Starting /dee2/code/volunteer_pipeline.sh SRR5031030
    current disk space = 160545882112
    free memory = 73949320 
SRR5031030 SRAfilesize
7adcfb6492c7cc422a853b0495991ef8  SRR5031030.sra
SRR5031030.sra file validated
SRR5031030 is single end
SRR5031030 is conventional basespace
SRR5031030 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031030_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	53
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	32.3365	33.0	31.0	34.0	31.0	34.0
2	32.52725	34.0	31.0	34.0	31.0	34.0
3	32.62675	34.0	31.0	34.0	31.0	34.0
4	36.18325	37.0	35.0	37.0	35.0	37.0
5	35.896	37.0	35.0	37.0	35.0	37.0
6	35.86325	37.0	35.0	37.0	35.0	37.0
7	36.0075	37.0	35.0	37.0	35.0	37.0
8	35.74675	37.0	35.0	37.0	33.0	37.0
9	37.54475	39.0	37.0	39.0	35.0	39.0
10	37.757	39.0	37.0	39.0	35.0	39.0
11	37.63225	39.0	37.0	39.0	35.0	39.0
12	37.6375	39.0	37.0	39.0	35.0	39.0
13	37.61525	39.0	37.0	39.0	35.0	39.0
14	39.01175	40.0	38.0	41.0	35.0	41.0
15	38.911	40.0	38.0	41.0	35.0	41.0
16	38.96275	40.0	38.0	41.0	35.0	41.0
17	38.88525	40.0	38.0	41.0	35.0	41.0
18	38.99575	40.0	38.0	41.0	35.0	41.0
19	38.567	40.0	38.0	41.0	34.0	41.0
20	38.7815	40.0	38.0	41.0	34.0	41.0
21	38.7815	40.0	38.0	41.0	34.0	41.0
22	38.921	40.0	39.0	41.0	35.0	41.0
23	38.69725	40.0	38.0	41.0	34.0	41.0
24	38.75075	40.0	38.0	41.0	34.0	41.0
25	38.9245	40.0	38.0	41.0	35.0	41.0
26	38.55475	40.0	38.0	41.0	34.0	41.0
27	38.5375	40.0	38.0	41.0	34.0	41.0
28	38.6295	40.0	38.0	41.0	34.0	41.0
29	38.132	40.0	38.0	41.0	33.0	41.0
30	37.99975	40.0	38.0	41.0	32.0	41.0
31	38.391	40.0	38.0	41.0	33.0	41.0
32	38.36025	40.0	38.0	41.0	34.0	41.0
33	38.28725	40.0	38.0	41.0	33.0	41.0
34	38.462	40.0	38.0	41.0	34.0	41.0
35	38.27825	40.0	38.0	41.0	34.0	41.0
36	37.82825	40.0	37.0	41.0	33.0	41.0
37	37.27675	39.0	37.0	41.0	31.0	41.0
38	36.57225	39.0	35.0	40.0	30.0	41.0
39	37.008	39.0	36.0	41.0	31.0	41.0
40	37.41	39.0	37.0	41.0	31.0	41.0
41	37.49675	40.0	37.0	41.0	32.0	41.0
42	37.8535	40.0	37.0	41.0	33.0	41.0
43	38.0535	40.0	37.0	41.0	33.0	41.0
44	37.7535	40.0	37.0	41.0	33.0	41.0
45	37.663	40.0	37.0	41.0	33.0	41.0
46	37.56575	40.0	37.0	41.0	33.0	41.0
47	36.944	40.0	36.0	41.0	31.0	41.0
48	36.62675	39.0	35.0	41.0	31.0	41.0
49	36.6675	39.0	35.0	41.0	31.0	41.0
50	36.038	38.0	35.0	41.0	30.0	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
7	1.0
8	0.0
9	0.0
10	0.0
11	0.0
12	0.0
13	0.0
14	0.0
15	1.0
16	0.0
17	0.0
18	2.0
19	2.0
20	4.0
21	8.0
22	7.0
23	3.0
24	5.0
25	14.0
26	12.0
27	16.0
28	26.0
29	39.0
30	57.0
31	76.0
32	61.0
33	114.0
34	171.0
35	199.0
36	255.0
37	483.0
38	778.0
39	1666.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	11.0	25.6	45.425	17.974999999999998
2	22.785445420326223	28.48180677540778	20.02509410288582	28.707653701380174
3	23.875	15.950000000000001	22.725	37.45
4	36.7	28.249999999999996	13.850000000000001	21.2
5	21.925	36.425000000000004	27.875	13.775
6	28.999999999999996	16.150000000000002	38.375	16.475
7	20.0	19.950000000000003	18.95	41.099999999999994
8	21.075	28.9	18.55	31.474999999999998
9	23.625	32.75	24.575	19.05
10	20.974999999999998	20.200000000000003	29.2	29.625
11	33.375	14.399999999999999	15.525	36.7
12	17.299999999999997	22.175	28.65	31.874999999999996
13	27.85	16.45	34.949999999999996	20.75
14	30.349999999999998	28.425	21.5	19.725
15	34.75	22.400000000000002	27.500000000000004	15.35
16	20.575	19.0	22.525000000000002	37.9
17	27.05	24.525	34.25	14.174999999999999
18	25.5	15.35	31.025000000000002	28.125
19	34.675	14.499999999999998	33.625	17.2
20	43.55	14.875	26.724999999999998	14.85
