Starting /dee2/code/volunteer_pipeline.sh SRR5031007
    current disk space = 160546226176
    free memory = 73948896 
SRR5031007 SRAfilesize
8332b12076694fef5f1d9f94c5f79f29  SRR5031007.sra
SRR5031007.sra file validated
SRR5031007 is single end
SRR5031007 is conventional basespace
SRR5031007 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031007_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	32.3275	33.0	31.0	34.0	31.0	34.0
2	32.5355	34.0	31.0	34.0	31.0	34.0
3	32.55125	34.0	31.0	34.0	31.0	34.0
4	36.22525	37.0	35.0	37.0	35.0	37.0
5	36.13025	37.0	35.0	37.0	35.0	37.0
6	35.87475	37.0	35.0	37.0	35.0	37.0
7	35.792	37.0	35.0	37.0	35.0	37.0
8	35.962	37.0	35.0	37.0	35.0	37.0
9	37.51	39.0	37.0	39.0	35.0	39.0
10	37.49025	39.0	37.0	39.0	34.0	39.0
11	37.20575	39.0	37.0	39.0	33.0	39.0
12	37.4825	39.0	37.0	39.0	34.0	39.0
13	37.50675	39.0	37.0	39.0	35.0	39.0
14	38.87475	40.0	38.0	41.0	34.0	41.0
15	38.88575	40.0	38.0	41.0	35.0	41.0
16	38.908	40.0	38.0	41.0	35.0	41.0
17	39.00275	40.0	38.0	41.0	35.0	41.0
18	38.94325	40.0	38.0	41.0	35.0	41.0
19	38.81525	40.0	38.0	41.0	34.0	41.0
20	38.7805	40.0	38.0	41.0	34.0	41.0
21	38.8425	40.0	38.0	41.0	35.0	41.0
22	38.914	40.0	38.0	41.0	35.0	41.0
23	38.6525	40.0	38.0	41.0	34.0	41.0
24	38.8455	40.0	38.0	41.0	35.0	41.0
25	38.93925	40.0	38.0	41.0	35.0	41.0
26	38.80525	40.0	38.0	41.0	35.0	41.0
27	38.86875	40.0	38.0	41.0	35.0	41.0
28	38.65575	40.0	38.0	41.0	34.0	41.0
29	38.4545	40.0	38.0	41.0	34.0	41.0
30	38.39375	40.0	38.0	41.0	34.0	41.0
31	38.602	40.0	38.0	41.0	34.0	41.0
32	38.60825	40.0	38.0	41.0	34.0	41.0
33	37.99625	40.0	38.0	41.0	33.0	41.0
34	38.09825	40.0	38.0	41.0	33.0	41.0
35	37.92775	40.0	37.0	41.0	33.0	41.0
36	37.94275	40.0	37.0	41.0	33.0	41.0
37	37.38275	40.0	37.0	41.0	32.0	41.0
38	37.47675	40.0	37.0	41.0	32.0	41.0
39	37.84225	40.0	37.0	41.0	33.0	41.0
40	37.93575	40.0	37.0	41.0	33.0	41.0
41	38.0355	40.0	38.0	41.0	33.0	41.0
42	37.944	40.0	37.0	41.0	33.0	41.0
43	37.937	40.0	38.0	41.0	33.0	41.0
44	37.9915	40.0	37.0	41.0	33.0	41.0
45	37.84375	40.0	37.0	41.0	33.0	41.0
46	37.485	40.0	37.0	41.0	32.0	41.0
47	37.178	40.0	36.0	41.0	31.0	41.0
48	36.95025	40.0	36.0	41.0	31.0	41.0
49	36.991	40.0	36.0	41.0	31.0	41.0
50	36.408	39.0	35.0	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
15	1.0
16	1.0
17	1.0
18	1.0
19	4.0
20	6.0
21	2.0
22	1.0
23	6.0
24	7.0
25	7.0
26	13.0
27	14.0
28	28.0
29	45.0
30	44.0
31	49.0
32	89.0
33	112.0
34	162.0
35	211.0
36	286.0
37	417.0
38	735.0
39	1758.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	8.725	24.349999999999998	52.349999999999994	14.575
2	24.680210684725356	26.21018309505894	17.63230499122147	31.477301228994232
3	26.224999999999998	21.55	22.400000000000002	29.825000000000003
4	34.449999999999996	26.75	14.000000000000002	24.8
5	21.875	41.65	26.125	10.35
6	35.775	15.8	34.599999999999994	13.825000000000001
7	15.6	20.674999999999997	23.474999999999998	40.25
8	24.425	27.85	14.825	32.9
9	21.9	33.6	28.475	16.025
10	19.575	24.15	28.349999999999998	27.925
11	29.075	10.775	18.25	41.9
12	15.775	17.65	32.15	34.425
13	34.375	17.275	31.324999999999996	17.025000000000002
14	31.525	31.374999999999996	21.5	15.6
15	36.5	24.099999999999998	26.224999999999998	13.175
16	18.25	18.3	22.375	41.075
17	22.900000000000002	22.2	41.449999999999996	13.450000000000001
18	24.85	17.849999999999998	29.075	28.225
19	35.625	13.675	31.45	19.25
20	43.2	15.024999999999999	28.249999999999996	13.525
21	22.75	19.975	28.775000000000002	28.499999999999996
22	28.825	12.975	47.9	10.299999999999999
23	27.800000000000004	12.15	44.65	15.4
24	53.425	13.225000000000001	25.074999999999996	8.275
25	52.225	25.624999999999996	13.725000000000001	8.425
26	28.4	48.65	12.85	10.100000000000001
27	15.525	48.0	24.375	12.1
28	11.0	24.45	49.475	15.075
29	10.325	12.15	56.45	21.075
30	9.25	6.0249999999999995	38.2	46.525
31	13.925	4.75	45.125	36.199999999999996
32	29.275000000000002	5.325	22.35	43.05
33	56.25	7.025	12.075	24.65
34	63.925	7.425	14.825	13.825000000000001
35	64.3	6.925000000000001	19.650000000000002	9.125
36	42.875	7.124999999999999	37.35	12.65
