Starting /dee2/code/volunteer_pipeline.sh SRR5031055
    current disk space = 160512835584
    free memory = 73933560 
SRR5031055 SRAfilesize
bed374c40810212776e75bfa8541503f  SRR5031055.sra
SRR5031055.sra file validated
SRR5031055 is single end
SRR5031055 is conventional basespace
SRR5031055 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031055_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	32.3375	33.0	31.0	34.0	31.0	34.0
2	32.65425	34.0	31.0	34.0	31.0	34.0
3	32.66825	34.0	31.0	34.0	31.0	34.0
4	36.23775	37.0	37.0	37.0	35.0	37.0
5	35.999	37.0	35.0	37.0	35.0	37.0
6	35.837	37.0	35.0	37.0	35.0	37.0
7	35.894	37.0	35.0	37.0	35.0	37.0
8	35.81425	37.0	35.0	37.0	35.0	37.0
9	37.61	39.0	37.0	39.0	35.0	39.0
10	37.796	39.0	38.0	39.0	35.0	39.0
11	37.618	39.0	37.0	39.0	35.0	39.0
12	37.652	39.0	37.0	39.0	35.0	39.0
13	37.58225	39.0	37.0	39.0	35.0	39.0
14	39.06475	41.0	38.0	41.0	36.0	41.0
15	39.0765	40.0	38.0	41.0	36.0	41.0
16	38.9205	40.0	38.0	41.0	35.0	41.0
17	38.8595	40.0	38.0	41.0	35.0	41.0
18	38.99375	40.0	38.0	41.0	35.0	41.0
19	38.688	40.0	38.0	41.0	34.0	41.0
20	38.9055	40.0	39.0	41.0	35.0	41.0
21	38.77475	40.0	38.0	41.0	34.0	41.0
22	38.99775	40.0	39.0	41.0	35.0	41.0
23	38.862	40.0	39.0	41.0	36.0	41.0
24	38.85625	40.0	38.0	41.0	35.0	41.0
25	39.116	41.0	39.0	41.0	36.0	41.0
26	38.81975	40.0	38.0	41.0	35.0	41.0
27	38.735	40.0	38.0	41.0	34.0	41.0
28	38.75375	40.0	38.0	41.0	34.0	41.0
29	38.37075	40.0	38.0	41.0	33.0	41.0
30	38.3205	40.0	38.0	41.0	33.0	41.0
31	38.529	40.0	38.0	41.0	34.0	41.0
32	38.34675	40.0	38.0	41.0	33.0	41.0
33	38.188	40.0	38.0	41.0	34.0	41.0
34	38.3665	40.0	38.0	41.0	34.0	41.0
35	38.1935	40.0	38.0	41.0	34.0	41.0
36	38.078	40.0	38.0	41.0	34.0	41.0
37	37.787	40.0	37.0	41.0	33.0	41.0
38	37.06975	40.0	36.0	41.0	30.0	41.0
39	37.3775	40.0	37.0	41.0	31.0	41.0
40	37.64525	40.0	37.0	41.0	32.0	41.0
41	37.94575	40.0	38.0	41.0	33.0	41.0
42	38.19825	40.0	38.0	41.0	33.0	41.0
43	38.4885	40.0	38.0	41.0	34.0	41.0
44	38.224	40.0	38.0	41.0	33.0	41.0
45	38.0895	40.0	38.0	41.0	33.0	41.0
46	37.9345	40.0	37.0	41.0	33.0	41.0
47	37.535	40.0	37.0	41.0	32.0	41.0
48	37.16125	40.0	37.0	41.0	31.0	41.0
49	37.3805	40.0	37.0	41.0	32.0	41.0
50	37.01375	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
12	1.0
13	0.0
14	1.0
15	1.0
16	1.0
17	2.0
18	0.0
19	2.0
20	2.0
21	1.0
22	5.0
23	5.0
24	5.0
25	14.0
26	11.0
27	15.0
28	24.0
29	43.0
30	54.0
31	56.0
32	77.0
33	92.0
34	142.0
35	189.0
36	249.0
37	437.0
38	710.0
39	1861.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	8.9	25.4	50.675000000000004	15.024999999999999
2	24.85607008760951	26.132665832290364	20.876095118898625	28.1351689612015
3	22.650000000000002	22.0	20.349999999999998	35.0
4	33.125	28.349999999999998	14.374999999999998	24.15
5	23.75	38.425	26.900000000000002	10.925
6	34.975	14.249999999999998	35.9	14.875
7	15.975	23.275000000000002	23.3	37.45
8	26.6	29.349999999999998	16.75	27.3
9	19.5	35.199999999999996	29.925	15.375
10	20.225	24.875	28.075	26.825
11	33.95	9.6	17.0	39.45
12	15.675	19.325	29.675	35.325
13	28.525	18.75	35.25	17.474999999999998
14	31.424999999999997	29.45	23.474999999999998	15.65
15	36.3	24.6	25.974999999999998	13.125
16	19.025	19.875	24.575	36.525
17	25.55	25.5	36.6	12.35
18	24.099999999999998	19.625	29.025000000000002	27.250000000000004
19	35.925000000000004	14.975	32.275	16.825000000000003
20	44.65	14.475	28.025	12.85
21	23.225	20.05	28.875	27.85
22	27.725	11.975	49.3	11.0
23	25.924999999999997	12.675	46.875	14.524999999999999