21	25.6	22.875	21.925	29.599999999999998
22	31.324999999999996	14.424999999999999	43.05	11.200000000000001
23	24.375	13.725000000000001	44.725	17.175
24	49.5	15.0	25.374999999999996	10.125
25	50.425	23.150000000000002	15.625	10.8
26	28.000000000000004	43.1	14.7	14.2
27	16.3	45.324999999999996	22.0	16.375
28	13.125	23.400000000000002	46.125	17.349999999999998
29	15.024999999999999	13.475000000000001	52.175000000000004	19.325
30	10.875	7.5249999999999995	34.125	47.475
31	14.475	5.800000000000001	45.800000000000004	33.925
32	27.275	6.3	24.6	41.825
33	50.824999999999996	10.25	14.374999999999998	24.55
34	58.85	8.3	17.974999999999998	14.875
35	62.8	8.575000000000001	17.65	10.975
36	41.25	10.05	36.0	12.7
37	43.175000000000004	13.0	22.05	21.775
38	25.674999999999997	17.974999999999998	13.775	42.575
39	16.5	22.025	13.65	47.825
40	16.075	44.525	14.35	25.05
41	23.625	46.725	10.6	19.05
42	45.35	28.95	14.249999999999998	11.450000000000001
43	51.9	25.674999999999997	9.575	12.85
44	33.875	43.25	9.925	12.950000000000001
45	20.775	47.675	13.5	18.05
46	17.9	25.3	17.1	39.7
47	11.200000000000001	14.05	38.7	36.05
48	14.299999999999999	11.774999999999999	22.175	51.74999999999999
49	13.675	17.549999999999997	15.0	53.77499999999999
50	19.225	35.55	12.975	32.25
>>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	0.5
14	1.0
15	0.5
16	0.0
17	0.0
18	0.0
19	0.5
20	1.0
21	1.5
22	2.0
23	1.0
24	0.0
25	0.5
26	1.0
27	1.5
28	2.0
29	3.5
30	5.0
31	7.0
32	9.0
33	12.0
34	15.0
35	23.0
36	31.0
37	29.0
38	27.0
39	42.0
40	57.0
41	65.0
42	73.0
43	95.5
44	118.0
45	135.0
46	152.0
47	264.0
48	376.0
49	466.5
50	557.0
51	711.5
52	866.0
53	620.0
54	374.0
55	447.5
56	521.0
57	409.5
58	298.0
59	182.5
60	67.0
61	59.5
62	52.0
63	132.5
64	213.0
65	123.5
66	34.0
67	23.0
68	12.0
69	18.5
70	25.0
71	65.5
72	106.0
73	53.5
74	1.0
75	1.0
76	1.0
77	0.5
78	0.0
79	0.5
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	0.375
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	38.800000000000004
#Duplication Level	Percentage of deduplicated	Percentage of total
1	75.45103092783505	29.275000000000002
2	10.051546391752577	7.8
3	4.574742268041237	5.325
4	2.190721649484536	3.4000000000000004
5	1.2242268041237114	2.375
6	1.2886597938144329	3.0
7	0.7731958762886598	2.1
8	0.5798969072164949	1.7999999999999998
9	0.3865979381443299	1.35
>10	2.899484536082474	20.325
>50	0.3221649484536082	9.45
>100	0.25773195876288657	13.8
>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	165	4.125	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	145	3.6249999999999996	RNA PCR Primer, Index 1 (100% over 27bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	124	3.1	No Hit
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	118	2.9499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	89	2.225	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	84	2.1	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	75	1.875	RNA PCR Primer, Index 1 (100% over 30bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	71	1.775	RNA PCR Primer, Index 1 (100% over 28bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	59	1.4749999999999999	No Hit
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	50	1.25	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	49	1.225	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	41	1.0250000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
GGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	29	0.7250000000000001	No Hit
