41.0	33.0	41.0
43	38.1205	40.0	38.0	41.0	34.0	41.0
44	37.98875	40.0	38.0	41.0	33.0	41.0
45	37.98025	40.0	38.0	41.0	33.0	41.0
46	37.8825	40.0	38.0	41.0	33.0	41.0
47	37.493	40.0	37.0	41.0	33.0	41.0
48	37.43625	40.0	37.0	41.0	33.0	41.0
49	37.535	40.0	37.0	41.0	33.0	41.0
50	37.01925	40.0	36.0	41.0	31.0	41.0
>>END_MODULE
>>Per tile sequence quality	pass
#Tile	Base	Mean
1101	1	0.0
1101	2	0.0
1101	3	0.0
1101	4	0.0
1101	5	0.0
1101	6	0.0
1101	7	0.0
1101	8	0.0
1101	9	0.0
1101	10	0.0
1101	11	0.0
1101	12	0.0
1101	13	0.0
1101	14	0.0
1101	15	0.0
1101	16	0.0
1101	17	0.0
1101	18	0.0
1101	19	0.0
1101	20	0.0
1101	21	0.0
1101	22	0.0
1101	23	0.0
1101	24	0.0
1101	25	0.0
1101	26	0.0
1101	27	0.0
1101	28	0.0
1101	29	0.0
1101	30	0.0
1101	31	0.0
1101	32	0.0
1101	33	0.0
1101	34	0.0
1101	35	0.0
1101	36	0.0
1101	37	0.0
1101	38	0.0
1101	39	0.0
1101	40	0.0
1101	41	0.0
1101	42	0.0
1101	43	0.0
1101	44	0.0
1101	45	0.0
1101	46	0.0
1101	47	0.0
1101	48	0.0
1101	49	0.0
1101	50	0.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
14	1.0
15	0.0
16	2.0
17	0.0
18	4.0
19	2.0
20	1.0
21	1.0
22	8.0
23	5.0
24	5.0
25	8.0
26	10.0
27	17.0
28	26.0
29	41.0
30	48.0
31	44.0
32	69.0
33	97.0
34	115.0
35	182.0
36	279.0
37	410.0
38	670.0
39	1955.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	7.025	22.35	59.35	11.275
2	26.04010025062657	27.994987468671678	22.305764411027567	23.659147869674186
3	16.150000000000002	21.349999999999998	20.825	41.675000000000004
4	28.95	37.85	12.075	21.125
5	23.549999999999997	37.525	29.15	9.775
6	35.075	15.4	38.75	10.775
7	13.125	25.5	24.325	37.05
8	25.025	40.375	14.299999999999999	20.3
9	16.25	39.375	32.7	11.675
10	15.725	22.875	27.725	33.675
11	34.699999999999996	9.175	13.925	42.199999999999996
12	15.6	17.375	23.200000000000003	43.824999999999996
13	19.45	21.775	41.325	17.45
14	40.35	20.724999999999998	26.275	12.65
15	41.099999999999994	20.424999999999997	26.85	11.625
16	13.8	25.0	23.575	37.625
17	26.224999999999998	24.55	38.35	10.875
18	29.799999999999997	19.325	27.125	23.75
19	37.75	15.049999999999999	32.45	14.75
20	51.949999999999996	16.275000000000002	21.025	10.75
21	18.8	26.025	26.474999999999998	28.7
22	31.65	11.15	49.825	7.375
23	27.1	11.450000000000001	49.75	11.700000000000001
24	54.175	11.15	29.325000000000003	5.35
25	56.39999999999999	23.425	13.100000000000001	7.074999999999999
26	31.025000000000002	49.925000000000004	11.275	7.775
27	13.5	53.77499999999999	23.200000000000003	9.525
28	8.575000000000001	26.75	52.625	12.049999999999999
29	9.3	10.5	60.925	19.275000000000002
30	8.075000000000001	4.5	41.05	46.375
31	12.049999999999999	3.9	46.525	37.525
32	26.450000000000003	4.65	24.224999999999998	44.675
33	57.4	5.625	12.1	24.875
34	69.575	5.2749999999999995	12.725	12.425
35	68.85	5.575	18.375	7.199999999999999
36	44.525	5.8999999999999995	38.775	10.8
37	45.475	7.675	23.674999999999997	23.175
38	25.1	11.825	11.325000000000001	51.74999999999999
39	13.200000000000001	23.0	7.875	55.925000000000004
40	11.95	51.625	7.6499999999999995	28.775000000000002
41	24.2	54.949999999999996	7.199999999999999	13.65
42	52.15	32.25	8.15	7.449999999999999
43	58.375	27.900000000000002	6.175	7.55
44	31.4	50.7	6.925000000000001	10.975
45	14.674999999999999	55.60000000000001	9.75	19.975
46	8.95	28.799999999999997	18.925	43.325
47	6.25	12.3	39.975	41.475
48	7.375	9.625	24.224999999999998	58.775
49	9.575	19.025	12.9	58.5
50	18.25	39.050000000000004	10.5	32.2
>>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	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	0.5
24	1.0
25	1.5
26	2.0
27	1.5
28	1.0
29	0.5
30	0.0
31	2.0
32	4.0
33	7.5
34	11.0
35	13.5
36	16.0
37	19.5
38	23.0
39	27.0
40	31.0
41	33.5
42	36.0
43	102.5
44	169.0
45	232.0
46	295.0
47	473.5
48	652.0
49	637.5
50	623.0
51	815.5
52	1008.0
53	668.0
54	328.0
55	334.5
56	341.0
57	282.5
58	224.0
59	133.0
60	42.0
61	30.0
62	18.0
63	46.0
64	74.0
65	46.5
66	19.0
67	12.0
68	5.0
69	9.0
70	13.0
71	37.0
72	61.0
73	32.0
74	3.0
75	1.5
76	0.0
77	0.0
78	0.0
79	0.0
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	0.0
2	0.25
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	34.225
#Duplication Level	Percentage of deduplicated	Percentage of total
1	75.38349159970782	25.8
2	9.130752373995616	6.25
3	4.894083272461651	5.025
4	2.483564645726808	3.4000000000000004
5	0.9495982468955442	1.625
6	0.8765522279035792	1.7999999999999998
7	0.5113221329437546	1.225
8	0.6574141709276844	1.7999999999999998
9	0.7304601899196494	2.25
>10	3.7253469685902116	25.775
>50	0.3652300949598247	8.025
>100	0.2921840759678598	17.025000000000002
