Starting /dee2/code/volunteer_pipeline.sh SRR5031061
    current disk space = 160498515968
    free memory = 73932740 
SRR5031061 SRAfilesize
2cedb7ac4a3e751b2879e3cca8ea62cf  SRR5031061.sra
SRR5031061.sra file validated
SRR5031061 is single end
SRR5031061 is conventional basespace
SRR5031061 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031061_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	32.22175	33.0	31.0	34.0	31.0	34.0
2	32.56175	34.0	31.0	34.0	31.0	34.0
3	32.51425	34.0	31.0	34.0	31.0	34.0
4	36.154	37.0	35.0	37.0	35.0	37.0
5	35.9445	37.0	35.0	37.0	35.0	37.0
6	35.7075	37.0	35.0	37.0	33.0	37.0
7	35.837	37.0	35.0	37.0	35.0	37.0
8	35.7045	37.0	35.0	37.0	33.0	37.0
9	37.413	39.0	37.0	39.0	34.0	39.0
10	37.69725	39.0	37.0	39.0	35.0	39.0
11	37.568	39.0	37.0	39.0	35.0	39.0
12	37.47175	39.0	37.0	39.0	35.0	39.0
13	37.599	39.0	37.0	39.0	35.0	39.0
14	38.97325	40.0	38.0	41.0	35.0	41.0
15	38.87975	40.0	38.0	41.0	35.0	41.0
16	38.78775	40.0	38.0	41.0	35.0	41.0
17	38.7705	40.0	38.0	41.0	34.0	41.0
18	38.93125	40.0	38.0	41.0	35.0	41.0
19	38.54825	40.0	38.0	41.0	34.0	41.0
20	38.8505	40.0	38.0	41.0	35.0	41.0
21	38.72525	40.0	38.0	41.0	34.0	41.0
22	38.93975	40.0	38.0	41.0	35.0	41.0
23	38.63475	40.0	38.0	41.0	34.0	41.0
24	38.67025	40.0	38.0	41.0	34.0	41.0
25	38.9155	40.0	38.0	41.0	35.0	41.0
26	38.67875	40.0	38.0	41.0	34.0	41.0
27	38.656	40.0	38.0	41.0	34.0	41.0
28	38.65725	40.0	38.0	41.0	34.0	41.0
29	38.156	40.0	38.0	41.0	33.0	41.0
30	38.15075	40.0	38.0	41.0	33.0	41.0
31	38.3615	40.0	38.0	41.0	34.0	41.0
32	38.25025	40.0	38.0	41.0	33.0	41.0
33	38.38225	40.0	38.0	41.0	34.0	41.0
34	38.46975	40.0	38.0	41.0	34.0	41.0
35	38.2825	40.0	38.0	41.0	34.0	41.0
36	38.03125	40.0	38.0	41.0	33.0	41.0
37	37.75875	40.0	37.0	41.0	32.0	41.0
38	36.93425	40.0	36.0	41.0	30.0	41.0
39	37.262	39.0	37.0	41.0	31.0	41.0
40	37.51075	40.0	37.0	41.0	32.0	41.0
41	37.70675	40.0	37.0	41.0	33.0	41.0
42	37.91925	40.0	38.0	41.0	33.0	41.0
43	38.2195	40.0	38.0	41.0	33.0	41.0
44	38.094	40.0	38.0	41.0	33.0	41.0
45	38.003	40.0	38.0	41.0	33.0	41.0
46	37.74175	40.0	37.0	41.0	33.0	41.0
47	37.44425	40.0	37.0	41.0	32.0	41.0
48	36.9335	40.0	36.0	41.0	31.0	41.0
49	37.21725	40.0	37.0	41.0	32.0	41.0
50	36.8145	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
10	1.0
11	0.0
12	0.0
13	1.0
14	0.0
15	1.0
16	0.0
17	0.0
18	1.0
19	3.0
20	2.0
21	1.0
22	7.0
23	9.0
24	8.0
25	5.0
26	18.0
27	16.0
28	31.0
29	43.0
30	60.0
31	62.0
32	86.0
33	106.0
34	154.0
35	196.0
36	278.0
37	410.0
38	665.0
39	1836.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	7.475	23.825	55.825	12.875
2	23.375	28.299999999999997	20.775	27.55
3	15.049999999999999	19.675	17.825	47.449999999999996
4	25.75	37.325	13.325000000000001	23.599999999999998
5	23.075000000000003	34.775	31.8	10.35
6	37.475	13.4	39.050000000000004	10.075000000000001
7	12.75	26.150000000000002	25.4	35.699999999999996
8	26.5	40.025	13.625000000000002	19.85
9	17.575	42.475	28.599999999999998	11.35
10	18.25	21.65	25.45	34.65
11	34.25	11.700000000000001	12.45	41.6
12	15.15	16.225	21.625	47.0
13	19.5	20.525	42.325	17.65
14	40.1	20.3	27.450000000000003	12.15
15	38.125	19.125	31.674999999999997	11.075
16	12.65	26.125	21.45	39.775
17	27.450000000000003	24.675	35.275	12.6
18	29.099999999999998	17.9	27.3	25.7
19	36.25	13.950000000000001	32.574999999999996	17.224999999999998
20	52.0	15.325	23.025000000000002	9.65
21	21.875	27.650000000000002	23.575	26.900000000000002
22	31.825	12.0	49.85	6.325
23	24.4	12.075	51.949999999999996	11.575000000000001
