Starting /dee2/code/volunteer_pipeline.sh SRR5031073
    current disk space = 160501071872
    free memory = 73930900 
SRR5031073 SRAfilesize
9cf7824251088283ff5c8cb2ada3b78d  SRR5031073.sra
SRR5031073.sra file validated
SRR5031073 is single end
SRR5031073 is conventional basespace
SRR5031073 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031073_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	32.354	33.0	31.0	34.0	31.0	34.0
2	32.61325	34.0	31.0	34.0	31.0	34.0
3	32.58025	34.0	31.0	34.0	31.0	34.0
4	36.20075	37.0	35.0	37.0	35.0	37.0
5	35.8435	37.0	35.0	37.0	35.0	37.0
6	35.8145	37.0	35.0	37.0	35.0	37.0
7	35.88775	37.0	35.0	37.0	35.0	37.0
8	35.776	37.0	35.0	37.0	33.0	37.0
9	37.5245	39.0	37.0	39.0	34.0	39.0
10	37.76	39.0	37.0	39.0	35.0	39.0
11	37.5965	39.0	37.0	39.0	35.0	39.0
12	37.54	39.0	37.0	39.0	35.0	39.0
13	37.559	39.0	37.0	39.0	35.0	39.0
14	39.05025	40.0	38.0	41.0	36.0	41.0
15	38.91725	40.0	38.0	41.0	35.0	41.0
16	38.95	40.0	38.0	41.0	35.0	41.0
17	38.88875	40.0	38.0	41.0	35.0	41.0
18	39.015	40.0	38.0	41.0	35.0	41.0
19	38.659	40.0	38.0	41.0	34.0	41.0
20	38.87625	40.0	38.0	41.0	35.0	41.0
21	38.8815	40.0	38.0	41.0	35.0	41.0
22	38.9325	40.0	39.0	41.0	35.0	41.0
23	38.72425	40.0	38.0	41.0	34.0	41.0
24	38.785	40.0	38.0	41.0	34.0	41.0
25	39.0505	40.0	39.0	41.0	35.0	41.0
26	38.7345	40.0	38.0	41.0	34.0	41.0
27	38.70225	40.0	38.0	41.0	34.0	41.0
28	38.692	40.0	38.0	41.0	35.0	41.0
29	38.292	40.0	38.0	41.0	34.0	41.0
30	38.0935	40.0	38.0	41.0	33.0	41.0
31	38.3485	40.0	38.0	41.0	33.0	41.0
32	38.1875	40.0	38.0	41.0	33.0	41.0
33	38.329	40.0	38.0	41.0	34.0	41.0
34	38.43225	40.0	38.0	41.0	34.0	41.0
35	38.23225	40.0	38.0	41.0	34.0	41.0
36	37.83775	40.0	37.0	41.0	33.0	41.0
37	37.332	40.0	37.0	41.0	31.0	41.0
38	36.7065	39.0	36.0	41.0	30.0	41.0
39	37.2385	39.0	37.0	41.0	31.0	41.0
40	37.55125	40.0	37.0	41.0	32.0	41.0
41	37.6825	40.0	37.0	41.0	32.0	41.0
42	37.92375	40.0	38.0	41.0	33.0	41.0
43	38.10875	40.0	38.0	41.0	33.0	41.0
44	37.776	40.0	37.0	41.0	33.0	41.0
45	37.74	40.0	37.0	41.0	33.0	41.0
46	37.63425	40.0	37.0	41.0	33.0	41.0
47	37.25625	40.0	37.0	41.0	31.0	41.0
48	36.9905	40.0	36.0	41.0	31.0	41.0
49	37.1705	40.0	36.0	41.0	32.0	41.0
50	36.66925	39.0	36.0	41.0	31.0	41.0
>>END_MODULE
>>Per tile sequence quality	pass
#Tile	Base	Mean
1101	1	0.0
1101	2	0.0
1101	3	0.0
1101	4	0.0
1101	5	0.0
1101	6	0.0
1101	7	0.0
1101	8	0.0
1101	9	0.0
1101	10	0.0
1101	11	0.0
1101	12	0.0
1101	13	0.0
1101	14	0.0
1101	15	0.0
1101	16	0.0
1101	17	0.0
1101	18	0.0
1101	19	0.0
1101	20	0.0
1101	21	0.0
1101	22	0.0
1101	23	0.0
1101	24	0.0
1101	25	0.0
1101	26	0.0
1101	27	0.0
1101	28	0.0
1101	29	0.0
1101	30	0.0
1101	31	0.0
1101	32	0.0
1101	33	0.0
1101	34	0.0
1101	35	0.0
1101	36	0.0
1101	37	0.0
1101	38	0.0
1101	39	0.0
1101	40	0.0
1101	41	0.0
1101	42	0.0
1101	43	0.0
1101	44	0.0
1101	45	0.0
1101	46	0.0
1101	47	0.0
1101	48	0.0
1101	49	0.0
1101	50	0.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
14	1.0
15	1.0
16	2.0
17	0.0
18	1.0
19	3.0
20	2.0
21	4.0
22	5.0
23	4.0
24	9.0
25	12.0
26	19.0
27	23.0
28	28.0
29	38.0
30	46.0
31	69.0
32	70.0
33	103.0
34	160.0
35	207.0
36	273.0
37	401.0
38	726.0
39	1793.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	9.0	25.575	51.1	14.325