37	44.0	9.2	20.575	26.224999999999998
38	23.25	14.825	12.375	49.55
39	14.799999999999999	24.55	9.65	51.0
40	14.85	49.9	10.100000000000001	25.15
41	25.924999999999997	48.825	8.725	16.525000000000002
42	49.625	29.925	11.225	9.225
43	51.87500000000001	29.825000000000003	7.95	10.35
44	30.625000000000004	48.525	7.3	13.55
45	17.175	49.25	13.850000000000001	19.725
46	12.7	25.6	19.5	42.199999999999996
47	7.55	14.725	38.3	39.425
48	9.625	12.425	20.825	57.125
49	11.975	21.4	14.000000000000002	52.625
50	18.875	37.025000000000006	14.025000000000002	30.075000000000003
>>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	0.5
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	0.5
26	1.0
27	1.5
28	2.0
29	2.5
30	3.0
31	7.5
32	12.0
33	10.0
34	8.0
35	14.0
36	20.0
37	18.0
38	16.0
39	20.5
40	25.0
41	31.0
42	37.0
43	76.0
44	115.0
45	165.5
46	216.0
47	333.5
48	451.0
49	581.5
50	712.0
51	796.0
52	880.0
53	649.5
54	419.0
55	457.5
56	496.0
57	351.0
58	206.0
59	132.5
60	59.0
61	46.5
62	34.0
63	82.5
64	131.0
65	84.5
66	38.0
67	27.0
68	16.0
69	19.0
70	22.0
71	45.5
72	69.0
73	36.5
74	4.0
75	4.0
76	4.0
77	2.5
78	1.0
79	1.5
80	2.0
81	1.0
82	0.0
83	0.0
84	0.0
85	0.0
86	0.0
87	0.0
88	0.0
89	0.0
90	0.0
91	0.0
92	0.0
93	0.0
94	0.0
95	0.0
96	0.0
97	0.0
98	0.0
99	0.0
100	0.0
>>END_MODULE
>>Per base N content	pass
#Base	N-Count
1	0.0
2	0.325
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	34.775
#Duplication Level	Percentage of deduplicated	Percentage of total
1	75.19769949676491	26.150000000000002
2	9.489575844716033	6.6000000000000005
3	3.8102084831056793	3.975
4	2.7318475916606757	3.8
5	1.3659237958303379	2.375
6	0.9345794392523363	1.95
7	0.9345794392523363	2.275
8	0.5751258087706687	1.6
9	0.503235082674335	1.575
>10	3.7383177570093453	24.925
>50	0.35945363048166784	8.799999999999999
>100	0.35945363048166784	15.975
>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
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	165	4.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	124	3.1	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	122	3.05	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	120	3.0	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	108	2.7	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	89	2.225	RNA PCR Primer, Index 1 (100% over 30bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	84	2.1	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	67	1.675	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	57	1.425	No Hit
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	55	1.375	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	48	1.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	44	1.0999999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	36	0.8999999999999999	RNA PCR Primer, Index 1 (100% over 29bp)
GGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	36	0.8999999999999999	No Hit
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	34	0.8500000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	31	0.775	RNA PCR Primer, Index 1 (100% over 26bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	30	0.75	No Hit
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAT	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 35bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	27	0.675	RNA PCR Primer, Index 1 (100% over 28bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATTCCTATCTCGTATGC	26	0.65	RNA PCR Primer, Index 27 (100% over 50bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	25	0.625	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)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	23	0.575	RNA PCR Primer, Index 1 (100% over 27bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 29bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATTCCTATCTC	21	0.525	RNA PCR Primer, Index 27 (100% over 44bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	19	0.475	No Hit
