Starting /dee2/code/volunteer_pipeline.sh SRR5031072
    current disk space = 160502464512
    free memory = 73914276 
SRR5031072 SRAfilesize
dec9288b8b5e719b115dbfd0a445126d  SRR5031072.sra
SRR5031072.sra file validated
SRR5031072 is single end
SRR5031072 is conventional basespace
SRR5031072 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031072_1.fastq
File type	Conventional base calls
Encoding	Sanger / Illumina 1.9
Total Sequences	4000
Sequences flagged as poor quality	0
Sequence length	50
%GC	52
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	32.37425	33.0	31.0	34.0	31.0	34.0
2	32.59225	34.0	31.0	34.0	31.0	34.0
3	32.65925	34.0	31.0	34.0	31.0	34.0
4	36.20975	37.0	37.0	37.0	35.0	37.0
5	36.05675	37.0	35.0	37.0	35.0	37.0
6	35.89375	37.0	35.0	37.0	35.0	37.0
7	35.9935	37.0	35.0	37.0	35.0	37.0
8	35.84975	37.0	35.0	37.0	35.0	37.0
9	37.58575	39.0	37.0	39.0	35.0	39.0
10	37.87225	39.0	38.0	39.0	35.0	39.0
11	37.76375	39.0	38.0	39.0	35.0	39.0
12	37.7025	39.0	37.0	39.0	35.0	39.0
13	37.68175	39.0	37.0	39.0	35.0	39.0
14	39.09725	41.0	38.0	41.0	36.0	41.0
15	39.011	40.0	38.0	41.0	35.0	41.0
16	38.96175	40.0	38.0	41.0	35.0	41.0
17	38.9765	40.0	38.0	41.0	35.0	41.0
18	39.07	41.0	38.0	41.0	36.0	41.0
19	38.7395	40.0	38.0	41.0	34.0	41.0
20	38.88	40.0	38.0	41.0	35.0	41.0
21	38.88875	40.0	38.0	41.0	34.0	41.0
22	39.00675	40.0	39.0	41.0	36.0	41.0
23	38.78475	40.0	38.0	41.0	34.0	41.0
24	38.7825	40.0	38.0	41.0	34.0	41.0
25	39.032	41.0	39.0	41.0	35.0	41.0
26	38.798	40.0	38.0	41.0	35.0	41.0
27	38.87525	40.0	38.0	41.0	35.0	41.0
28	38.87475	40.0	38.0	41.0	35.0	41.0
29	38.5585	40.0	38.0	41.0	34.0	41.0
30	38.38775	40.0	38.0	41.0	34.0	41.0
31	38.6465	40.0	38.0	41.0	34.0	41.0
32	38.72875	40.0	38.0	41.0	35.0	41.0
33	38.753	40.0	38.0	41.0	35.0	41.0
34	38.6595	40.0	38.0	41.0	34.0	41.0
35	38.53875	40.0	38.0	41.0	35.0	41.0
36	38.099	40.0	38.0	41.0	33.0	41.0
37	37.78175	40.0	37.0	41.0	33.0	41.0
38	36.98025	39.0	36.0	41.0	30.0	41.0
39	37.343	39.0	37.0	41.0	31.0	41.0
40	37.5535	40.0	37.0	41.0	32.0	41.0
41	37.87475	40.0	38.0	41.0	33.0	41.0
42	38.14375	40.0	38.0	41.0	33.0	41.0
43	38.404	40.0	38.0	41.0	34.0	41.0
44	38.17725	40.0	38.0	41.0	34.0	41.0
45	38.0125	40.0	38.0	41.0	33.0	41.0
46	37.9605	40.0	38.0	41.0	33.0	41.0
47	37.43625	40.0	37.0	41.0	31.0	41.0
48	37.12525	40.0	36.0	41.0	31.0	41.0
49	37.409	40.0	37.0	41.0	32.0	41.0
50	36.92	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
13	1.0
14	0.0
15	0.0
16	0.0
17	0.0
18	0.0
19	1.0
20	1.0
21	5.0
22	3.0
23	5.0
24	10.0
25	6.0
26	12.0
27	17.0
28	21.0
29	31.0
30	57.0
31	60.0
32	86.0
33	94.0
34	147.0
35	183.0
36	286.0
37	376.0
38	695.0
39	1903.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	8.0	25.7	51.800000000000004	14.499999999999998
2	22.93807971922788	28.07721233391828	18.601153171220858	30.383554775632994
3	23.974999999999998	20.525	21.875	33.625
4	31.5	27.950000000000003	14.549999999999999	26.0
5	22.05	40.275	26.525	11.15
6	36.05	14.924999999999999	33.475	15.55
7	13.375	22.325	24.7	39.6
8	25.15	30.575000000000003	14.524999999999999	29.75
9	22.025	34.875	28.999999999999996	14.099999999999998
10	21.5	22.1	28.075	28.325
11	29.725	9.425	18.925	41.925000000000004
12	14.2	17.2	31.924999999999997	36.675000000000004
13	30.425	18.675	31.525	19.375
14	32.0	31.874999999999996	19.575	16.55
15	35.15	26.875	25.374999999999996	12.6
16	18.025	22.725	21.525	37.724999999999994
17	24.474999999999998	22.275	38.425	14.825
18	25.3	18.775	29.275000000000002	26.650000000000002