>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	258	6.45	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	200	5.0	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	120	3.0	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	103	2.5749999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	96	2.4	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	65	1.625	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	56	1.4000000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	52	1.3	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	52	1.3	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	45	1.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	42	1.05	RNA PCR Primer, Index 1 (100% over 30bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	42	1.05	RNA PCR Primer, Index 1 (100% over 29bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	42	1.05	No Hit
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	39	0.975	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	38	0.95	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	37	0.9249999999999999	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	37	0.9249999999999999	RNA PCR Primer, Index 1 (100% over 26bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	35	0.8750000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	32	0.8	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	31	0.775	RNA PCR Primer, Index 1 (100% over 28bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	31	0.775	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	30	0.75	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	29	0.7250000000000001	No Hit
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	23	0.575	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	23	0.575	RNA PCR Primer, Index 1 (100% over 29bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	16	0.4	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	15	0.375	RNA PCR Primer, Index 1 (100% over 26bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTC	15	0.375	RNA PCR Primer, Index 5 (97% over 35bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
TCCTGTACTGAGCTGCCCCGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TCCTGTACTGAGCTGCCCCGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	12	0.3	No Hit
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	11	0.27499999999999997	No Hit
TTCAAGTAATTCAGGATAGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 33bp)
TGTAAACATCCTACACTCAGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAATGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGATTGTATAGTTTTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGATGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	10	0.25	No Hit
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCATTCATCTC	9	0.22499999999999998	RNA PCR Primer, Index 45 (100% over 44bp)
TATTGCACTCGTCCCGGCCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTGGAATTCTCGGGTGCCA	9	0.22499999999999998	No Hit
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	9	0.22499999999999998	No Hit
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCATTCATCTCGTATGC	9	0.22499999999999998	RNA PCR Primer, Index 45 (100% over 50bp)
TGTAAACATCCTCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGTTTGTGCTGTTATGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (100% over 30bp)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
TCCTGTACTGAGCTGCCCCGAGATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGATGAAGCACTGTAGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (100% over 30bp)
TTCCCTTTGTCATCCTATGCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
CCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCA	8	0.2	RNA PCR Primer, Index 3 (97% over 36bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	7	0.17500000000000002	No Hit
TTCAAGTAATCCAGGATAGTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 31bp)
TCCTGTACTGAGCTGCCCCGATGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
ACTGGACTTGGAGTCAGAAGGCTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTGCTGTTTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	6	0.15	No Hit
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
CACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACT	6	0.15	RNA PCR Primer, Index 3 (100% over 34bp)
AACATTCAACGCTGTCGGTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
GCATTTGTGGTTCAGTGGTAGAATTCTCGCCTGGAATTCTCGGGTGCCAA	6	0.15	No Hit
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATAGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGTTTGTACAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TTCAAGTAATTCAGGATAGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGGAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGGAATTCTCGGGTGCCAAG	5	0.125	No Hit