2	24.28035043804756	27.30913642052566	17.99749687108886	30.413016270337923
3	23.575	20.65	22.900000000000002	32.875
4	30.85	28.025	15.25	25.874999999999996
5	22.5	39.1	26.674999999999997	11.725
6	36.35	15.925	31.624999999999996	16.1
7	15.35	24.175	23.275000000000002	37.2
8	25.874999999999996	28.175	16.45	29.5
9	20.525	34.875	28.15	16.45
10	22.75	23.849999999999998	26.55	26.85
11	31.674999999999997	10.100000000000001	18.7	39.525
12	17.1	17.575	30.3	35.025
13	30.775000000000002	18.65	32.2	18.375
14	31.65	30.425	21.075	16.85
15	35.85	24.825	26.150000000000002	13.175
16	19.175	20.9	23.400000000000002	36.525
17	25.75	23.9	37.0	13.350000000000001
18	25.575	18.075	28.475	27.875
19	34.775	15.2	31.0	19.025
20	41.25	15.825	28.95	13.975000000000001
21	24.025	19.825	28.349999999999998	27.800000000000004
22	28.000000000000004	13.65	48.575	9.775
23	26.375	14.224999999999998	43.8	15.6
24	50.55	15.2	26.974999999999998	7.2749999999999995
25	49.225	24.575	15.75	10.45
26	28.625	45.675	14.45	11.25
27	15.525	46.1	25.674999999999997	12.7
28	11.35	25.124999999999996	47.625	15.9
29	11.55	13.425	55.125	19.900000000000002
30	10.875	6.7250000000000005	37.925	44.474999999999994
31	13.925	5.65	45.2	35.225
32	28.575	6.425	22.400000000000002	42.6
33	53.849999999999994	8.924999999999999	15.174999999999999	22.05
34	61.675000000000004	7.8	16.275000000000002	14.249999999999998
35	64.2	7.475	18.75	9.575
36	43.025000000000006	8.450000000000001	35.099999999999994	13.425
37	43.4	11.225	21.325	24.05
38	23.3	16.675	13.975000000000001	46.050000000000004
39	15.55	23.225	11.1	50.125
40	14.7	46.475	12.45	26.375
41	24.525	47.525	9.85	18.099999999999998
42	48.1	30.099999999999998	11.975	9.825000000000001
43	51.425	29.175	8.375	11.025
44	32.75	46.949999999999996	7.074999999999999	13.225000000000001
45	19.1	48.6	12.875	19.425
46	13.025	26.125	19.575	41.275
47	9.55	15.2	37.974999999999994	37.275000000000006
48	11.450000000000001	12.2	20.525	55.825
49	12.2	20.200000000000003	15.075	52.525
50	17.525	36.525	13.175	32.775
>>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	1.0
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	0.0
26	0.0
27	1.5
28	3.0
29	4.0
30	5.0
31	12.0
32	19.0
33	14.0
34	9.0
35	17.0
36	25.0
37	28.5
38	32.0
39	36.0
40	40.0
41	42.0
42	44.0
43	76.0
44	108.0
45	150.5
46	193.0
47	332.5
48	472.0
49	592.5
50	713.0
51	816.0
52	919.0
53	662.5
54	406.0
55	420.5
56	435.0
57	331.0
58	227.0
59	149.0
60	71.0
61	55.5
62	40.0
63	75.0
64	110.0
65	75.0
66	40.0
67	24.5
68	9.0
69	10.5
70	12.0
71	33.5
72	55.0
73	29.5
74	4.0
75	2.0
76	0.0
77	0.5
78	1.0
79	1.5
80	2.0
81	2.5
82	3.0
83	2.0
84	1.0
85	0.5
86	0.0
87	0.0
88	0.0
89	0.0
90	0.0
91	0.0
92	0.0
93	0.0
94	0.0
95	0.0
96	0.0
97	0.0
98	0.0
99	0.0
100	0.0
>>END_MODULE
>>Per base N content	pass
#Base	N-Count
1	0.0
2	0.125
3	0.0
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.0
10	0.0
11	0.0
12	0.0
13	0.0
14	0.0
15	0.0
16	0.0
17	0.0
18	0.0
19	0.0
20	0.0
21	0.0
22	0.0
23	0.0
24	0.0
25	0.0
26	0.0
27	0.0
28	0.0
29	0.0
30	0.0
31	0.0
32	0.0
33	0.0
34	0.0
35	0.0
36	0.0
37	0.0
38	0.0
39	0.0
40	0.0
41	0.0
42	0.0
43	0.0
44	0.0
45	0.0
46	0.0
47	0.0
48	0.0
49	0.0
50	0.0