24	53.574999999999996	12.25	29.025000000000002	5.1499999999999995
25	57.699999999999996	22.175	13.425	6.7
26	30.525000000000002	50.025	10.975	8.475000000000001
27	12.375	56.074999999999996	22.400000000000002	9.15
28	8.15	27.975	51.725	12.15
29	8.825	11.325000000000001	62.824999999999996	17.025000000000002
30	7.449999999999999	5.475	40.050000000000004	47.025
31	11.5	3.75	48.35	36.4
32	24.099999999999998	4.3	24.675	46.925
33	56.699999999999996	6.35	12.049999999999999	24.9
34	70.025	5.6000000000000005	12.0	12.375
35	70.625	5.7250000000000005	17.299999999999997	6.35
36	43.8	5.4	40.400000000000006	10.4
37	48.0	7.6499999999999995	23.7	20.65
38	25.724999999999998	11.575000000000001	11.425	51.275000000000006
39	13.5	20.9	7.75	57.85
40	11.95	51.65	7.825	28.575
41	22.400000000000002	57.175	6.65	13.775
42	52.65	31.45	8.450000000000001	7.449999999999999
43	60.35	26.575	6.0249999999999995	7.049999999999999
44	33.15	51.275000000000006	5.1	10.475
45	15.6	57.550000000000004	10.0	16.85
46	9.950000000000001	29.15	16.375	44.525
47	7.6499999999999995	12.525	41.425	38.4
48	8.175	9.9	22.975	58.95
49	10.5	17.150000000000002	11.675	60.675000000000004
50	16.825000000000003	40.725	9.700000000000001	32.75
>>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	0.5
10	1.0
11	0.5
12	0.0
13	0.0
14	0.0
15	0.5
16	1.0
17	0.5
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	3.0
30	4.0
31	4.5
32	5.0
33	7.0
34	9.0
35	14.5
36	20.0
37	22.0
38	24.0
39	29.0
40	34.0
41	39.5
42	45.0
43	90.0
44	135.0
45	189.0
46	243.0
47	400.5
48	558.0
49	577.5
50	597.0
51	852.5
52	1108.0
53	722.0
54	336.0
55	345.0
56	354.0
57	317.0
58	280.0
59	164.5
60	49.0
61	46.0
62	43.0
63	56.5
64	70.0
65	45.5
66	21.0
67	17.0
68	13.0
69	12.5
70	12.0
71	21.5
72	31.0
73	17.0
74	3.0
75	1.5
76	0.0
77	0.5
78	1.0
79	1.0
80	1.0
81	0.5
82	0.0
83	0.0
84	0.0
85	0.0
86	0.0
87	0.0
88	0.0
89	0.0
90	0.0
91	0.0
92	0.0
93	0.0
94	0.0
95	0.0
96	0.0
97	0.0
98	0.0
99	0.0
100	0.0
>>END_MODULE
>>Per base N content	pass
#Base	N-Count
1	0.0
2	0.0
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	0.0
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
50	4000.0
>>END_MODULE
>>Sequence Duplication Levels	fail
#Total Deduplicated Percentage	34.25
#Duplication Level	Percentage of deduplicated	Percentage of total
1	75.83941605839416	25.974999999999998
2	8.686131386861314	5.949999999999999
3	4.890510948905109	5.025
4	1.9708029197080292	2.7
5	1.4598540145985401	2.5
6	1.094890510948905	2.25
7	0.7299270072992701	1.7500000000000002
8	0.36496350364963503	1.0
9	0.656934306569343	2.025
>10	3.722627737226277	25.5
>50	0.291970802919708	5.7
>100	0.291970802919708	19.625
>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	260	6.5	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	218	5.45	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	172	4.3	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	135	3.375	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	65	1.625	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	61	1.525	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	51	1.275	RNA PCR Primer, Index 1 (100% over 29bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	51	1.275	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	41	1.0250000000000001	No Hit