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AGAGGTAGTAGGTTGCATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	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	0.275	0.0	0.0	0.0
2	0.0	0.3	0.0	0.0	0.0
3	0.0	0.325	0.0	0.0	0.0
4	0.0	0.35	0.0	0.0	0.0
5	0.0	0.375	0.0	0.0	0.0
6	0.0	0.425	0.0	0.0	0.0
7	0.0	0.7	0.0	0.0	0.0
8	0.0	0.875	0.0	0.0	0.0
9	0.0	0.9	0.0	0.0	0.0
10	0.0	1.025	0.0	0.0	0.0
11	0.0	1.175	0.0	0.0	0.0
12	0.0	1.45	0.0	0.0	0.0
13	0.0	1.75	0.0	0.0	0.0
14	0.0	2.125	0.0	0.0	0.0
15	0.0	2.55	0.0	0.0	0.0
16	0.0	3.275	0.0	0.0	0.0
17	0.0	3.9	0.0	0.0	0.0
18	0.0	4.675	0.0	0.0	0.0
19	0.0	5.15	0.0	0.0	0.0
20	0.0	6.075	0.0	0.0	0.0
21	0.0	10.725	0.0	0.0	0.0
22	0.0	23.975	0.0	0.0	0.0
23	0.0	57.0	0.0	0.0	0.0
24	0.0	74.675	0.0	0.0	0.0
25	0.0	80.45	0.0	0.0	0.0
26	0.0	81.4	0.0	0.0	0.0
27	0.0	81.8	0.0	0.0	0.0
28	0.0	82.375	0.0	0.0	0.0
29	0.0	83.075	0.0	0.0	0.0
30	0.0	83.375	0.0	0.0	0.0
31	0.0	84.25	0.0	0.0	0.0
32	0.0	85.05	0.0	0.0	0.0
33	0.0	85.975	0.0	0.0	0.0
34	0.0	87.975	0.0	0.0	0.0
35	0.0	88.75	0.0	0.0	0.0
36	0.0	89.35	0.0	0.0	0.0
37	0.0	89.825	0.0	0.0	0.0
38	0.0	90.375	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TAAACAT	40	5.315087E-9	44.000004	3
AAACATC	40	5.315087E-9	44.000004	4
CATTCAA	40	5.315087E-9	44.000004	3
ACATTCA	40	5.315087E-9	44.000004	2
CTTTGGT	20	6.952051E-4	44.000004	2
ATTCAAC	40	5.315087E-9	44.000004	4
GTAGTAG	45	2.728484E-10	44.000004	5
AACATTC	40	5.315087E-9	44.000004	1
TGTAAAC	40	5.315087E-9	44.000004	1
GTAAACA	40	5.315087E-9	44.000004	2
AACATCC	40	5.315087E-9	44.000004	5
GTAGATT	35	1.02281774E-7	44.0	8
AACGCTG	35	1.02281774E-7	44.0	8
GAGGTAG	50	1.4551915E-11	44.0	2
GTTTGGA	35	1.02281774E-7	44.0	20
AAGTAAT	35	1.02281774E-7	44.0	4
TCAAGTA	35	1.02281774E-7	44.0	2
ACGCTGT	35	1.02281774E-7	44.0	9
ATCCAGG	35	1.02281774E-7	44.0	9
TTGTATA	35	1.02281774E-7	44.0	13
>>END_MODULE
Read 145461 spots for SRR5031025.sra
Written 145461 spots for SRR5031025.sra
Read 145483 spots for SRR5031025.sra
Written 145483 spots for SRR5031025.sra
Read 145461 spots for SRR5031025.sra
Written 145461 spots for SRR5031025.sra
Read 145461 spots for SRR5031025.sra
Written 145461 spots for SRR5031025.sra
Read 145461 spots for SRR5031025.sra
Written 145461 spots for SRR5031025.sra
Read 145461 spots for SRR5031025.sra
Written 145461 spots for SRR5031025.sra
Read 145461 spots for SRR5031025.sra
Written 145461 spots for SRR5031025.sra
Read 145461 spots for SRR5031025.sra
Written 145461 spots for SRR5031025.sra
Read 145461 spots for SRR5031025.sra
Written 145461 spots for SRR5031025.sra
Read 145461 spots for SRR5031025.sra
Written 145461 spots for SRR5031025.sra
Read 145461 spots for SRR5031025.sra
Written 145461 spots for SRR5031025.sra
Read 145461 spots for SRR5031025.sra
Written 145461 spots for SRR5031025.sra
Read 145461 spots for SRR5031025.sra
Written 145461 spots for SRR5031025.sra
Read 145461 spots for SRR5031025.sra
Written 145461 spots for SRR5031025.sra
Read 145461 spots for SRR5031025.sra
Written 145461 spots for SRR5031025.sra
Read 145461 spots for SRR5031025.sra
Written 145461 spots for SRR5031025.sra
Read 145461 spots for SRR5031025.sra
Written 145461 spots for SRR5031025.sra
Read 145461 spots for SRR5031025.sra
Written 145461 spots for SRR5031025.sra
Read 145461 spots for SRR5031025.sra
Written 145461 spots for SRR5031025.sra
Read 145461 spots for SRR5031025.sra
Written 145461 spots for SRR5031025.sra
Read 145461 spots for SRR5031025.sra
Written 145461 spots for SRR5031025.sra
Read 145461 spots for SRR5031025.sra
Written 145461 spots for SRR5031025.sra
Read 145461 spots for SRR5031025.sra
Written 145461 spots for SRR5031025.sra
Read 145461 spots for SRR5031025.sra
Written 145461 spots for SRR5031025.sra
SRR ids: ['SRR5031025.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_dkekq5ex
SRR5031025.sra spots: 3491086
blocks: [[1, 145461], [145462, 290922], [290923, 436383], [436384, 581844], [581845, 727305], [727306, 872766], [872767, 1018227], [1018228, 1163688], [1163689, 1309149], [1309150, 1454610], [1454611, 1600071], [1600072, 1745532], [1745533, 1890993], [1890994, 2036454], [2036455, 2181915], [2181916, 2327376], [2327377, 2472837], [2472838, 2618298], [2618299, 2763759], [2763760, 2909220], [2909221, 3054681], [3054682, 3200142], [3200143, 3345603], [3345604, 3491086]]
SRR5031025 file size 602116
SRR5031025 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 24 -o SRR5031025 SRR5031025_1.fastq
Input file:	SRR5031025_1.fastq
trimmed:	SRR5031025-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):	24
Wed Jan  8 16:41:53 2020 >> started

