Starting /dee2/code/volunteer_pipeline.sh SRR5030944
    current disk space = 160605470720
    free memory = 73945652 
SRR5030944 SRAfilesize
390cbd5e3bdec61e1bc7365461a181db  SRR5030944.sra
SRR5030944.sra file validated
SRR5030944 is single end
SRR5030944 is conventional basespace
SRR5030944 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030944_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	32.49225	34.0	31.0	34.0	31.0	34.0
2	32.7345	34.0	31.0	34.0	31.0	34.0
3	32.8945	34.0	31.0	34.0	31.0	34.0
4	36.3155	37.0	37.0	37.0	35.0	37.0
5	36.3215	37.0	37.0	37.0	35.0	37.0
6	36.19525	37.0	37.0	37.0	35.0	37.0
7	36.1435	37.0	36.0	37.0	35.0	37.0
8	36.26525	37.0	37.0	37.0	35.0	37.0
9	38.03575	39.0	38.0	39.0	35.0	39.0
10	38.06	39.0	39.0	39.0	35.0	39.0
11	37.89175	39.0	38.0	39.0	35.0	39.0
12	37.95725	39.0	38.0	39.0	35.0	39.0
13	37.87175	39.0	38.0	39.0	35.0	39.0
14	39.33075	41.0	39.0	41.0	36.0	41.0
15	39.3505	41.0	39.0	41.0	36.0	41.0
16	39.3105	41.0	39.0	41.0	36.0	41.0
17	39.50275	41.0	39.0	41.0	36.0	41.0
18	39.432	41.0	39.0	41.0	36.0	41.0
19	39.239	41.0	39.0	41.0	36.0	41.0
20	39.155	41.0	39.0	41.0	35.0	41.0
21	39.23925	40.0	39.0	41.0	36.0	41.0
22	39.10275	41.0	39.0	41.0	36.0	41.0
23	39.027	41.0	39.0	41.0	35.0	41.0
24	38.82975	40.0	38.0	41.0	34.0	41.0
25	39.14075	41.0	39.0	41.0	36.0	41.0
26	39.18125	41.0	39.0	41.0	36.0	41.0
27	39.2135	41.0	39.0	41.0	36.0	41.0
28	38.9775	41.0	39.0	41.0	35.0	41.0
29	38.15775	40.0	38.0	41.0	33.0	41.0
30	38.3925	40.0	38.0	41.0	34.0	41.0
31	38.71775	40.0	38.0	41.0	34.0	41.0
32	39.021	40.0	39.0	41.0	35.0	41.0
33	38.20775	40.0	38.0	41.0	33.0	41.0
34	38.006	40.0	38.0	41.0	33.0	41.0
35	37.459	39.0	37.0	40.0	32.0	41.0
36	34.356	38.0	31.0	40.0	23.0	41.0
37	35.18925	38.0	33.0	40.0	26.0	41.0
38	36.82175	39.0	36.0	40.0	31.0	41.0
39	36.3995	39.0	36.0	40.0	30.0	41.0
40	36.7005	39.0	36.0	40.0	30.0	41.0
41	36.8555	39.0	37.0	40.0	31.0	41.0
42	37.0925	40.0	37.0	40.0	31.0	41.0
43	36.8875	40.0	37.0	41.0	31.0	41.0
44	36.85025	39.0	37.0	41.0	31.0	41.0
45	36.40525	39.0	36.0	41.0	30.0	41.0
46	34.81075	38.0	34.0	40.0	24.0	41.0
47	35.559	39.0	35.0	40.0	28.0	41.0
48	35.83	39.0	36.0	40.0	30.0	41.0
49	35.0435	39.0	35.0	40.0	27.0	41.0
50	30.27225	34.0	27.0	38.0	2.0	40.0
>>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	0.0
17	1.0
18	1.0
19	2.0
20	2.0
21	5.0
22	5.0
23	13.0
24	11.0
25	17.0
26	26.0
27	23.0
28	35.0
29	38.0
30	59.0
31	68.0
32	92.0
33	104.0
34	154.0
35	191.0
36	279.0
37	528.0
38	1085.0
39	1260.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	12.283780396089245	23.364251692153424	48.68388067184758	15.668087239909752
2	21.85	25.424999999999997	20.3	32.425
3	26.174999999999997	16.0	23.125	34.699999999999996
4	33.925	28.675	14.099999999999998	23.3
5	19.475	41.825	23.25	15.45
6	27.025	18.55	40.625	13.8
7	20.025000000000002	19.55	21.9	38.525
8	22.25	30.8	15.325	31.624999999999996
9	27.175	30.4	27.55	14.875
10	24.725	17.9	33.15	24.224999999999998
11	29.225	16.675	14.85	39.25
12	14.625	21.05	34.025	30.3
13	29.125	19.725	29.075	22.075
14	25.124999999999996	34.150000000000006	20.724999999999998	20.0
15	35.699999999999996	23.5	24.275	16.525000000000002
16	16.625	22.55	21.95	38.875
17	23.95	21.099999999999998	39.425	15.525
18	22.25	17.0	36.425000000000004	24.325
19	38.15	15.1	29.075	17.675
20	42.075	17.4	24.575	15.950000000000001
21	24.6	20.375	25.374999999999996	29.65
22	28.199999999999996	15.625	45.2	10.975
23	26.700000000000003	14.475	41.9	16.925
24	46.975	18.425	24.425	10.174999999999999
25	45.275	25.05	16.150000000000002	13.525
26	25.55	43.675000000000004	17.150000000000002	13.625000000000002