19	38.45	13.200000000000001	29.799999999999997	18.55
20	43.6	15.9	27.250000000000004	13.25
21	23.275000000000002	20.5	27.150000000000002	29.075
22	29.725	12.325	48.325	9.625
23	26.5	13.65	44.45	15.4
24	51.975	15.2	25.55	7.2749999999999995
25	50.824999999999996	24.6	15.5	9.075
26	28.249999999999996	47.625	13.625000000000002	10.5
27	15.7	48.925000000000004	24.45	10.925
28	9.925	25.15	49.625	15.299999999999999
29	11.0	13.350000000000001	57.85	17.8
30	9.425	6.8500000000000005	37.4	46.325
31	14.05	5.075	48.425000000000004	32.45
32	27.150000000000002	5.775	21.425	45.65
33	54.925000000000004	7.95	14.274999999999999	22.85
34	62.2	7.000000000000001	15.875	14.924999999999999
35	66.60000000000001	5.675	18.075	9.65
36	42.4	6.625	37.85	13.125
37	47.425	10.549999999999999	19.125	22.900000000000002
38	24.2	16.025	12.275	47.5
39	16.2	23.225	9.75	50.824999999999996
40	15.725	47.949999999999996	10.4	25.924999999999997
41	23.825	50.2	9.075	16.900000000000002
42	48.85	30.85	10.775	9.525
43	51.975	30.599999999999998	7.875	9.55
44	31.424999999999997	49.65	6.15	12.775
45	18.95	51.37500000000001	12.375	17.299999999999997
46	12.049999999999999	27.3	17.275	43.375
47	8.175	16.175	40.45	35.199999999999996
48	9.45	13.200000000000001	20.65	56.699999999999996
49	12.049999999999999	18.075	15.0	54.87499999999999
50	16.725	38.7	13.675	30.9
>>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	0.0
16	0.0
17	0.5
18	1.0
19	0.5
20	0.0
21	0.0
22	0.0
23	0.5
24	1.0
25	0.5
26	0.0
27	0.5
28	1.0
29	1.5
30	2.0
31	6.5
32	11.0
33	11.5
34	12.0
35	15.0
36	18.0
37	23.0
38	28.0
39	29.5
40	31.0
41	37.0
42	43.0
43	81.0
44	119.0
45	167.5
46	216.0
47	356.0
48	496.0
49	597.0
50	698.0
51	793.0
52	888.0
53	662.5
54	437.0
55	451.5
56	466.0
57	347.0
58	228.0
59	141.5
60	55.0
61	49.0
62	43.0
63	77.5
64	112.0
65	63.5
66	15.0
67	16.5
68	18.0
69	13.5
70	9.0
71	26.0
72	43.0
73	23.0
74	3.0
75	2.0
76	1.0
77	1.5
78	2.0
79	1.5
80	1.0
81	1.0
82	1.0
83	0.5
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	0.27499999999999997
3	0.0
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.0
10	0.0
11	0.0
12	0.0
13	0.0
14	0.0
15	0.0
16	0.0
17	0.0
18	0.0
19	0.0
20	0.0
21	0.0
22	0.0
23	0.0
24	0.0
25	0.0
26	0.0
27	0.0
28	0.0
29	0.0
30	0.0
31	0.0
32	0.0
33	0.0
34	0.0
35	0.0
36	0.0
37	0.0
38	0.0
39	0.0
40	0.0
41	0.0
42	0.0
43	0.0
44	0.0
45	0.0
46	0.0
47	0.0
48	0.0
49	0.0
50	0.0
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
50	4000.0
>>END_MODULE
>>Sequence Duplication Levels	fail
#Total Deduplicated Percentage	37.1
#Duplication Level	Percentage of deduplicated	Percentage of total
1	76.21293800539084	28.275
2	8.288409703504044	6.15
3	4.8517520215633425	5.4
4	2.8301886792452833	4.2
5	1.5498652291105122	2.875
6	0.6064690026954178	1.35
7	0.8086253369272237	2.1
8	0.7412398921832885	2.1999999999999997
9	0.8086253369272237	2.7
>10	2.560646900269542	18.625
>50	0.5390835579514826	14.799999999999999
>100	0.20215633423180593	11.325000000000001
>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	174	4.35	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	163	4.075	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	116	2.9000000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	98	2.45	RNA PCR Primer, Index 1 (100% over 30bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	94	2.35	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	92	2.3	RNA PCR Primer, Index 1 (100% over 27bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	68	1.7000000000000002	No Hit