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	39	0.975	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	38	0.95	RNA PCR Primer, Index 1 (100% over 26bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	35	0.8750000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	34	0.8500000000000001	RNA PCR Primer, Index 1 (100% over 30bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	31	0.775	RNA PCR Primer, Index 1 (100% over 27bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	30	0.75	RNA PCR Primer, Index 1 (100% over 29bp)
TCCTGTACTGAGCTGCCCCGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	27	0.675	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	26	0.65	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	25	0.625	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	24	0.6	RNA PCR Primer, Index 1 (100% over 26bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	24	0.6	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	24	0.6	RNA PCR Primer, Index 1 (100% over 26bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	24	0.6	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	23	0.575	RNA PCR Primer, Index 1 (100% over 28bp)
TCCTGTACTGAGCTGCCCCGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	21	0.525	RNA PCR Primer, Index 1 (100% over 27bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	20	0.5	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	20	0.5	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	20	0.5	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	19	0.475	RNA PCR Primer, Index 1 (100% over 29bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	19	0.475	No Hit
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 29bp)
TCCTGTACTGAGCTGCCCCGATGGAATTCTCGGGTGCCAAGGAACTCCAG	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	16	0.4	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGATGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	15	0.375	RNA PCR Primer, Index 1 (100% over 30bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	13	0.325	RNA PCR Primer, Index 1 (100% over 33bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGGCGATCTCGTATGC	13	0.325	RNA PCR Primer, Index 33 (100% over 50bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	12	0.3	RNA PCR Primer, Index 1 (100% over 30bp)
TCCTGTACTGAGCTGCCCCGAGATGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 26bp)
TCACAGTGAACCGGTCTCTTTATGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATTCAGGATAGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	10	0.25	RNA PCR Primer, Index 1 (100% over 30bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	10	0.25	No Hit
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGGAATTCTCGGGTGCCA	10	0.25	No Hit
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	9	0.22499999999999998	No Hit
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	9	0.22499999999999998	No Hit
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGGAATTCTCGGGTGCCAA	9	0.22499999999999998	No Hit
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGGAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	9	0.22499999999999998	No Hit
TTCCCTTTGTCATCCTATGCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGGCGATCTC	8	0.2	RNA PCR Primer, Index 33 (100% over 44bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCA	8	0.2	RNA PCR Primer, Index 7 (100% over 35bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTATTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGATTGTATAGTTATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTTGGAATTCTCGGGTGCCA	7	0.17500000000000002	No Hit
TGTAAACATCCCCGACTGGAAATGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TGCGGGGCTAGGGCTAACAGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTTTGGAATTCTCGGGTGCCAAGGAACT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 25bp)