27	18.05	43.05	25.7	13.200000000000001
28	14.000000000000002	23.925	45.375	16.7
29	12.1	15.125	54.15	18.625
30	11.55	8.875	33.1	46.475
31	17.299999999999997	7.375	45.175	30.15
32	28.775000000000002	9.45	20.200000000000003	41.575
33	52.2	10.674999999999999	14.774999999999999	22.35
34	55.60000000000001	10.2	18.325	15.875
35	60.175	8.5	18.95	12.375
36	40.775	10.6	33.650000000000006	14.975
37	44.224999999999994	12.025	19.15	24.6
38	22.325	18.4	14.000000000000002	45.275
39	17.45	26.55	10.025	45.975
40	17.775	46.150000000000006	13.200000000000001	22.875
41	26.625	44.75	10.8	17.825
42	47.325	30.025000000000002	12.25	10.4
43	45.625	32.65	11.700000000000001	10.025
44	27.474999999999998	47.625	8.475000000000001	16.425
45	18.7	47.199999999999996	15.950000000000001	18.15
46	13.025	27.175	19.25	40.550000000000004
47	10.25	17.4	38.3	34.050000000000004
48	11.774999999999999	15.7	18.975	53.55
49	16.35	21.6	15.375	46.675
50	19.975	35.575	15.049999999999999	29.4
>>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	0.5
14	1.0
15	2.0
16	3.0
17	2.0
18	1.0
19	1.0
20	1.0
21	0.5
22	0.0
23	0.0
24	0.0
25	0.0
26	0.0
27	1.5
28	3.0
29	4.5
30	6.0
31	18.0
32	30.0
33	33.0
34	36.0
35	47.5
36	59.0
37	66.0
38	73.0
39	71.0
40	69.0
41	65.0
42	61.0
43	101.5
44	142.0
45	160.5
46	179.0
47	283.0
48	387.0
49	486.5
50	586.0
51	654.0
52	722.0
53	575.0
54	428.0
55	499.5
56	571.0
57	452.0
58	333.0
59	212.0
60	91.0
61	65.5
62	40.0
63	67.0
64	94.0
65	61.5
66	29.0
67	20.0
68	11.0
69	10.5
70	10.0
71	13.5
72	17.0
73	12.0
74	7.0
75	5.0
76	3.0
77	3.0
78	3.0
79	3.0
80	3.0
81	2.0
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	0.27499999999999997
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	42.4
#Duplication Level	Percentage of deduplicated	Percentage of total
1	75.4127358490566	31.974999999999998
2	10.25943396226415	8.7
3	4.068396226415095	5.175
4	2.8301886792452833	4.8
5	1.1202830188679245	2.375
6	1.2971698113207548	3.3000000000000003
7	0.589622641509434	1.7500000000000002
8	0.589622641509434	2.0
9	0.41273584905660377	1.575
>10	2.94811320754717	21.675
>50	0.3537735849056604	10.325
>100	0.1179245283018868	6.35
>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
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	150	3.75	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	104	2.6	RNA PCR Primer, Index 1 (100% over 30bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	87	2.175	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	81	2.025	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	67	1.675	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	64	1.6	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	57	1.425	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	57	1.425	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	46	1.15	No Hit
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	45	1.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	35	0.8750000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 33bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCATCTC	26	0.65	RNA PCR Primer, Index 14 (100% over 44bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	25	0.625	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	25	0.625	RNA PCR Primer, Index 1 (100% over 26bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	24	0.6	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	24	0.6	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	23	0.575	RNA PCR Primer, Index 1 (100% over 28bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAG	23	0.575	RNA PCR Primer, Index 2 (97% over 35bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	20	0.5	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	19	0.475	RNA PCR Primer, Index 1 (100% over 26bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 29bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 30bp)