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCG	25	0.625	RNA PCR Primer, Index 2 (100% over 35bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	25	0.625	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	24	0.6	RNA PCR Primer, Index 1 (100% over 27bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	23	0.575	RNA PCR Primer, Index 1 (100% over 33bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	23	0.575	RNA PCR Primer, Index 1 (100% over 26bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	23	0.575	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	21	0.525	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	19	0.475	RNA PCR Primer, Index 1 (100% over 26bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	18	0.44999999999999996	No Hit
TACCCTGTAGAACCGAATTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	16	0.4	No Hit
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGATGTATCTC	16	0.4	RNA PCR Primer, Index 2 (100% over 44bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	15	0.375	No Hit
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	13	0.325	RNA PCR Primer, Index 1 (100% over 30bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	13	0.325	RNA PCR Primer, Index 1 (100% over 30bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGATGTATCTCGTATGC	12	0.3	RNA PCR Primer, Index 2 (100% over 50bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	12	0.3	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 26bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	11	0.27499999999999997	No Hit
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TACCCTGTAGATCCGAATTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	10	0.25	No Hit
TGAGATGAAGCACTGTAGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	10	0.25	RNA PCR Primer, Index 1 (100% over 30bp)
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	10	0.25	No Hit
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	10	0.25	RNA PCR Primer, Index 1 (100% over 31bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	9	0.22499999999999998	No Hit
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
AGAGGTAGTAGGTTGCATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCTGGAATTCTCGGGTGC	9	0.22499999999999998	No Hit
TATTGCACTTGTCCCGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGT	8	0.2	No Hit
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGGAATTCTCGGGTGCCA	8	0.2	No Hit
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
TGCGGGGCTAGGGCTAACAGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
CCGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGC	8	0.2	No Hit
AACCCGTAGATCCGAACTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
GTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGA	7	0.17500000000000002	RNA PCR Primer, Index 2 (100% over 36bp)
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 25bp)
TCGGATCCGTCTGAGCTTGGCTTTTTGGAATTCTCGGGTGCCAAGGAACT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 25bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	7	0.17500000000000002	No Hit
TGACTTGATGAAAGTACTTTTGAACCCTTTTCCATCTGATGTGGAATTCT	7	0.17500000000000002	No Hit
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTATGG	7	0.17500000000000002	No Hit
TCTCCCAACCCTTGTACCAGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
AACCCGTAGATCCGAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
AACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTTGGAATTCTCGGGTGCCA	6	0.15	No Hit
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGTGGAATTCTCGGGTGCC	6	0.15	No Hit
AGAAATGCGGATATGGGACTGAGATGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
CAAAGAATTCTCCTTTTGGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGGTCTAGTGGTTAGGATTCGGCGCTCTCTGGAATTCTCGGGTGCC	6	0.15	No Hit
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTTGGAATTCTCGGGTGCCA	6	0.15	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGGAATTCTCGGGTGCCAA	6	0.15	No Hit
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TACCCTGTAGAACCGAATTTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	6	0.15	No Hit
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTC	6	0.15	No Hit
TAAGGCACGCGGTGAATGCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	6	0.15	No Hit
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTACAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCT	5	0.125	No Hit
ACGCCCTTCCCCCCCTTCTTCATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGGTAGTTCAATGGTAGAATTCTCGCCTCCCTGGAATTCTCGGGTG	5	0.125	No Hit
AAGCCCTTACCCCAAAAAGCATTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTCACTGGAATTCTCGGGT	5	0.125	No Hit
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCCAGCATCAGTGATTTTGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	5	0.125	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGGAATTCTCGGGTGCCAA	5	0.125	No Hit
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TCCCTGTGGTCTAGTGGTTAGGATTCGGCGCTCTCTGGAATTCTCGGGTG	5	0.125	No Hit
CATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGATGTATCTCGTAT	5	0.125	RNA PCR Primer, Index 2 (100% over 48bp)
TGAGGTAGGAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATGGAATTCTCGGGTGC	5	0.125	No Hit
CTAGACTGAGGCTCCTTGAGGAATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
CATGCTCAATAGGATTACGCTGAGGCCCTGGAATTCTCGGGTGCCAAGGA	5	0.125	RNA PCR Primer, Index 1 (100% over 22bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
>>END_MODULE
>>Adapter Content	fail
#Position	Illumina Universal Adapter	Illumina Small RNA 3' Adapter	Illumina Small RNA 5' Adapter	Nextera Transposase Sequence	SOLID Small RNA Adapter
1	0.0	0.3	0.0	0.0	0.0
2	0.0	0.3	0.0	0.0	0.0
3	0.0	0.425	0.0	0.0	0.0
4	0.0	0.525	0.0	0.0	0.0
5	0.0	0.55	0.0	0.0	0.0
6	0.0	0.675	0.0	0.0	0.0
7	0.0	1.125	0.0	0.0	0.0
8	0.0	1.225	0.0	0.0	0.0
9	0.0	1.3	0.0	0.0	0.0
10	0.0	1.4	0.0	0.0	0.0
11	0.0	1.575	0.0	0.0	0.0
12	0.0	1.725	0.0	0.0	0.0
13	0.0	1.9	0.0	0.0	0.0
14	0.0	2.175	0.0	0.0	0.0
15	0.0	2.75	0.0	0.0	0.0
16	0.0	3.725	0.0	0.0	0.0
17	0.0	4.4	0.0	0.0	0.0
18	0.0	5.525	0.0	0.0	0.0
19	0.0	6.075	0.0	0.0	0.0
20	0.0	7.1	0.0	0.0	0.0
21	0.0	11.625	0.0	0.0	0.0
22	0.0	20.9	0.0	0.0	0.0
23	0.0	47.95	0.0	0.0	0.0
24	0.0	60.95	0.0	0.0	0.0
25	0.0	66.025	0.0	0.0	0.0
26	0.0	67.8	0.0	0.0	0.0
27	0.0	68.45	0.0	0.0	0.0
28	0.0	69.25	0.0	0.0	0.0
29	0.0	69.85	0.0	0.0	0.0
30	0.0	70.375	0.0	0.0	0.0
31	0.0	71.375	0.0	0.0	0.0
32	0.0	73.325	0.0	0.0	0.0
33	0.0	74.825	0.0	0.0	0.0
34	0.0	79.65	0.0	0.0	0.0
35	0.0	81.3	0.0	0.0	0.0
36	0.0	82.675	0.0	0.0	0.0
37	0.0	84.025	0.0	0.0	0.0
38	0.0	84.7	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
GAGGTAG	20	6.952051E-4	44.000004	2
CTGAGCT	45	2.728484E-10	44.000004	11
CCTGTTG	20	6.952051E-4	44.000004	18
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
AACCTGT	20	6.952051E-4	44.000004	16
CGGATCC	45	2.728484E-10	44.000004	2
ACCTGTT	20	6.952051E-4	44.000004	17
GATCCGT	45	2.728484E-10	44.000004	4
GGTAGTA	20	6.952051E-4	44.000004	4
GCTTGGC	45	2.728484E-10	44.000004	15
TGAGGTA	20	6.952051E-4	44.000004	1
TTGGCTT	20	6.952051E-4	44.000004	17
TCCGTCT	45	2.728484E-10	44.000004	6