24	52.725	13.475000000000001	25.825	7.9750000000000005
25	51.4	23.849999999999998	15.375	9.375
26	27.375	47.125	13.950000000000001	11.55
27	15.35	48.75	23.075000000000003	12.825000000000001
28	10.174999999999999	24.5	50.1	15.225
29	12.625	12.425	56.925000000000004	18.025
30	9.3	7.3	36.55	46.85
31	13.65	5.55	48.35	32.45
32	26.900000000000002	5.675	22.2	45.225
33	54.900000000000006	8.95	13.350000000000001	22.8
34	62.324999999999996	7.199999999999999	15.6	14.875
35	65.075	6.6000000000000005	18.725	9.6
36	41.8	7.000000000000001	38.175	13.025
37	47.275	10.0	20.349999999999998	22.375
38	23.7	14.825	12.049999999999999	49.425000000000004
39	16.150000000000002	22.900000000000002	10.625	50.324999999999996
40	15.1	49.55	10.35	25.0
41	23.35	50.2	9.15	17.299999999999997
42	49.675000000000004	28.925	11.975	9.425
43	52.949999999999996	27.875	8.649999999999999	10.525
44	30.099999999999998	49.475	7.475	12.950000000000001
45	18.575	51.725	11.600000000000001	18.099999999999998
46	13.25	26.25	18.4	42.1
47	9.049999999999999	14.75	40.475	35.725
48	10.674999999999999	12.275	20.424999999999997	56.625
49	11.875	18.85	14.524999999999999	54.75
50	16.900000000000002	38.0	13.5	31.6
>>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	0.5
18	1.0
19	0.5
20	0.0
21	0.0
22	0.0
23	0.0
24	0.0
25	0.0
26	0.0
27	1.5
28	3.0
29	3.0
30	3.0
31	3.5
32	4.0
33	7.0
34	10.0
35	18.5
36	27.0
37	27.5
38	28.0
39	37.0
40	46.0
41	48.0
42	50.0
43	98.0
44	146.0
45	183.0
46	220.0
47	368.5
48	517.0
49	610.5
50	704.0
51	780.5
52	857.0
53	636.0
54	415.0
55	427.0
56	439.0
57	327.0
58	215.0
59	137.0
60	59.0
61	48.5
62	38.0
63	81.0
64	124.0
65	72.5
66	21.0
67	15.0
68	9.0
69	13.0
70	17.0
71	28.0
72	39.0
73	20.5
74	2.0
75	1.5
76	1.0
77	0.5
78	0.0
79	1.5
80	3.0
81	2.5
82	2.0
83	1.0
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	0.125
3	0.0
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.0
10	0.0
11	0.0
12	0.0
13	0.0
14	0.0
15	0.0
16	0.0
17	0.0
18	0.0
19	0.0
20	0.0
21	0.0
22	0.0
23	0.0
24	0.0
25	0.0
26	0.0
27	0.0
28	0.0
29	0.0
30	0.0
31	0.0
32	0.0
33	0.0
34	0.0
35	0.0
36	0.0
37	0.0
38	0.0
39	0.0
40	0.0
41	0.0
42	0.0
43	0.0
44	0.0
45	0.0
46	0.0
47	0.0
48	0.0
49	0.0
50	0.0
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
50	4000.0
>>END_MODULE
>>Sequence Duplication Levels	fail
#Total Deduplicated Percentage	37.4
#Duplication Level	Percentage of deduplicated	Percentage of total
1	76.00267379679144	28.425
2	9.893048128342247	7.3999999999999995
3	4.077540106951872	4.575
4	2.406417112299465	3.5999999999999996
5	1.7379679144385027	3.25
6	0.7352941176470588	1.6500000000000001
7	0.4010695187165776	1.05
8	0.8689839572192514	2.6
9	0.53475935828877	1.7999999999999998
>10	2.606951871657754	19.2
>50	0.53475935828877	15.4
>100	0.2005347593582888	11.05
>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	159	3.975	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	155	3.875	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	128	3.2	RNA PCR Primer, Index 1 (100% over 27bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	89	2.225	No Hit