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
50	4000.0
>>END_MODULE
>>Sequence Duplication Levels	fail
#Total Deduplicated Percentage	37.974999999999994
#Duplication Level	Percentage of deduplicated	Percentage of total
1	73.14022383146808	27.775
2	11.454904542462147	8.7
3	4.805793285055958	5.475
4	2.9624753127057275	4.5
5	0.9216589861751152	1.7500000000000002
6	1.5141540487162608	3.45
7	0.5924950625411455	1.575
8	0.5924950625411455	1.7999999999999998
9	0.32916392363396973	1.125
>10	3.0941408821593153	22.825
>50	0.39499670836076367	10.875
>100	0.19749835418038184	10.15
>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	157	3.925	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	129	3.225	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	120	3.0	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	82	2.0500000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	78	1.95	RNA PCR Primer, Index 1 (100% over 30bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	74	1.8499999999999999	RNA PCR Primer, Index 1 (100% over 29bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	71	1.775	No Hit
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	66	1.6500000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	64	1.6	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	46	1.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	45	1.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	38	0.95	RNA PCR Primer, Index 1 (100% over 28bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTC	35	0.8750000000000001	RNA PCR Primer, Index 5 (97% over 35bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	31	0.775	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	30	0.75	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	27	0.675	RNA PCR Primer, Index 1 (100% over 28bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	25	0.625	RNA PCR Primer, Index 1 (100% over 29bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	24	0.6	RNA PCR Primer, Index 1 (100% over 33bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	24	0.6	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	21	0.525	RNA PCR Primer, Index 1 (100% over 27bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 29bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 29bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	18	0.44999999999999996	No Hit
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	16	0.4	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	16	0.4	RNA PCR Primer, Index 1 (100% over 26bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCATTCATCTC	16	0.4	RNA PCR Primer, Index 45 (100% over 44bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCATTCATCTCGTATGC	16	0.4	RNA PCR Primer, Index 45 (100% over 50bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	15	0.375	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	13	0.325	RNA PCR Primer, Index 1 (100% over 30bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	13	0.325	No Hit
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	11	0.27499999999999997	No Hit
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTTGGAATTCTCGGGTGCCA	11	0.27499999999999997	No Hit