TGAACTGATGATATCATTTCTTTCCCCGTCAGATCGACCCTGTTGATCTC	18	0.44999999999999996	No Hit
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 30bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 29bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	16	0.4	RNA PCR Primer, Index 1 (100% over 27bp)
GCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCA	16	0.4	RNA PCR Primer, Index 1 (100% over 32bp)
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	16	0.4	No Hit
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (96% over 28bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
GGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	15	0.375	No Hit
TACCCTGTAGATCCGAATTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	14	0.35000000000000003	No Hit
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	13	0.325	No Hit
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCATCTCGTATGC	13	0.325	RNA PCR Primer, Index 14 (100% over 50bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
GGTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCG	12	0.3	No Hit
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
GACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGCT	11	0.27499999999999997	No Hit
TTCCCTTTGTCATCCTATGCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTTGTCCCGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
CATTATTACTTTTGGTACGCGTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	10	0.25	RNA PCR Primer, Index 1 (100% over 30bp)
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
GTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCGG	10	0.25	No Hit
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	9	0.22499999999999998	No Hit
TACCCTGTAGAACCGAATTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
GCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAATTC	9	0.22499999999999998	No Hit
AGCCCATGATGGTATGAGAGTAGTGGACAGAAGGGATTTCTGAAAAACAC	9	0.22499999999999998	No Hit
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
AACCCGTAGATCCGAACTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (96% over 28bp)
TGCTGTGATGAGATGACTAAGTAGGAAGTGCCGTCAGAGTCGATAACTGA	8	0.2	No Hit
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
GTAAATGATGAGATTCCATTGGTCCGTGTTTCTGAACTACATGATTTTCC	8	0.2	No Hit
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGAAATCAAA	8	0.2	No Hit
ACTAATCCTAGCCCTAGCCCTACACTGGAATTCTCGGGTGCCAAGGAACT	8	0.2	RNA PCR Primer, Index 1 (100% over 25bp)
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
AACCCGTAGATCCGAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
GCATGTGATGACATTATTTAGCGACCAAAGTCTGATAAAGATGATTGTGA	7	0.17500000000000002	No Hit
CACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGT	7	0.17500000000000002	No Hit
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
CACCCTGATGAACTGAATACCGCCCCAGTCTGATAGCTGTGGAGAAAGGT	7	0.17500000000000002	No Hit
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTTGGAATTCTCGGGTGCCA	7	0.17500000000000002	No Hit
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 31bp)
CATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCATCTCGTAT	7	0.17500000000000002	RNA PCR Primer, Index 14 (100% over 48bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCTGGAATTCTCGGGTGC	7	0.17500000000000002	No Hit