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	85	2.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	83	2.075	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	78	1.95	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	76	1.9	RNA PCR Primer, Index 1 (100% over 30bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	76	1.9	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	73	1.825	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	56	1.4000000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	40	1.0	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	39	0.975	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	38	0.95	RNA PCR Primer, Index 1 (100% over 27bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	37	0.9249999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	27	0.675	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	26	0.65	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	25	0.625	RNA PCR Primer, Index 1 (100% over 26bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	24	0.6	RNA PCR Primer, Index 1 (100% over 27bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	21	0.525	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	21	0.525	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	21	0.525	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	21	0.525	RNA PCR Primer, Index 1 (100% over 26bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATTCCTATCTCGTATGC	20	0.5	RNA PCR Primer, Index 27 (100% over 50bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	19	0.475	No Hit
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	19	0.475	RNA PCR Primer, Index 1 (100% over 26bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	18	0.44999999999999996	No Hit
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAT	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 35bp)
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	16	0.4	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	15	0.375	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	13	0.325	RNA PCR Primer, Index 1 (100% over 33bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	13	0.325	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	12	0.3	RNA PCR Primer, Index 1 (100% over 30bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	10	0.25	No Hit
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	9	0.22499999999999998	No Hit
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATTCCTATCTC	9	0.22499999999999998	RNA PCR Primer, Index 27 (100% over 44bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	9	0.22499999999999998	No Hit
CACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 34bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	9	0.22499999999999998	No Hit
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (100% over 30bp)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
CTGGCCCTCTCTGCCCTTCCGTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TATTGCACTTGTCCCGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	8	0.2	No Hit
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TGACTTGATGAAAGTACTTTTGAACCCTTTTCCATCTGATGTGGAATTCT	8	0.2	No Hit
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	7	0.17500000000000002	No Hit
TTCAAGTAATTCAGGATAGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTTGGAATTCTCGGGTGCCA	7	0.17500000000000002	No Hit
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTCACTGGAATTCTCGGGT	7	0.17500000000000002	No Hit
CAAAGAATTCTCCTTTTGGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCTGGAATTCTCGGGTGC	7	0.17500000000000002	No Hit
TATTGCACTCGTCCCGGCCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	6	0.15	No Hit
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
GTGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCA	6	0.15	No Hit
TAGCACCATCTGAAATCGGTTATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AACCCGTAGATCCGAACTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AGAGGTAGTAGGTTGCATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	6	0.15	No Hit
TGAGGTAGTAGTTTGTGCTGTTATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
CTAGACTGAGGCTCCTTGAGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
GTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATT	6	0.15	RNA PCR Primer, Index 8 (97% over 36bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	5	0.125	No Hit
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TGTAAACATCCTACACTCAGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTACAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTAATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	5	0.125	RNA PCR Primer, Index 1 (100% over 31bp)
TCACAGTGAACCGGTCTCTTTAATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGTTTGTGCTGTTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
CCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATT	5	0.125	RNA PCR Primer, Index 8 (97% over 36bp)
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
AGAAATGCGGATATGGGACTGAGATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TGCGGGGCTAGGGCTAACAGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	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)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTC	5	0.125	No Hit
TCACAGTGAACCGGTCTCTTTATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TAAGGCACGCGGTGAATGCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	5	0.125	No Hit
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	5	0.125	No Hit
AACATTCAACGCTGTCGGTGAGTTTTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
AGACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
>>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	0.525	0.0	0.0	0.0
2	0.0	0.525	0.0	0.0	0.0
3	0.0	0.65	0.0	0.0	0.0
4	0.0	0.675	0.0	0.0	0.0
5	0.0	0.675	0.0	0.0	0.0
6	0.0	0.725	0.0	0.0	0.0
7	0.0	1.0	0.0	0.0	0.0
8	0.0	1.075	0.0	0.0	0.0
9	0.0	1.175	0.0	0.0	0.0
10	0.0	1.25	0.0	0.0	0.0
11	0.0	1.4	0.0	0.0	0.0
12	0.0	1.675	0.0	0.0	0.0
13	0.0	1.975	0.0	0.0	0.0
14	0.0	2.125	0.0	0.0	0.0
15	0.0	2.6	0.0	0.0	0.0
16	0.0	3.45	0.0	0.0	0.0
17	0.0	4.1	0.0	0.0	0.0
18	0.0	5.2	0.0	0.0	0.0
19	0.0	5.75	0.0	0.0	0.0
20	0.0	6.625	0.0	0.0	0.0
21	0.0	11.6	0.0	0.0	0.0
22	0.0	22.7	0.0	0.0	0.0
23	0.0	54.05	0.0	0.0	0.0
24	0.0	67.3	0.0	0.0	0.0
25	0.0	73.7	0.0	0.0	0.0
26	0.0	75.425	0.0	0.0	0.0
27	0.0	76.3	0.0	0.0	0.0
28	0.0	76.925	0.0	0.0	0.0
29	0.0	77.725	0.0	0.0	0.0
30	0.0	78.05	0.0	0.0	0.0
31	0.0	78.775	0.0	0.0	0.0
32	0.0	79.775	0.0	0.0	0.0
33	0.0	80.625	0.0	0.0	0.0
34	0.0	83.9	0.0	0.0	0.0
35	0.0	85.025	0.0	0.0	0.0
36	0.0	85.85	0.0	0.0	0.0
37	0.0	87.025	0.0	0.0	0.0
38	0.0	87.7	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
ACAGTGA	20	6.952051E-4	44.000004	3
ACCGGTC	20	6.952051E-4	44.000004	10
CGCTGAT	20	6.952051E-4	44.000004	28
AACCGGT	20	6.952051E-4	44.000004	9
TTGTATA	20	6.952051E-4	44.000004	13
GGTCTCT	20	6.952051E-4	44.000004	13
GCTGGAA	20	6.952051E-4	44.000004	20
GGCTGGA	20	6.952051E-4	44.000004	19
CATTCAA	40	5.315087E-9	44.000004	3
CTGATGG	20	6.952051E-4	44.000004	30
ACATTCA	40	5.315087E-9	44.000004	2
GTATAGT	20	6.952051E-4	44.000004	15
GAACCGG	20	6.952051E-4	44.000004	8
GTCTCTT	20	6.952051E-4	44.000004	14
GCTGATG	20	6.952051E-4	44.000004	29
AGTGAAC	20	6.952051E-4	44.000004	5
TCTCTTT	20	6.952051E-4	44.000004	15
GTGAACC	20	6.952051E-4	44.000004	6
CGGTCTC	20	6.952051E-4	44.000004	12
TGTATAG	20	6.952051E-4	44.000004	14
>>END_MODULE