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	67	1.675	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	64	1.6	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	57	1.425	RNA PCR Primer, Index 1 (100% over 28bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	52	1.3	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	38	0.95	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	38	0.95	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	35	0.8750000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTA	33	0.8250000000000001	RNA PCR Primer, Index 7 (97% over 35bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	32	0.8	RNA PCR Primer, Index 1 (100% over 29bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	32	0.8	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	32	0.8	RNA PCR Primer, Index 1 (100% over 26bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	32	0.8	RNA PCR Primer, Index 1 (100% over 27bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	25	0.625	RNA PCR Primer, Index 1 (100% over 33bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	24	0.6	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	23	0.575	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	21	0.525	RNA PCR Primer, Index 1 (100% over 26bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	21	0.525	RNA PCR Primer, Index 1 (100% over 29bp)
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (100% over 28bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	20	0.5	RNA PCR Primer, Index 1 (100% over 27bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	17	0.42500000000000004	No Hit
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 30bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTATAATATCTC	14	0.35000000000000003	RNA PCR Primer, Index 44 (100% over 44bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	13	0.325	No Hit
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTATAATATCTCGTATGC	13	0.325	RNA PCR Primer, Index 44 (100% over 50bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	12	0.3	RNA PCR Primer, Index 1 (100% over 26bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TATTGCACTCGTCCCGGCCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	10	0.25	No Hit
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 30bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 30bp)
AAGCCCTTACCCCAAAAAGCATTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTTGGAATTCTCGGGTGCC	9	0.22499999999999998	No Hit
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	9	0.22499999999999998	No Hit
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	9	0.22499999999999998	No Hit
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	9	0.22499999999999998	No Hit
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCAATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	8	0.2	No Hit
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	8	0.2	RNA PCR Primer, Index 1 (100% over 25bp)
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
AGAGGTAGTAGGTTGCATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	7	0.17500000000000002	No Hit
TCACAGTGAACCGGTCTCTTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	7	0.17500000000000002	No Hit
CATTATTACTTTTGGTACGCGTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	7	0.17500000000000002	No Hit
TGAGATGAAGCACTGTAGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
AACCCGTAGATCCGAACTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TGACTTGATGAAAGTACTTTTGAACCCTTTTCCATCTGATGTGGAATTCT	7	0.17500000000000002	No Hit
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGGCAATGGTAGAACTCACACCGTGGAATTCTCGGGTGCCAAGGAACT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 25bp)
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	7	0.17500000000000002	No Hit
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTTGGAATTCTCGGGTGCCA	6	0.15	No Hit
CGCACGGGGTCGGCGGCGATGTCGGCTGGAATTCTCGGGTGCCAAGGAAC	6	0.15	RNA PCR Primer, Index 1 (100% over 24bp)
TCACAGTGAACCGGTCTCTTTATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
CAACGGAATCCCAAAAGCAGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TAATACTGTCTGGTAATGCCGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	5	0.125	No Hit
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCTC	5	0.125	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTTGGAATTCTCGGGTGCCA	5	0.125	No Hit
TCGGATCCGTCTGAGCTTGGCTAATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTAATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
ACTAATCCTAGCCCTAGCCCTACACTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AACCCGTAGATCCGAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TAAGGCACGCGGTGAATGCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
CGCTAAACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGG	5	0.125	Illumina Small RNA Adapter 2 (100% over 21bp)
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGGAATTCTCGGGTGCCA	5	0.125	No Hit
AGCAGCATTGTACAGGGCTATGTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
CTAGACTGAGGCTCCTTGAGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCTGGAATTCTCGGGTGC	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	0.475	0.0	0.0	0.0
4	0.0	0.5	0.0	0.0	0.0
5	0.0	0.55	0.0	0.0	0.0
6	0.0	0.625	0.0	0.0	0.0
7	0.0	1.15	0.0	0.0	0.0
8	0.0	1.375	0.0	0.0	0.0
9	0.0	1.45	0.0	0.0	0.0
10	0.0	1.625	0.0	0.0	0.0
11	0.0	1.75	0.0	0.0	0.0
12	0.0	1.925	0.0	0.0	0.0
13	0.0	2.125	0.0	0.0	0.0
14	0.0	2.375	0.0	0.0	0.0
15	0.0	2.625	0.0	0.0	0.0
16	0.0	3.775	0.0	0.0	0.0
17	0.0	4.3	0.0	0.0	0.0
18	0.0	5.3	0.0	0.0	0.0
19	0.0	5.9	0.0	0.0	0.0
20	0.0	6.875	0.0	0.0	0.0
21	0.0	12.65	0.0	0.0	0.0
22	0.0	23.85	0.0	0.0	0.0
23	0.0	55.2	0.0	0.0	0.0
24	0.0	68.725	0.0	0.0	0.0
25	0.0	75.725	0.0	0.0	0.0
26	0.0	77.625	0.0	0.0	0.0
27	0.0	78.375	0.0	0.0	0.0
28	0.0	79.175	0.0	0.0	0.0
29	0.0	79.8	0.0	0.0	0.0
30	0.0	80.525	0.0	0.0	0.0
31	0.0	81.175	0.0	0.0	0.0
32	0.0	81.75	0.0	0.0	0.0
33	0.0	82.875	0.0	0.0	0.0
34	0.0	85.9	0.0	0.0	0.0
35	0.0	86.975	0.0	0.0	0.0
36	0.0	87.625	0.0	0.0	0.0
37	0.0	88.275	0.0	0.0	0.0
38	0.0	88.725	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
ACAGTGA	20	6.952051E-4	44.000004	3
AACGCTG	40	5.315087E-9	44.000004	8
GTTTGGA	20	6.952051E-4	44.000004	20
GTTGAAG	20	6.952051E-4	44.000004	10
ACGCTGT	40	5.315087E-9	44.000004	9
CAGTTGA	20	6.952051E-4	44.000004	8
CCAGTTG	20	6.952051E-4	44.000004	7
AACTGTT	20	6.952051E-4	44.000004	17
TTCAACG	40	5.315087E-9	44.000004	5
CTCTTTT	20	6.952051E-4	44.000004	16
CATTCAA	40	5.315087E-9	44.000004	3
TCAACGC	40	5.315087E-9	44.000004	6
GAAGAAC	20	6.952051E-4	44.000004	13
AGAACTG	20	6.952051E-4	44.000004	15
GCCAGTT	20	6.952051E-4	44.000004	6
ACATTCA	45	2.728484E-10	44.000004	2
GCTGCCA	20	6.952051E-4	44.000004	3
GCTGTCG	40	5.315087E-9	44.000004	11
GAACTGT	20	6.952051E-4	44.000004	16
>>END_MODULE
Read 342412 spots for SRR5031072.sra
Written 342412 spots for SRR5031072.sra