GGTTAATTCCGATAACGAACGAGACTCTGGCATGCTAACTAGTTACGCGA	6	0.15	No Hit
TGTAAACATCCTACACTCTCAGCTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
ATCGATGTGGTGCTCCGGAGTTCTCTTCGGGCCAGGGCCTAAGCCGCGCC	6	0.15	No Hit
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAC	6	0.15	No Hit
TGAGATGAAGCACTGTAGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	6	0.15	No Hit
GACACAAGGGTTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAG	6	0.15	RNA PCR Primer, Index 2 (97% over 35bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (96% over 28bp)
ACTAATCCTAGCCCTAGCCCTACACAAATATAATTATACTATTATATGGA	6	0.15	No Hit
TCGGATCCGTCTGAGCTTGGCAATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATTCAGGATAGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGC	6	0.15	RNA PCR Primer, Index 1 (96% over 29bp)
TTGCAATGATGACTTATATATCTGTCAATCCCCTGAGAGATCACTGACGA	6	0.15	No Hit
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTATGG	6	0.15	No Hit
TGCGGGGCTAGGGCTAACAGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
GTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAAT	6	0.15	No Hit
AAGGGATTCTGATGTTGGTCACACTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGTGGAATTCTCGGGTGCC	5	0.125	No Hit
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
TCGGATCCGTCTGAGCTTGGCTTTTTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
CACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACA	5	0.125	RNA PCR Primer, Index 1 (100% over 34bp)
TTCACAGTGGCTAAGTTCTGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ACTAATCCTAGCCCTAGCCCTACACAAATATAATTATACTATTATGGAAT	5	0.125	No Hit
ACTAATCCTAGCCCTAGCCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
CTAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGGAATTCTCGGGTGCCAA	5	0.125	No Hit
CTGCAGTGATGACTATCTTAGGACACCTTTGGATTTACCGTGAAAAGAAG	5	0.125	No Hit
ATTCTGTGATGACTTTACCAAATGACTTTCGTTCTTCTGAGTTTGCTGAA	5	0.125	No Hit
CACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATT	5	0.125	No Hit
TCCCTGAGACCCTAACTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CGCACGGGGTCGGCGGCGATGTCGGCTGGAATTCTCGGGTGCCAAGGAAC	5	0.125	RNA PCR Primer, Index 1 (100% over 24bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	5	0.125	No Hit
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
>>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	0.55	0.0	0.0	0.0
4	0.0	0.6	0.0	0.0	0.0
5	0.0	0.625	0.0	0.0	0.0
6	0.0	0.675	0.0	0.0	0.0
7	0.0	1.45	0.0	0.0	0.0
8	0.0	1.5	0.0	0.0	0.0
9	0.0	1.6	0.0	0.0	0.0
10	0.0	1.675	0.0	0.0	0.0
11	0.0	1.9	0.0	0.0	0.0
12	0.0	2.05	0.0	0.0	0.0
13	0.0	2.225	0.0	0.0	0.0
14	0.0	2.45	0.0	0.0	0.0
15	0.0	2.925	0.0	0.0	0.0
16	0.0	4.3	0.0	0.0	0.0
17	0.0	5.05	0.0	0.0	0.0
18	0.0	6.4	0.0	0.0	0.0
19	0.0	7.2	0.0	0.0	0.0
20	0.0	8.05	0.0	0.0	0.0
21	0.0	14.675	0.0	0.0	0.0
22	0.0	24.875	0.0	0.0	0.0
23	0.0	51.575	0.0	0.0	0.0
24	0.0	61.6	0.0	0.0	0.0
25	0.0	67.425	0.0	0.0	0.0
26	0.0	68.975	0.0	0.0	0.0
27	0.0	69.675	0.0	0.0	0.0
28	0.0	70.325	0.0	0.0	0.0
29	0.0	70.875	0.0	0.0	0.0
30	0.0	71.275	0.0	0.0	0.0
31	0.0	72.0	0.0	0.0	0.0
32	0.0	73.2	0.0	0.0	0.0
33	0.0	73.95	0.0	0.0	0.0
34	0.0	75.925	0.0	0.0	0.0
35	0.0	76.925	0.0	0.0	0.0
36	0.0	77.725	0.0	0.0	0.0
37	0.0	78.35	0.0	0.0	0.0
38	0.0	78.95	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TGAGACC	40	5.315087E-9	44.000004	5
ACTGTTG	20	6.952051E-4	44.000004	18
AACGCTG	20	6.952051E-4	44.000004	8
GTTGAAG	20	6.952051E-4	44.000004	10
AAGTAAT	20	6.952051E-4	44.000004	4
TCAAGTA	20	6.952051E-4	44.000004	2
ACGCTGT	20	6.952051E-4	44.000004	9
AATCCAG	20	6.952051E-4	44.000004	8
CAGTTGA	20	6.952051E-4	44.000004	8
CTGAGAC	40	5.315087E-9	44.000004	4