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	19	0.475	RNA PCR Primer, Index 1 (100% over 26bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 33bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 26bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 29bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	16	0.4	No Hit
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	16	0.4	RNA PCR Primer, Index 1 (100% over 30bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGCTGGAATTCTCGGGTGCC	16	0.4	No Hit
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	15	0.375	No Hit
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTATGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	12	0.3	RNA PCR Primer, Index 1 (100% over 30bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	12	0.3	No Hit
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 30bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	11	0.27499999999999997	No Hit
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	11	0.27499999999999997	No Hit
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	10	0.25	No Hit
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTACACTCTCAGCTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 31bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCAATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	7	0.17500000000000002	No Hit
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
CGCACGGGGTCGGCGGCGATGTCGGCTGGAATTCTCGGGTGCCAAGGAAC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 24bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
CATTATTACTTTTGGTACGCGTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
CAAGGGTTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATTCCT	7	0.17500000000000002	RNA PCR Primer, Index 27 (100% over 39bp)
TGAGATGAAGCACTGTAGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
ACTAATCCTAGCCCTAGCCCTACACTGGAATTCTCGGGTGCCAAGGAACT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 25bp)
TCTCCCAACCCTTGTACCAGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGATTGTATAGTTATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
CATCATCGTCTCAAATGAGTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCC	6	0.15	No Hit
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
CACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAAT	6	0.15	No Hit
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TTTGGCAATGGTAGAACTCACACCGTGGAATTCTCGGGTGCCAAGGAACT	6	0.15	RNA PCR Primer, Index 1 (100% over 25bp)
TGTAAACATCCTCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAAGTTGTATTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGAATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCCAGGAACTCCAGTCACAT	5	0.125	RNA PCR Primer, Index 1 (97% over 35bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TTATAAAGCAATGAGACTGATTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCT	5	0.125	No Hit
CATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATTCCTATCTCGTAT	5	0.125	RNA PCR Primer, Index 27 (100% over 48bp)
TATTGCACTTGTCCCGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGGAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CAGGATCACAGAAAAAGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	5	0.125	RNA PCR Primer, Index 1 (100% over 33bp)
TAGCACCATCTGAAATCGGTTATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ACTAATCCTAGCCCTAGCCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
CACCCGTAGAACCGACCTTGCGATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
AAGGGATTCTGATGTTGGTCACATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TAAGGCACGCGGTGAATGCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
AGCTACATCTGGCTACTGGGTCTCTTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCTGGAATT	5	0.125	No Hit
CTAGACTGAGGCTCCTTGAGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
>>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	0.725	0.0	0.0	0.0
2	0.0	0.725	0.0	0.0	0.0
3	0.0	0.975	0.0	0.0	0.0
4	0.0	1.075	0.0	0.0	0.0
5	0.0	1.125	0.0	0.0	0.0
6	0.0	1.2	0.0	0.0	0.0
7	0.0	1.875	0.0	0.0	0.0
8	0.0	2.05	0.0	0.0	0.0
9	0.0	2.125	0.0	0.0	0.0
10	0.0	2.3	0.0	0.0	0.0
11	0.0	2.55	0.0	0.0	0.0
12	0.0	2.9	0.0	0.0	0.0
13	0.0	3.1	0.0	0.0	0.0
14	0.0	3.375	0.0	0.0	0.0