AGGTAGT	20	6.952051E-4	44.000004	3
ATCCGTC	45	2.728484E-10	44.000004	5
TTAACCT	20	6.952051E-4	44.000004	14
TGAGCTT	45	2.728484E-10	44.000004	12
>>END_MODULE
Read 253563 spots for SRR5031030.sra
Written 253563 spots for SRR5031030.sra
Read 253563 spots for SRR5031030.sra
Written 253563 spots for SRR5031030.sra
Read 253563 spots for SRR5031030.sra
Written 253563 spots for SRR5031030.sra
Read 253563 spots for SRR5031030.sra
Written 253563 spots for SRR5031030.sra
Read 253563 spots for SRR5031030.sra
Written 253563 spots for SRR5031030.sra
Read 253563 spots for SRR5031030.sra
Written 253563 spots for SRR5031030.sra
Read 253563 spots for SRR5031030.sra
Written 253563 spots for SRR5031030.sra
Read 253563 spots for SRR5031030.sra
Written 253563 spots for SRR5031030.sra
Read 253563 spots for SRR5031030.sra
Written 253563 spots for SRR5031030.sra
Read 253563 spots for SRR5031030.sra
Written 253563 spots for SRR5031030.sra
Read 253563 spots for SRR5031030.sra
Written 253563 spots for SRR5031030.sra
Read 253570 spots for SRR5031030.sra
Written 253570 spots for SRR5031030.sra
SRR ids: ['SRR5031030.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_4ne0zpyy
SRR5031030.sra spots: 3042763
blocks: [[1, 253563], [253564, 507126], [507127, 760689], [760690, 1014252], [1014253, 1267815], [1267816, 1521378], [1521379, 1774941], [1774942, 2028504], [2028505, 2282067], [2282068, 2535630], [2535631, 2789193], [2789194, 3042763]]
SRR5031030 file size 526315
SRR5031030 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031030 SRR5031030_1.fastq
Input file:	SRR5031030_1.fastq
trimmed:	SRR5031030-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 07:09:35 2020 >> started

Wed Mar  4 07:09:37 2020 >> done (1.856s)
3042763 reads processed; of these:
    324 ( 0.01%) short reads filtered out after trimming by size control
     13 ( 0.00%) empty reads filtered out after trimming by size control
3042426 (99.99%) reads available; of these:
 161508 ( 5.31%) trimmed reads available after processing
2880918 (94.69%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     94	  0.00%
 19	    102	  0.00%
 20	    160	  0.01%
 21	    252	  0.01%
 22	    349	  0.01%
 23	    431	  0.01%
 24	    480	  0.02%
 25	    659	  0.02%
 26	    517	  0.02%
 27	    610	  0.02%
 28	    654	  0.02%
 29	    973	  0.03%
 30	    689	  0.02%
 31	    823	  0.03%
 32	    903	  0.03%
 33	   1218	  0.04%
 34	   1524	  0.05%
 35	   2962	  0.10%
 36	   2743	  0.09%
 37	   2959	  0.10%
 38	   2845	  0.09%
 39	   2935	  0.10%
 40	   3394	  0.11%
 41	   3327	  0.11%
 42	   4272	  0.14%
 43	   6157	  0.20%
 44	   8418	  0.28%
 45	  10658	  0.35%
 46	  17256	  0.57%
 47	  20208	  0.66%
 48	  30645	  1.01%
 49	  32291	  1.06%
 50	2880918	 94.69%
3042426 reads passed initial QC


criterion=sequence-density
sequence-density=84.49
sequence-density-rank=1
fanout-score=21.99
fanout-score-rank=1
prefix-density=86.87
prefix-fanout=21.4
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGATGTATCTCGTATGCC


criterion=fanout-score
sequence-density=84.49
sequence-density-rank=1
fanout-score=21.99
fanout-score-rank=1
prefix-density=86.87
prefix-fanout=21.4
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGATGTATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGATGTATCTCGTATGCC -o SRR5031030 -
Input file:	STDIN
trimmed:	SRR5031030-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGATGTATCTCGTATGCC
-- 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 07:09:58 2020 >> started