Wed Jan  8 16:41:55 2020 >> done (1.801s)
3491086 reads processed; of these:
    189 ( 0.01%) short reads filtered out after trimming by size control
      9 ( 0.00%) empty reads filtered out after trimming by size control
3490888 (99.99%) reads available; of these:
 171945 ( 4.93%) trimmed reads available after processing
3318943 (95.07%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     53	  0.00%
 19	     56	  0.00%
 20	    149	  0.00%
 21	    192	  0.01%
 22	    353	  0.01%
 23	    427	  0.01%
 24	    409	  0.01%
 25	    552	  0.02%
 26	    476	  0.01%
 27	    567	  0.02%
 28	    763	  0.02%
 29	   1361	  0.04%
 30	    802	  0.02%
 31	    777	  0.02%
 32	    949	  0.03%
 33	   1259	  0.04%
 34	   1614	  0.05%
 35	   3141	  0.09%
 36	   2836	  0.08%
 37	   3060	  0.09%
 38	   2740	  0.08%
 39	   2899	  0.08%
 40	   3362	  0.10%
 41	   3676	  0.11%
 42	   4815	  0.14%
 43	   7115	  0.20%
 44	   8810	  0.25%
 45	  11118	  0.32%
 46	  15017	  0.43%
 47	  18920	  0.54%
 48	  33660	  0.96%
 49	  40017	  1.15%
 50	3318943	 95.07%
3490888 reads passed initial QC