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCTTTGGTTATCTAGCTGTATGTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
GGAATACCGGGTGCTGTAGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	6	0.15	No Hit
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTGGAATTCTCGGGTGCCA	6	0.15	No Hit
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGTGGAATTCTCGGGTGCC	6	0.15	No Hit
AAGGGATTCTGATGTTGGTCACTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTCTCTGGAATTCTCGGGT	6	0.15	No Hit
TGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	6	0.15	No Hit
AGAGGTAGTAGGTTGCATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
GCATTGTGGTTCAGTGGTAGAATTCTCGCCTGGAATTCTCGGGTGCCAAG	6	0.15	No Hit
AACATTCAACCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
CTAGACTGAGGCTCCTTGAGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTTTAACCTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTACACTCTCAGCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTGTGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGTGGTCTAGTGGTTAGGATTCGGCGCTGGAATTCTCGGGTGCCAA	5	0.125	No Hit
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
CACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC	5	0.125	RNA PCR Primer, Index 2 (100% over 34bp)
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGACCTTGCGATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
AGAGGTAGTAGGTTGCATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TAAGGCACGCGGTGAATGCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
CTAGACTGAGGCTCCTTGAGGAATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	5	0.125	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGGAATTCTCGGGTGCCAA	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	0.35	0.0	0.0	0.0
4	0.0	0.375	0.0	0.0	0.0
5	0.0	0.4	0.0	0.0	0.0
6	0.0	0.4	0.0	0.0	0.0
7	0.0	0.625	0.0	0.0	0.0
8	0.0	0.625	0.0	0.0	0.0
9	0.0	0.75	0.0	0.0	0.0
10	0.0	0.825	0.0	0.0	0.0
11	0.0	0.875	0.0	0.0	0.0
12	0.0	1.15	0.0	0.0	0.0
13	0.0	1.3	0.0	0.0	0.0
14	0.0	1.35	0.0	0.0	0.0
15	0.0	1.55	0.0	0.0	0.0
16	0.0	2.125	0.0	0.0	0.0
17	0.0	2.5	0.0	0.0	0.0
18	0.0	3.25	0.0	0.0	0.0
19	0.0	3.6	0.0	0.0	0.0
20	0.0	4.175	0.0	0.0	0.0
21	0.0	8.725	0.0	0.0	0.0
22	0.0	20.1	0.0	0.0	0.0
23	0.0	54.7	0.0	0.0	0.0
24	0.0	72.575	0.0	0.0	0.0
25	0.0	78.625	0.0	0.0	0.0
26	0.0	79.725	0.0	0.0	0.0
27	0.0	80.3	0.0	0.0	0.0
28	0.0	80.55	0.0	0.0	0.0
29	0.0	81.275	0.0	0.0	0.0
30	0.0	81.875	0.0	0.0	0.0
31	0.0	82.575	0.0	0.0	0.0
32	0.0	83.65	0.0	0.0	0.0
33	0.0	84.8	0.0	0.0	0.0
34	0.0	87.0	0.0	0.0	0.0
35	0.0	87.875	0.0	0.0	0.0
36	0.0	88.575	0.0	0.0	0.0
37	0.0	89.475	0.0	0.0	0.0
38	0.0	89.85	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
ACTGTTG	20	6.952051E-4	44.000004	18
GAGGTAG	40	5.315087E-9	44.000004	2
GGTTGTA	20	6.952051E-4	44.000004	11
GGTGAGT	45	2.728484E-10	44.000004	17
GTTGAAG	20	6.952051E-4	44.000004	10
AAGTAAT	45	2.728484E-10	44.000004	4
TCAAGTA	45	2.728484E-10	44.000004	2
CAGTTGA	20	6.952051E-4	44.000004	8
CTTTAAC	20	6.952051E-4	44.000004	12
CCAGTTG	20	6.952051E-4	44.000004	7
AACTGTT	20	6.952051E-4	44.000004	17
AGTAGGT	20	6.952051E-4	44.000004	7
TTCAAGT	45	2.728484E-10	44.000004	1
AGGATAG	45	2.728484E-10	44.000004	13
GAGCTTG	20	6.952051E-4	44.000004	13
GGATCCG	20	6.952051E-4	44.000004	3
CCGTCTG	20	6.952051E-4	44.000004	7
GGTTTGG	20	6.952051E-4	44.000004	19
TCGGATC	20	6.952051E-4	44.000004	1
CGGATCC	20	6.952051E-4	44.000004	2
>>END_MODULE