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	10	0.25	No Hit
TCGGATCCGTCTGAGCTTGGCTTTTTGGAATTCTCGGGTGCCAAGGAACT	10	0.25	RNA PCR Primer, Index 1 (100% over 25bp)
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTTGGAATTCTCGGGTGCC	9	0.22499999999999998	No Hit
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
AGAGGTAGTAGGTTGCATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	8	0.2	No Hit
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	8	0.2	No Hit
TGCGGGGCTAGGGCTAACAGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TAGCACCATCTGAAATCGGTTATGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	8	0.2	No Hit
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	7	0.17500000000000002	No Hit
TTCAAGTAATTCAGGATAGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
CATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCATTCATCTCGTAT	7	0.17500000000000002	RNA PCR Primer, Index 45 (100% over 48bp)
TCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCC	7	0.17500000000000002	No Hit
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGGAATTCTCGGGTGCCAA	7	0.17500000000000002	No Hit
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
ACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTC	6	0.15	RNA PCR Primer, Index 5 (97% over 35bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGGAATTCTCGGGTGCCAA	6	0.15	No Hit
TCACAGTGAACCGGTCTCTTTTTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	6	0.15	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCTGGAATTCTCGGGTG	6	0.15	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGTGGAATTCTCGGGTGCC	6	0.15	No Hit
TGAGGTAGGAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTGAAATGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
GGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	6	0.15	No Hit
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
ACTAATCCTAGCCCTAGCCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
TGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	6	0.15	No Hit
TCACAGTGAACCGGTCTCTTTATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTATTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGGAATTCTCGGGTGCCA	6	0.15	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATGGAATTCTCGGGTGCCAAG	6	0.15	No Hit
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	6	0.15	No Hit
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCAATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
CACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCAT	5	0.125	RNA PCR Primer, Index 42 (97% over 37bp)
TGTCTGAGCGTCGCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACT	5	0.125	RNA PCR Primer, Index 3 (100% over 34bp)
TGCGGGGCTAGGGCTAACAGCATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTACATTGTCTGCTGGGTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGATGAAGCACTGTAGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TTTGGCAATGGTAGAACTCACTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGACTGGAATTCTCGGGT	5	0.125	No Hit
ACTAATCCTAGCCCTAGCCCTACACAAATATAATTATACTATTATTGGAA	5	0.125	No Hit
TCTCCCAACCCTTGTACCAGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AGCAGCATTGTACAGGGCTATGTTGGAATTCTCGGGTGCCAAGGAACTCC	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	0.4	0.0	0.0	0.0
2	0.0	0.425	0.0	0.0	0.0
3	0.0	0.6	0.0	0.0	0.0
4	0.0	0.625	0.0	0.0	0.0
5	0.0	0.725	0.0	0.0	0.0
6	0.0	0.8	0.0	0.0	0.0
7	0.0	1.25	0.0	0.0	0.0
8	0.0	1.3	0.0	0.0	0.0
9	0.0	1.325	0.0	0.0	0.0
10	0.0	1.325	0.0	0.0	0.0
11	0.0	1.575	0.0	0.0	0.0
12	0.0	1.775	0.0	0.0	0.0
13	0.0	2.125	0.0	0.0	0.0
14	0.0	2.55	0.0	0.0	0.0
15	0.0	2.825	0.0	0.0	0.0
16	0.0	4.2	0.0	0.0	0.0
17	0.0	4.825	0.0	0.0	0.0
18	0.0	5.875	0.0	0.0	0.0
19	0.0	6.175	0.0	0.0	0.0
20	0.0	7.225	0.0	0.0	0.0
21	0.0	12.675	0.0	0.0	0.0
22	0.0	24.625	0.0	0.0	0.0
23	0.0	52.825	0.0	0.0	0.0
24	0.0	66.3	0.0	0.0	0.0
25	0.0	72.75	0.0	0.0	0.0
26	0.0	74.25	0.0	0.0	0.0
27	0.0	74.975	0.0	0.0	0.0
28	0.0	75.775	0.0	0.0	0.0
29	0.0	76.6	0.0	0.0	0.0
30	0.0	77.2	0.0	0.0	0.0
31	0.0	78.1	0.0	0.0	0.0
32	0.0	79.4	0.0	0.0	0.0
33	0.0	81.125	0.0	0.0	0.0
34	0.0	84.6	0.0	0.0	0.0
35	0.0	85.6	0.0	0.0	0.0
36	0.0	86.45	0.0	0.0	0.0
37	0.0	87.5	0.0	0.0	0.0
38	0.0	88.025	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
ACAGTGA	20	6.952051E-4	44.000004	3
ACCGGTC	20	6.952051E-4	44.000004	10
AACCGGT	20	6.952051E-4	44.000004	9
TTGTATA	20	6.952051E-4	44.000004	13
GAGTTGG	20	6.952051E-4	44.000004	20
GTATAGT	20	6.952051E-4	44.000004	15
GAACCGG	20	6.952051E-4	44.000004	8
GTCTCTT	20	6.952051E-4	44.000004	14
GCTTGGC	45	2.728484E-10	44.000004	15
AGTGAAC	20	6.952051E-4	44.000004	5
TCTCTTT	20	6.952051E-4	44.000004	15
GTGAACC	20	6.952051E-4	44.000004	6
CGGTCTC	20	6.952051E-4	44.000004	12
CTGTTGG	20	6.952051E-4	44.000004	19
TGAACCG	20	6.952051E-4	44.000004	7
TGTATAG	20	6.952051E-4	44.000004	14
TGAGTTG	20	6.952051E-4	44.000004	19
TATAGTT	20	6.952051E-4	44.000004	16
CAGTGAA	20	6.952051E-4	44.000004	4
TGGCTTG	20	6.952051E-4	44.000004	18
>>END_MODULE
Read 227307 spots for SRR5031073.sra
Written 227307 spots for SRR5031073.sra
Read 227307 spots for SRR5031073.sra
Written 227307 spots for SRR5031073.sra
Read 227307 spots for SRR5031073.sra
Written 227307 spots for SRR5031073.sra
Read 227307 spots for SRR5031073.sra
Written 227307 spots for SRR5031073.sra
Read 227307 spots for SRR5031073.sra
Written 227307 spots for SRR5031073.sra
Read 227307 spots for SRR5031073.sra
Written 227307 spots for SRR5031073.sra
Read 227307 spots for SRR5031073.sra
Written 227307 spots for SRR5031073.sra
Read 227307 spots for SRR5031073.sra
Written 227307 spots for SRR5031073.sra
Read 227316 spots for SRR5031073.sra
Written 227316 spots for SRR5031073.sra
Read 227307 spots for SRR5031073.sra
Written 227307 spots for SRR5031073.sra
Read 227307 spots for SRR5031073.sra
Written 227307 spots for SRR5031073.sra
Read 227307 spots for SRR5031073.sra
Written 227307 spots for SRR5031073.sra
SRR ids: ['SRR5031073.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_6xpkxuug
SRR5031073.sra spots: 2727693
blocks: [[1, 227307], [227308, 454614], [454615, 681921], [681922, 909228], [909229, 1136535], [1136536, 1363842], [1363843, 1591149], [1591150, 1818456], [1818457, 2045763], [2045764, 2273070], [2273071, 2500377], [2500378, 2727693]]
SRR5031073 file size 471701
SRR5031073 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031073 SRR5031073_1.fastq