TAAACAT	20	6.952051E-4	44.000004	3
ATCCAGG	20	6.952051E-4	44.000004	9
CCAGTTG	20	6.952051E-4	44.000004	7
AAACATC	20	6.952051E-4	44.000004	4
AACTGTT	20	6.952051E-4	44.000004	17
TTCAAGT	20	6.952051E-4	44.000004	1
TTCAACG	20	6.952051E-4	44.000004	5
AGGATAG	20	6.952051E-4	44.000004	13
ATAGGCT	20	6.952051E-4	44.000004	16
GAGCTTG	45	2.728484E-10	44.000004	13
>>END_MODULE
Read 221881 spots for SRR5030944.sra
Written 221881 spots for SRR5030944.sra
Read 221881 spots for SRR5030944.sra
Written 221881 spots for SRR5030944.sra
Read 221881 spots for SRR5030944.sra
Written 221881 spots for SRR5030944.sra
Read 221881 spots for SRR5030944.sra
Written 221881 spots for SRR5030944.sra
Read 221881 spots for SRR5030944.sra
Written 221881 spots for SRR5030944.sra
Read 221881 spots for SRR5030944.sra
Written 221881 spots for SRR5030944.sra
Read 221881 spots for SRR5030944.sra
Written 221881 spots for SRR5030944.sra
Read 221881 spots for SRR5030944.sra
Written 221881 spots for SRR5030944.sra
Read 221883 spots for SRR5030944.sra
Written 221883 spots for SRR5030944.sra
Read 221881 spots for SRR5030944.sra
Written 221881 spots for SRR5030944.sra
Read 221881 spots for SRR5030944.sra
Written 221881 spots for SRR5030944.sra
Read 221881 spots for SRR5030944.sra
Written 221881 spots for SRR5030944.sra
SRR ids: ['SRR5030944.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_tjl5zcgb
SRR5030944.sra spots: 2662574
blocks: [[1, 221881], [221882, 443762], [443763, 665643], [665644, 887524], [887525, 1109405], [1109406, 1331286], [1331287, 1553167], [1553168, 1775048], [1775049, 1996929], [1996930, 2218810], [2218811, 2440691], [2440692, 2662574]]
SRR5030944 file size 460405
SRR5030944 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030944 SRR5030944_1.fastq
Input file:	SRR5030944_1.fastq
trimmed:	SRR5030944-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 06:50:34 2020 >> started

Wed Mar  4 06:50:36 2020 >> done (1.807s)
2662574 reads processed; of these:
    120 ( 0.00%) short reads filtered out after trimming by size control
      8 ( 0.00%) empty reads filtered out after trimming by size control
2662446 (100.00%) reads available; of these:
 154193 ( 5.79%) trimmed reads available after processing
2508253 (94.21%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     34	  0.00%
 19	     48	  0.00%
 20	    107	  0.00%
 21	    126	  0.00%
 22	    222	  0.01%
 23	    249	  0.01%
 24	    317	  0.01%
 25	    385	  0.01%
 26	    328	  0.01%
 27	    460	  0.02%
 28	    594	  0.02%
 29	    774	  0.03%
 30	    640	  0.02%
 31	    798	  0.03%
 32	    835	  0.03%
 33	   1174	  0.04%
 34	   3022	  0.11%
 35	   2608	  0.10%
 36	   1916	  0.07%
 37	   1989	  0.07%
 38	   2339	  0.09%
 39	   2457	  0.09%
 40	   2583	  0.10%
 41	   2913	  0.11%
 42	   3509	  0.13%
 43	   5081	  0.19%
 44	   9209	  0.35%
 45	  10566	  0.40%
 46	   9665	  0.36%
 47	  14395	  0.54%
 48	  28647	  1.08%
 49	  46203	  1.74%
 50	2508253	 94.21%
2662446 reads passed initial QC


criterion=sequence-density
sequence-density=78.38
sequence-density-rank=1
fanout-score=18.67
fanout-score-rank=1
prefix-density=80.54
prefix-fanout=18.2
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCATCTCGTATGCC


criterion=fanout-score
sequence-density=78.38
sequence-density-rank=1
fanout-score=18.67
fanout-score-rank=1
prefix-density=80.54
prefix-fanout=18.2
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCATCTCGTATGCC -o SRR5030944 -
Input file:	STDIN
trimmed:	SRR5030944-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCATCTCGTATGCC
-- 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 06:50:50 2020 >> started

Wed Mar  4 06:50:54 2020 >> done (4.057s)
2595042 reads processed; of these:
 155362 ( 5.99%) short reads filtered out after trimming by size control
  10167 ( 0.39%) empty reads filtered out after trimming by size control
2429513 (93.62%) reads available; of these:
2117508 (87.16%) trimmed reads available after processing
 312005 (12.84%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  27221	  1.12%
 19	  20470	  0.84%
 20	 143925	  5.92%
 21	 268301	 11.04%
 22	 701128	 28.86%
 23	 282830	 11.64%
 24	 149432	  6.15%
 25	  43070	  1.77%
 26	  20335	  0.84%
 27	  15786	  0.65%
 28	  17187	  0.71%
 29	  12746	  0.52%
 30	  18658	  0.77%
 31	  31403	  1.29%
 32	  23753	  0.98%
 33	  60078	  2.47%
 34	  23122	  0.95%
 35	  18912	  0.78%
 36	  19066	  0.78%
 37	  13713	  0.56%
 38	  15036	  0.62%
 39	  15981	  0.66%
 40	  24039	  0.99%
 41	  29387	  1.21%
 42	  33944	  1.40%
 43	  24066	  0.99%
 44	  19852	  0.82%
 45	  27728	  1.14%
 46	  19633	  0.81%
 47	  14850	  0.61%
 48	   3323	  0.14%
 49	  11937	  0.49%
 50	 278601	 11.47%


criterion=sequence-density
sequence-density=5.07
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=11
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.56
sequence-density-rank=24
fanout-score=18.65
fanout-score-rank=1
prefix-density=10.50
prefix-fanout=1.0
sequence=TGAGCTTGGCTTTT
                                 Started job on |	Mar 04 06:51:16
                             Started mapping on |	Mar 04 06:51:17
                                    Finished on |	Mar 04 06:51:39
       Mapping speed, Million of reads per hour |	408.59

                          Number of input reads |	2496917
                      Average input read length |	28
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1549289
                        Uniquely mapped reads % |	62.05%
                          Average mapped length |	27.78
                       Number of splices: Total |	1070
            Number of splices: Annotated (sjdb) |	184
                       Number of splices: GT/AG |	1002
                       Number of splices: GC/AG |	6
                       Number of splices: AT/AC |	1
               Number of splices: Non-canonical |	61
                      Mismatch rate per base, % |	0.19%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.61
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.02
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	657263
             % of reads mapped to multiple loci |	26.32%
        Number of reads mapped to too many loci |	57346
             % of reads mapped to too many loci |	2.30%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	8.36%
                     % of reads unmapped: other |	0.97%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	290365	290365	290365
N_multimapping	657263	657263	657263
N_noFeature	68414	87854	1034326
N_ambiguous	868532	414302	14285
UnstrandedReadsAssigned:612343 PositiveStrandReadsAssigned:1047133 NegativeStrandReadsAssigned:500678
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5030944 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: SRR5030944-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,496,917 reads, 692,264 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,104 rounds

 109283 SRR5030944.ke.tsv
  52636 SRR5030944.se.tsv
 161919 total
==> SRR5030944.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

==> SRR5030944.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030944 completed mapping pipeline successfully