15	0.0	3.75	0.0	0.0	0.0
16	0.0	4.825	0.0	0.0	0.0
17	0.0	5.45	0.0	0.0	0.0
18	0.0	6.5	0.0	0.0	0.0
19	0.0	6.8	0.0	0.0	0.0
20	0.0	7.775	0.0	0.0	0.0
21	0.0	13.275	0.0	0.0	0.0
22	0.0	26.375	0.0	0.0	0.0
23	0.0	56.3	0.0	0.0	0.0
24	0.0	70.125	0.0	0.0	0.0
25	0.0	75.925	0.0	0.0	0.0
26	0.0	77.45	0.0	0.0	0.0
27	0.0	78.05	0.0	0.0	0.0
28	0.0	78.575	0.0	0.0	0.0
29	0.0	79.2	0.0	0.0	0.0
30	0.0	79.725	0.0	0.0	0.0
31	0.0	80.525	0.0	0.0	0.0
32	0.0	82.1	0.0	0.0	0.0
33	0.0	82.825	0.0	0.0	0.0
34	0.0	85.65	0.0	0.0	0.0
35	0.0	86.475	0.0	0.0	0.0
36	0.0	87.175	0.0	0.0	0.0
37	0.0	88.0	0.0	0.0	0.0
38	0.0	88.575	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
CTTTTGG	20	6.952051E-4	44.000004	18
ATCCTCG	20	6.952051E-4	44.000004	8
TCCTCGA	20	6.952051E-4	44.000004	9
TCGACTG	20	6.952051E-4	44.000004	12
CATCCTC	20	6.952051E-4	44.000004	7
CTCTTTT	20	6.952051E-4	44.000004	16
CCTCGAC	20	6.952051E-4	44.000004	10
GAGCTTG	45	2.728484E-10	44.000004	13
GGATCCG	45	2.728484E-10	44.000004	3
CCGTCTG	45	2.728484E-10	44.000004	7
TCGGATC	45	2.728484E-10	44.000004	1
CGGATCC	45	2.728484E-10	44.000004	2
GTGAGTT	20	6.952051E-4	44.000004	18
CTTGGCT	20	6.952051E-4	44.000004	16
GATCCGT	45	2.728484E-10	44.000004	4
TCCGTCT	45	2.728484E-10	44.000004	6
ATCCGTC	45	2.728484E-10	44.000004	5
TCTTTTG	20	6.952051E-4	44.000004	17
TGAGCTT	45	2.728484E-10	44.000004	12
CGTCTGA	45	2.728484E-10	44.000004	8
>>END_MODULE
Read 226230 spots for SRR5031007.sra
Written 226230 spots for SRR5031007.sra
Read 226230 spots for SRR5031007.sra
Written 226230 spots for SRR5031007.sra
Read 226230 spots for SRR5031007.sra
Written 226230 spots for SRR5031007.sra
Read 226230 spots for SRR5031007.sra
Written 226230 spots for SRR5031007.sra
Read 226230 spots for SRR5031007.sra
Written 226230 spots for SRR5031007.sra
Read 226230 spots for SRR5031007.sra
Written 226230 spots for SRR5031007.sra
Read 226230 spots for SRR5031007.sra
Written 226230 spots for SRR5031007.sra
Read 226230 spots for SRR5031007.sra
Written 226230 spots for SRR5031007.sra
Read 226230 spots for SRR5031007.sra
Written 226230 spots for SRR5031007.sra
Read 226230 spots for SRR5031007.sra
Written 226230 spots for SRR5031007.sra
Read 226241 spots for SRR5031007.sra
Written 226241 spots for SRR5031007.sra
Read 226230 spots for SRR5031007.sra
Written 226230 spots for SRR5031007.sra
SRR ids: ['SRR5031007.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd___ic0i1e
SRR5031007.sra spots: 2714771
blocks: [[1, 226230], [226231, 452460], [452461, 678690], [678691, 904920], [904921, 1131150], [1131151, 1357380], [1357381, 1583610], [1583611, 1809840], [1809841, 2036070], [2036071, 2262300], [2262301, 2488530], [2488531, 2714771]]
SRR5031007 file size 469462
SRR5031007 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031007 SRR5031007_1.fastq
Input file:	SRR5031007_1.fastq
trimmed:	SRR5031007-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 07:05:11 2020 >> started

Wed Mar  4 07:05:14 2020 >> done (3.044s)
2714771 reads processed; of these:
    290 ( 0.01%) short reads filtered out after trimming by size control
      7 ( 0.00%) empty reads filtered out after trimming by size control
2714474 (99.99%) reads available; of these:
 146678 ( 5.40%) trimmed reads available after processing
2567796 (94.60%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     74	  0.00%
 19	     72	  0.00%
 20	    157	  0.01%
 21	    222	  0.01%
 22	    397	  0.01%
 23	    388	  0.01%
 24	    418	  0.02%
 25	    521	  0.02%
 26	    459	  0.02%
 27	    588	  0.02%
 28	    710	  0.03%
 29	   1058	  0.04%
 30	    788	  0.03%
 31	    784	  0.03%
 32	    901	  0.03%
 33	   1162	  0.04%
 34	   1319	  0.05%
 35	   2397	  0.09%
 36	   2106	  0.08%
 37	   2416	  0.09%
 38	   2362	  0.09%
 39	   2530	  0.09%
 40	   2752	  0.10%
 41	   3039	  0.11%
 42	   4260	  0.16%
 43	   6134	  0.23%
 44	   8619	  0.32%
 45	  10167	  0.37%
 46	  13759	  0.51%
 47	  16835	  0.62%
 48	  27153	  1.00%
 49	  32131	  1.18%
 50	2567796	 94.60%
2714474 reads passed initial QC


criterion=sequence-density
sequence-density=87.45
sequence-density-rank=1