Read 234357 spots for SRR5031055.sra
Written 234357 spots for SRR5031055.sra
Read 234357 spots for SRR5031055.sra
Written 234357 spots for SRR5031055.sra
Read 234357 spots for SRR5031055.sra
Written 234357 spots for SRR5031055.sra
Read 234357 spots for SRR5031055.sra
Written 234357 spots for SRR5031055.sra
Read 234357 spots for SRR5031055.sra
Written 234357 spots for SRR5031055.sra
Read 234357 spots for SRR5031055.sra
Written 234357 spots for SRR5031055.sra
Read 234357 spots for SRR5031055.sra
Written 234357 spots for SRR5031055.sra
Read 234357 spots for SRR5031055.sra
Written 234357 spots for SRR5031055.sra
Read 234357 spots for SRR5031055.sra
Written 234357 spots for SRR5031055.sra
Read 234357 spots for SRR5031055.sra
Written 234357 spots for SRR5031055.sra
Read 234358 spots for SRR5031055.sra
Written 234358 spots for SRR5031055.sra
Read 234357 spots for SRR5031055.sra
Written 234357 spots for SRR5031055.sra
SRR ids: ['SRR5031055.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_xndkpwe3
SRR5031055.sra spots: 2812285
blocks: [[1, 234357], [234358, 468714], [468715, 703071], [703072, 937428], [937429, 1171785], [1171786, 1406142], [1406143, 1640499], [1640500, 1874856], [1874857, 2109213], [2109214, 2343570], [2343571, 2577927], [2577928, 2812285]]
SRR5031055 file size 486365
SRR5031055 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031055 SRR5031055_1.fastq
Input file:	SRR5031055_1.fastq
trimmed:	SRR5031055-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 07:14:58 2020 >> started

Wed Mar  4 07:14:59 2020 >> done (1.782s)
2812285 reads processed; of these:
    181 ( 0.01%) short reads filtered out after trimming by size control
     12 ( 0.00%) empty reads filtered out after trimming by size control
2812092 (99.99%) reads available; of these:
 130467 ( 4.64%) trimmed reads available after processing
2681625 (95.36%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     40	  0.00%
 19	     67	  0.00%
 20	    143	  0.01%
 21	    180	  0.01%
 22	    326	  0.01%
 23	    395	  0.01%
 24	    406	  0.01%
 25	    569	  0.02%
 26	    434	  0.02%
 27	    583	  0.02%
 28	    706	  0.03%
 29	   1058	  0.04%
 30	    723	  0.03%
 31	    808	  0.03%
 32	    888	  0.03%
 33	   1038	  0.04%
 34	   1263	  0.04%
 35	   2409	  0.09%
 36	   2227	  0.08%
 37	   2349	  0.08%
 38	   2242	  0.08%
 39	   2460	  0.09%
 40	   2651	  0.09%
 41	   2630	  0.09%
 42	   3544	  0.13%
 43	   5421	  0.19%
 44	   7708	  0.27%
 45	   9492	  0.34%
 46	  12748	  0.45%
 47	  15854	  0.56%
 48	  24164	  0.86%
 49	  24941	  0.89%
 50	2681625	 95.36%
2812092 reads passed initial QC


criterion=sequence-density
sequence-density=86.86
sequence-density-rank=1
fanout-score=20.57
fanout-score-rank=1
prefix-density=88.83
prefix-fanout=20.1
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATTCCTATCTCGTATGCC


criterion=fanout-score
sequence-density=86.86
sequence-density-rank=1
fanout-score=20.57
fanout-score-rank=1
prefix-density=88.83
prefix-fanout=20.1
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATTCCTATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATTCCTATCTCGTATGCC -o SRR5031055 -
Input file:	STDIN
trimmed:	SRR5031055-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATTCCTATCTCGTATGCC
-- 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 07:15:15 2020 >> started

Wed Mar  4 07:15:20 2020 >> done (4.500s)
2747446 reads processed; of these:
 125373 ( 4.56%) short reads filtered out after trimming by size control