Wed Mar  4 07:10:02 2020 >> done (4.007s)
2970840 reads processed; of these:
 183016 ( 6.16%) short reads filtered out after trimming by size control
  15593 ( 0.52%) empty reads filtered out after trimming by size control
2772231 (93.31%) reads available; of these:
2609136 (94.12%) trimmed reads available after processing
 163095 ( 5.88%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  15781	  0.57%
 19	  27892	  1.01%
 20	 139818	  5.04%
 21	 286687	 10.34%
 22	 778502	 28.08%
 23	 377613	 13.62%
 24	 176225	  6.36%
 25	  50710	  1.83%
 26	  26664	  0.96%
 27	  22216	  0.80%
 28	  24259	  0.88%
 29	  20249	  0.73%
 30	  29007	  1.05%
 31	  56175	  2.03%
 32	  38272	  1.38%
 33	 148508	  5.36%
 34	  47596	  1.72%
 35	  40183	  1.45%
 36	  47293	  1.71%
 37	  20344	  0.73%
 38	  24305	  0.88%
 39	  19152	  0.69%
 40	  27190	  0.98%
 41	  32418	  1.17%
 42	  36470	  1.32%
 43	  26165	  0.94%
 44	  19821	  0.71%
 45	  28720	  1.04%
 46	  21923	  0.79%
 47	  16687	  0.60%
 48	   1428	  0.05%
 49	   1755	  0.06%
 50	 142203	  5.13%


criterion=sequence-density
sequence-density=8.64
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=15
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.48
sequence-density-rank=34
fanout-score=16.98
fanout-score-rank=1
prefix-density=8.05
prefix-fanout=1.0
sequence=TGAGCTTGGCTTTT
                                 Started job on |	Mar 04 07:10:27
                             Started mapping on |	Mar 04 07:10:28
                                    Finished on |	Mar 04 07:10:56
       Mapping speed, Million of reads per hour |	365.63

                          Number of input reads |	2843817
                      Average input read length |	27
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1442711
                        Uniquely mapped reads % |	50.73%
                          Average mapped length |	25.02
                       Number of splices: Total |	2243
            Number of splices: Annotated (sjdb) |	393
                       Number of splices: GT/AG |	2124
                       Number of splices: GC/AG |	33
                       Number of splices: AT/AC |	1
               Number of splices: Non-canonical |	85
                      Mismatch rate per base, % |	0.23%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.77
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.02
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	922675
             % of reads mapped to multiple loci |	32.44%
        Number of reads mapped to too many loci |	82187
             % of reads mapped to too many loci |	2.89%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	12.88%
                     % of reads unmapped: other |	1.05%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	478431	478431	478431
N_multimapping	922675	922675	922675
N_noFeature	97481	118132	968877
N_ambiguous	772684	352378	12977
UnstrandedReadsAssigned:572546 PositiveStrandReadsAssigned:972201 NegativeStrandReadsAssigned:460857
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5031030 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: SRR5031030-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,843,817 reads, 674,611 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,169 rounds

 109283 SRR5031030.ke.tsv
  52636 SRR5031030.se.tsv
 161919 total
==> SRR5031030.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

==> SRR5031030.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031030 completed mapping pipeline successfully