Read 342412 spots for SRR5031072.sra
Written 342412 spots for SRR5031072.sra
Read 342412 spots for SRR5031072.sra
Written 342412 spots for SRR5031072.sra
Read 342412 spots for SRR5031072.sra
Written 342412 spots for SRR5031072.sra
Read 342412 spots for SRR5031072.sra
Written 342412 spots for SRR5031072.sra
Read 342412 spots for SRR5031072.sra
Written 342412 spots for SRR5031072.sra
Read 342412 spots for SRR5031072.sra
Written 342412 spots for SRR5031072.sra
Read 342412 spots for SRR5031072.sra
Written 342412 spots for SRR5031072.sra
Read 342412 spots for SRR5031072.sra
Written 342412 spots for SRR5031072.sra
Read 342418 spots for SRR5031072.sra
Written 342418 spots for SRR5031072.sra
Read 342412 spots for SRR5031072.sra
Written 342412 spots for SRR5031072.sra
Read 342412 spots for SRR5031072.sra
Written 342412 spots for SRR5031072.sra
SRR ids: ['SRR5031072.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_xle1436o
SRR5031072.sra spots: 4108950
blocks: [[1, 342412], [342413, 684824], [684825, 1027236], [1027237, 1369648], [1369649, 1712060], [1712061, 2054472], [2054473, 2396884], [2396885, 2739296], [2739297, 3081708], [3081709, 3424120], [3424121, 3766532], [3766533, 4108950]]
SRR5031072 file size 711117
SRR5031072 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031072 SRR5031072_1.fastq
Input file:	SRR5031072_1.fastq
trimmed:	SRR5031072-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 07:18:30 2020 >> started

Wed Mar  4 07:18:34 2020 >> done (4.001s)
4108950 reads processed; of these:
    281 ( 0.01%) short reads filtered out after trimming by size control
     14 ( 0.00%) empty reads filtered out after trimming by size control
4108655 (99.99%) reads available; of these:
 193168 ( 4.70%) trimmed reads available after processing
3915487 (95.30%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	    105	  0.00%
 19	    118	  0.00%
 20	    233	  0.01%
 21	    269	  0.01%
 22	    597	  0.01%
 23	    615	  0.01%
 24	    667	  0.02%
 25	    879	  0.02%
 26	    647	  0.02%
 27	    924	  0.02%
 28	   1077	  0.03%
 29	   1802	  0.04%
 30	   1149	  0.03%
 31	   1200	  0.03%
 32	   1285	  0.03%
 33	   1729	  0.04%
 34	   2149	  0.05%
 35	   4266	  0.10%
 36	   3431	  0.08%
 37	   4032	  0.10%
 38	   3561	  0.09%
 39	   3871	  0.09%
 40	   4149	  0.10%
 41	   4254	  0.10%
 42	   5488	  0.13%
 43	   7762	  0.19%
 44	  10865	  0.26%
 45	  13110	  0.32%
 46	  18582	  0.45%
 47	  23829	  0.58%
 48	  35564	  0.87%
 49	  34959	  0.85%
 50	3915487	 95.30%
4108655 reads passed initial QC


criterion=sequence-density
sequence-density=88.49
sequence-density-rank=1
fanout-score=20.54
fanout-score-rank=1
prefix-density=90.30
prefix-fanout=20.1
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTATAATATCTCGTATGCC


criterion=fanout-score
sequence-density=88.49
sequence-density-rank=1
fanout-score=20.54
fanout-score-rank=1
prefix-density=90.30
prefix-fanout=20.1
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTATAATATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTATAATATCTCGTATGCC -o SRR5031072 -
Input file:	STDIN
trimmed:	SRR5031072-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTATAATATCTCGTATGCC
-- 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 07:19:03 2020 >> started

Wed Mar  4 07:19:11 2020 >> done (8.431s)
4016326 reads processed; of these:
 209879 ( 5.23%) short reads filtered out after trimming by size control