fanout-score=20.64
fanout-score-rank=1
prefix-density=88.81
prefix-fanout=20.3
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATTCCTATCTCGTATGCC


criterion=fanout-score
sequence-density=87.45
sequence-density-rank=1
fanout-score=20.64
fanout-score-rank=1
prefix-density=88.81
prefix-fanout=20.3
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 SRR5031007 -
Input file:	STDIN
trimmed:	SRR5031007-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 07:05:33 2020 >> started

Wed Mar  4 07:05:40 2020 >> done (6.658s)
2652782 reads processed; of these:
 160620 ( 6.05%) short reads filtered out after trimming by size control
  23000 ( 0.87%) empty reads filtered out after trimming by size control
2469162 (93.08%) reads available; of these:
2360701 (95.61%) trimmed reads available after processing
 108461 ( 4.39%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  12660	  0.51%
 19	  28180	  1.14%
 20	 146134	  5.92%
 21	 336318	 13.62%
 22	 789023	 31.96%
 23	 360776	 14.61%
 24	 172558	  6.99%
 25	  41943	  1.70%
 26	  21097	  0.85%
 27	  16562	  0.67%
 28	  17125	  0.69%
 29	  12922	  0.52%
 30	  20592	  0.83%
 31	  38219	  1.55%
 32	  24832	  1.01%
 33	  70520	  2.86%
 34	  23646	  0.96%
 35	  19418	  0.79%
 36	  23114	  0.94%
 37	  11939	  0.48%
 38	  12921	  0.52%
 39	  12378	  0.50%
 40	  19352	  0.78%
 41	  25434	  1.03%
 42	  30891	  1.25%
 43	  21826	  0.88%
 44	  15727	  0.64%
 45	  21423	  0.87%
 46	  15978	  0.65%
 47	  11614	  0.47%
 48	   1110	  0.04%
 49	   2020	  0.08%
 50	  90910	  3.68%


criterion=sequence-density
sequence-density=6.50
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=18
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.02
sequence-density-rank=38
fanout-score=88.84
fanout-score-rank=1
prefix-density=1.99
prefix-fanout=1.0
sequence=ATTGTATAGTTTAACAGTCTACAGCCATGGTCGT
                                 Started job on |	Mar 04 07:06:08
                             Started mapping on |	Mar 04 07:06:09
                                    Finished on |	Mar 04 07:06:34
       Mapping speed, Million of reads per hour |	364.44

                          Number of input reads |	2530854
                      Average input read length |	26
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1360655
                        Uniquely mapped reads % |	53.76%
                          Average mapped length |	24.30
                       Number of splices: Total |	1293
            Number of splices: Annotated (sjdb) |	271
                       Number of splices: GT/AG |	1213
                       Number of splices: GC/AG |	17
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	63
                      Mismatch rate per base, % |	0.18%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.84
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.11
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	863536
             % of reads mapped to multiple loci |	34.12%
        Number of reads mapped to too many loci |	49330
             % of reads mapped to too many loci |	1.95%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	9.52%
                     % of reads unmapped: other |	0.65%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	306663	306663	306663
N_multimapping	863536	863536	863536
N_noFeature	78865	92719	937740
N_ambiguous	747876	376710	13074
UnstrandedReadsAssigned:533914 PositiveStrandReadsAssigned:891226 NegativeStrandReadsAssigned:409841
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=21 echo kmer=19
SRR5031007 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: SRR5031007-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,530,854 reads, 645,577 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 800 rounds

 109283 SRR5031007.ke.tsv
  52636 SRR5031007.se.tsv
 161919 total
==> SRR5031007.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

==> SRR5031007.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	1
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031007 completed mapping pipeline successfully