criterion=sequence-density
sequence-density=90.02
sequence-density-rank=1
fanout-score=18.98
fanout-score-rank=1
prefix-density=91.48
prefix-fanout=18.7
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCATTCATCTCGTATGCC


criterion=fanout-score
sequence-density=90.02
sequence-density-rank=1
fanout-score=18.98
fanout-score-rank=1
prefix-density=91.48
prefix-fanout=18.7
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCATTCATCTCGTATGCC
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 24 -x TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCATTCATCTCGTATGCC -o SRR5031025 -
Input file:	STDIN
trimmed:	SRR5031025-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCATTCATCTCGTATGCC
-- 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):	24
Wed Jan  8 16:42:12 2020 >> started

Wed Jan  8 16:42:17 2020 >> done (4.278s)
3414165 reads processed; of these:
 156636 ( 4.59%) short reads filtered out after trimming by size control
  13829 ( 0.41%) empty reads filtered out after trimming by size control
3243700 (95.01%) reads available; of these:
3128686 (96.45%) trimmed reads available after processing
 115014 ( 3.55%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  17087	  0.53%
 19	  42957	  1.32%
 20	 162735	  5.02%
 21	 421420	 12.99%
 22	1138235	 35.09%
 23	 610183	 18.81%
 24	 201337	  6.21%
 25	  32405	  1.00%
 26	  16698	  0.51%
 27	  16906	  0.52%
 28	  19228	  0.59%
 29	  16105	  0.50%
 30	  25788	  0.80%
 31	  36585	  1.13%
 32	  38984	  1.20%
 33	  78728	  2.43%
 34	  31185	  0.96%
 35	  20274	  0.63%
 36	  21592	  0.67%
 37	  12470	  0.38%
 38	  14721	  0.45%
 39	  13047	  0.40%
 40	  18258	  0.56%
 41	  24170	  0.75%
 42	  26824	  0.83%
 43	  21461	  0.66%
 44	  17054	  0.53%
 45	  19483	  0.60%
 46	  14374	  0.44%
 47	  11269	  0.35%
 48	   1062	  0.03%
 49	   1944	  0.06%
 50	  99131	  3.06%


criterion=sequence-density
sequence-density=4.53
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=21
prefix-density=0.00
prefix-fanout=1.0
sequence=TCCCTGAGACCCTTTAACCTGTGAA


criterion=fanout-score
sequence-density=0.37
sequence-density-rank=33
fanout-score=10.89
fanout-score-rank=1
prefix-density=3.99
prefix-fanout=1.0
sequence=GTAGTAGGTTGCATAGTT
                                 Started job on |	Jan 08 16:42:36
                             Started mapping on |	Jan 08 16:42:36
                                    Finished on |	Jan 08 16:43:02
       Mapping speed, Million of reads per hour |	459.75

                          Number of input reads |	3320423
                      Average input read length |	25
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1502355
                        Uniquely mapped reads % |	45.25%
                          Average mapped length |	23.92
                       Number of splices: Total |	1552
            Number of splices: Annotated (sjdb) |	170
                       Number of splices: GT/AG |	1402
                       Number of splices: GC/AG |	13
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	137
                      Mismatch rate per base, % |	0.14%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.78
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.13
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1469764
             % of reads mapped to multiple loci |	44.26%
        Number of reads mapped to too many loci |	73306
             % of reads mapped to too many loci |	2.21%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	7.63%
                     % of reads unmapped: other |	0.65%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	348304	348304	348304
N_multimapping	1469764	1469764	1469764
N_noFeature	66202	80089	1156989
N_ambiguous	785218	488610	9999
UnstrandedReadsAssigned:650935 PositiveStrandReadsAssigned:933656 NegativeStrandReadsAssigned:335367
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=22 echo kmer=19
SRR5031025 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: SRR5031025-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,320,423 reads, 605,208 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,111 rounds

 109283 SRR5031025.ke.tsv
  52636 SRR5031025.se.tsv
 161919 total
==> SRR5031025.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

==> SRR5031025.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031025 completed mapping pipeline successfully