  16572 ( 0.41%) empty reads filtered out after trimming by size control
3789875 (94.36%) reads available; of these:
3656952 (96.49%) trimmed reads available after processing
 132923 ( 3.51%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  20901	  0.55%
 19	  39141	  1.03%
 20	 218203	  5.76%
 21	 491926	 12.98%
 22	1250392	 32.99%
 23	 555380	 14.65%
 24	 267868	  7.07%
 25	  73247	  1.93%
 26	  36979	  0.98%
 27	  27840	  0.73%
 28	  30853	  0.81%
 29	  23151	  0.61%
 30	  32948	  0.87%
 31	  38036	  1.00%
 32	  48429	  1.28%
 33	 120534	  3.18%
 34	  40930	  1.08%
 35	  29586	  0.78%
 36	  32839	  0.87%
 37	  18288	  0.48%
 38	  20009	  0.53%
 39	  19700	  0.52%
 40	  31970	  0.84%
 41	  41507	  1.10%
 42	  47343	  1.25%
 43	  31369	  0.83%
 44	  22561	  0.60%
 45	  29519	  0.78%
 46	  21313	  0.56%
 47	  15530	  0.41%
 48	   1374	  0.04%
 49	   1812	  0.05%
 50	 108397	  2.86%


criterion=sequence-density
sequence-density=6.41
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=14
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.02
sequence-density-rank=40
fanout-score=100.32
fanout-score-rank=1
prefix-density=1.63
prefix-fanout=1.0
sequence=ATTGTATAGTTTAACAGTCTACAGCCATGGTCGT
                                 Started job on |	Mar 04 07:19:44
                             Started mapping on |	Mar 04 07:19:45
                                    Finished on |	Mar 04 07:20:10
       Mapping speed, Million of reads per hour |	559.04

                          Number of input reads |	3882204
                      Average input read length |	26
                                    UNIQUE READS:
                   Uniquely mapped reads number |	2119667
                        Uniquely mapped reads % |	54.60%
                          Average mapped length |	24.20
                       Number of splices: Total |	2426
            Number of splices: Annotated (sjdb) |	651
                       Number of splices: GT/AG |	2290
                       Number of splices: GC/AG |	29
                       Number of splices: AT/AC |	3
               Number of splices: Non-canonical |	104
                      Mismatch rate per base, % |	0.19%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.78
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.06
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1305582
             % of reads mapped to multiple loci |	33.63%
        Number of reads mapped to too many loci |	69107
             % of reads mapped to too many loci |	1.78%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	9.43%
                     % of reads unmapped: other |	0.56%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	456955	456955	456955
N_multimapping	1305582	1305582	1305582
N_noFeature	92310	115734	1465894
N_ambiguous	1194911	633831	17878
UnstrandedReadsAssigned:832446 PositiveStrandReadsAssigned:1370102 NegativeStrandReadsAssigned:635895
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=21 echo kmer=19
SRR5031072 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: SRR5031072-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,882,204 reads, 1,022,950 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,166 rounds

 109283 SRR5031072.ke.tsv
  52636 SRR5031072.se.tsv
 161919 total
==> SRR5031072.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

==> SRR5031072.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031072 completed mapping pipeline successfully