Read 281458 spots for SRR5031061.sra
Written 281458 spots for SRR5031061.sra
Read 281458 spots for SRR5031061.sra
Written 281458 spots for SRR5031061.sra
Read 281458 spots for SRR5031061.sra
Written 281458 spots for SRR5031061.sra
Read 281458 spots for SRR5031061.sra
Written 281458 spots for SRR5031061.sra
Read 281458 spots for SRR5031061.sra
Written 281458 spots for SRR5031061.sra
Read 281458 spots for SRR5031061.sra
Written 281458 spots for SRR5031061.sra
Read 281458 spots for SRR5031061.sra
Written 281458 spots for SRR5031061.sra
Read 281458 spots for SRR5031061.sra
Written 281458 spots for SRR5031061.sra
Read 281458 spots for SRR5031061.sra
Written 281458 spots for SRR5031061.sra
Read 281465 spots for SRR5031061.sra
Written 281465 spots for SRR5031061.sra
Read 281458 spots for SRR5031061.sra
Written 281458 spots for SRR5031061.sra
Read 281458 spots for SRR5031061.sra
Written 281458 spots for SRR5031061.sra
SRR ids: ['SRR5031061.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_gkc9l0fj
SRR5031061.sra spots: 3377503
blocks: [[1, 281458], [281459, 562916], [562917, 844374], [844375, 1125832], [1125833, 1407290], [1407291, 1688748], [1688749, 1970206], [1970207, 2251664], [2251665, 2533122], [2533123, 2814580], [2814581, 3096038], [3096039, 3377503]]
SRR5031061 file size 584333
SRR5031061 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031061 SRR5031061_1.fastq
Input file:	SRR5031061_1.fastq
trimmed:	SRR5031061-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 07:16:07 2020 >> started

Wed Mar  4 07:16:09 2020 >> done (1.999s)
3377503 reads processed; of these:
    216 ( 0.01%) short reads filtered out after trimming by size control
     11 ( 0.00%) empty reads filtered out after trimming by size control
3377276 (99.99%) reads available; of these:
 157163 ( 4.65%) trimmed reads available after processing
3220113 (95.35%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     77	  0.00%
 19	     73	  0.00%
 20	    160	  0.00%
 21	    250	  0.01%
 22	    427	  0.01%
 23	    512	  0.02%
 24	    488	  0.01%
 25	    610	  0.02%
 26	    501	  0.01%
 27	    737	  0.02%
 28	    900	  0.03%
 29	   1736	  0.05%
 30	    799	  0.02%
 31	    880	  0.03%
 32	    865	  0.03%
 33	   1163	  0.03%
 34	   1518	  0.04%
 35	   2998	  0.09%
 36	   2675	  0.08%
 37	   2752	  0.08%
 38	   2535	  0.08%
 39	   2860	  0.08%
 40	   3270	  0.10%
 41	   3495	  0.10%
 42	   4388	  0.13%
 43	   6455	  0.19%
 44	   8978	  0.27%
 45	  12081	  0.36%
 46	  14661	  0.43%
 47	  19606	  0.58%
 48	  29878	  0.88%
 49	  28835	  0.85%
 50	3220113	 95.35%
3377276 reads passed initial QC


criterion=sequence-density
sequence-density=89.92
sequence-density-rank=1
fanout-score=18.54
fanout-score-rank=1
prefix-density=91.74
prefix-fanout=18.2
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGGCGATCTCGTATGCC


criterion=fanout-score
sequence-density=89.92
sequence-density-rank=1
fanout-score=18.54
fanout-score-rank=1
prefix-density=91.74
prefix-fanout=18.2
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGGCGATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGGCGATCTCGTATGCC -o SRR5031061 -
Input file:	STDIN
trimmed:	SRR5031061-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGGCGATCTCGTATGCC
-- 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 07:16:24 2020 >> started

Wed Mar  4 07:16:30 2020 >> done (5.060s)
3302226 reads processed; of these:
  98167 ( 2.97%) short reads filtered out after trimming by size control