  16746 ( 0.61%) empty reads filtered out after trimming by size control
2605327 (94.83%) reads available; of these:
2478489 (95.13%) trimmed reads available after processing
 126838 ( 4.87%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  12857	  0.49%
 19	  25534	  0.98%
 20	 126965	  4.87%
 21	 320365	 12.30%
 22	 863740	 33.15%
 23	 382062	 14.66%
 24	 166575	  6.39%
 25	  42184	  1.62%
 26	  21037	  0.81%
 27	  19322	  0.74%
 28	  21561	  0.83%
 29	  16520	  0.63%
 30	  21378	  0.82%
 31	  25004	  0.96%
 32	  29811	  1.14%
 33	  99764	  3.83%
 34	  33599	  1.29%
 35	  25774	  0.99%
 36	  33215	  1.27%
 37	  14353	  0.55%
 38	  15927	  0.61%
 39	  14497	  0.56%
 40	  21883	  0.84%
 41	  27070	  1.04%
 42	  29735	  1.14%
 43	  20899	  0.80%
 44	  15461	  0.59%
 45	  19294	  0.74%
 46	  14097	  0.54%
 47	  12592	  0.48%
 48	   1235	  0.05%
 49	   1633	  0.06%
 50	 109384	  4.20%


criterion=sequence-density
sequence-density=4.67
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=16
prefix-density=0.00
prefix-fanout=1.0
sequence=AAGCTGCCAGTTGAAGAACTGT


criterion=fanout-score
sequence-density=0.49
sequence-density-rank=24
fanout-score=13.22
fanout-score-rank=1
prefix-density=6.48
prefix-fanout=1.0
sequence=TGAGCTTGGCTTTT
                                 Started job on |	Mar 04 07:15:42
                             Started mapping on |	Mar 04 07:15:43
                                    Finished on |	Mar 04 07:16:08
       Mapping speed, Million of reads per hour |	384.48

                          Number of input reads |	2669973
                      Average input read length |	26
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1342056
                        Uniquely mapped reads % |	50.26%
                          Average mapped length |	24.72
                       Number of splices: Total |	1433
            Number of splices: Annotated (sjdb) |	199
                       Number of splices: GT/AG |	1330
                       Number of splices: GC/AG |	14
                       Number of splices: AT/AC |	2
               Number of splices: Non-canonical |	87
                      Mismatch rate per base, % |	0.20%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.66
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.08
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	983868
             % of reads mapped to multiple loci |	36.85%
        Number of reads mapped to too many loci |	54522
             % of reads mapped to too many loci |	2.04%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	10.33%
                     % of reads unmapped: other |	0.52%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	344049	344049	344049
N_multimapping	983868	983868	983868
N_noFeature	62383	77357	948251
N_ambiguous	763334	426065	10300
UnstrandedReadsAssigned:516339 PositiveStrandReadsAssigned:838634 NegativeStrandReadsAssigned:383505
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=22 echo kmer=19
SRR5031055 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: SRR5031055-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,669,973 reads, 670,364 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,133 rounds

 109283 SRR5031055.ke.tsv
  52636 SRR5031055.se.tsv
 161919 total
==> SRR5031055.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

==> SRR5031055.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031055 completed mapping pipeline successfully