   7552 ( 0.23%) empty reads filtered out after trimming by size control
3196507 (96.80%) reads available; of these:
3086516 (96.56%) trimmed reads available after processing
 109991 ( 3.44%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  14736	  0.46%
 19	  31642	  0.99%
 20	 141876	  4.44%
 21	 378324	 11.84%
 22	1156216	 36.17%
 23	 620440	 19.41%
 24	 202749	  6.34%
 25	  34617	  1.08%
 26	  17044	  0.53%
 27	  16830	  0.53%
 28	  19774	  0.62%
 29	  17565	  0.55%
 30	  29450	  0.92%
 31	  36223	  1.13%
 32	  42480	  1.33%
 33	  70602	  2.21%
 34	  34382	  1.08%
 35	  21409	  0.67%
 36	  24781	  0.78%
 37	  13526	  0.42%
 38	  15420	  0.48%
 39	  13895	  0.43%
 40	  19620	  0.61%
 41	  24516	  0.77%
 42	  25677	  0.80%
 43	  18837	  0.59%
 44	  14958	  0.47%
 45	  18833	  0.59%
 46	  13526	  0.42%
 47	  10906	  0.34%
 48	   1102	  0.03%
 49	   1610	  0.05%
 50	  92941	  2.91%


criterion=sequence-density
sequence-density=3.41
sequence-density-rank=1
fanout-score=1.00
fanout-score-rank=13
prefix-density=0.01
prefix-fanout=1.0
sequence=TGTAAACATCCTCGACTGGAAGC


criterion=fanout-score
sequence-density=0.01
sequence-density-rank=46
fanout-score=30.20
fanout-score-rank=1
prefix-density=0.18
prefix-fanout=1.0
sequence=TGGTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTTTT
                                 Started job on |	Mar 04 07:16:51
                             Started mapping on |	Mar 04 07:16:51
                                    Finished on |	Mar 04 07:17:17
       Mapping speed, Million of reads per hour |	452.98

                          Number of input reads |	3271557
                      Average input read length |	25
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1525072
                        Uniquely mapped reads % |	46.62%
                          Average mapped length |	24.25
                       Number of splices: Total |	1750
            Number of splices: Annotated (sjdb) |	182
                       Number of splices: GT/AG |	1561
                       Number of splices: GC/AG |	19
                       Number of splices: AT/AC |	1
               Number of splices: Non-canonical |	169
                      Mismatch rate per base, % |	0.16%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.71
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.00
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1437695
             % of reads mapped to multiple loci |	43.95%
        Number of reads mapped to too many loci |	57718
             % of reads mapped to too many loci |	1.76%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	7.08%
                     % of reads unmapped: other |	0.59%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	308790	308790	308790
N_multimapping	1437695	1437695	1437695
N_noFeature	65421	80267	1180030
N_ambiguous	823557	532163	9103
UnstrandedReadsAssigned:636094 PositiveStrandReadsAssigned:912642 NegativeStrandReadsAssigned:335939
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=22 echo kmer=19
SRR5031061 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: SRR5031061-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,271,557 reads, 637,688 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,129 rounds

 109283 SRR5031061.ke.tsv
  52636 SRR5031061.se.tsv
 161919 total
==> SRR5031061.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

==> SRR5031061.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031061 completed mapping pipeline successfully