Input file:	SRR5031073_1.fastq
trimmed:	SRR5031073-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
-- maximum error ratio allowed (-r):	0.100
-- maximum indel error ratio allowed (-d):	0.030
-- end quality threshold (-q):		10
-- minimum read length allowed after trimming (-l):	18
-- file format (-f):		Sanger/Illumina 1.8+ FASTQ (auto detected)
-- minimum overlap length for adapter detection (-k):	inf
-- number of concurrent threads (-t):	12
Wed Mar  4 07:18:06 2020 >> started

Wed Mar  4 07:18:07 2020 >> done (1.606s)
2727693 reads processed; of these:
    220 ( 0.01%) short reads filtered out after trimming by size control
     12 ( 0.00%) empty reads filtered out after trimming by size control
2727461 (99.99%) reads available; of these:
 122656 ( 4.50%) trimmed reads available after processing
2604805 (95.50%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     57	  0.00%
 19	     65	  0.00%
 20	    153	  0.01%
 21	    190	  0.01%
 22	    333	  0.01%
 23	    409	  0.01%
 24	    420	  0.02%
 25	    562	  0.02%
 26	    455	  0.02%
 27	    560	  0.02%
 28	    655	  0.02%
 29	   1033	  0.04%
 30	    712	  0.03%
 31	    697	  0.03%
 32	    836	  0.03%
 33	   1065	  0.04%
 34	   1283	  0.05%
 35	   2477	  0.09%
 36	   2197	  0.08%
 37	   2522	  0.09%
 38	   2329	  0.09%
 39	   2478	  0.09%
 40	   2754	  0.10%
 41	   2728	  0.10%
 42	   3552	  0.13%
 43	   5109	  0.19%
 44	   6668	  0.24%
 45	   7963	  0.29%
 46	  11783	  0.43%
 47	  14407	  0.53%
 48	  22877	  0.84%
 49	  23327	  0.86%
 50	2604805	 95.50%
2727461 reads passed initial QC


criterion=sequence-density
sequence-density=87.69
sequence-density-rank=1
fanout-score=21.06
fanout-score-rank=1
prefix-density=89.52
prefix-fanout=20.6
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCATTCATCTCGTATGCC


criterion=fanout-score
sequence-density=87.69
sequence-density-rank=1
fanout-score=21.06
fanout-score-rank=1
prefix-density=89.52
prefix-fanout=20.6
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCATTCATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCATTCATCTCGTATGCC -o SRR5031073 -
Input file:	STDIN
trimmed:	SRR5031073-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCATTCATCTCGTATGCC
-- 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 07:18:22 2020 >> started

Wed Mar  4 07:18:26 2020 >> done (3.967s)
2665473 reads processed; of these:
 145083 ( 5.44%) short reads filtered out after trimming by size control
  14999 ( 0.56%) empty reads filtered out after trimming by size control
2505391 (93.99%) reads available; of these:
2403377 (95.93%) trimmed reads available after processing
 102014 ( 4.07%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  13384	  0.53%
 19	  25708	  1.03%
 20	 130320	  5.20%
 21	 316667	 12.64%
 22	 819452	 32.71%
 23	 357046	 14.25%
 24	 170295	  6.80%
 25	  44958	  1.79%
 26	  22839	  0.91%
 27	  18605	  0.74%
 28	  20207	  0.81%
 29	  15731	  0.63%
 30	  25543	  1.02%
 31	  31339	  1.25%
 32	  39730	  1.59%
 33	  89313	  3.56%
 34	  29695	  1.19%
 35	  21203	  0.85%
 36	  24605	  0.98%
 37	  13933	  0.56%
 38	  13725	  0.55%
 39	  13550	  0.54%
 40	  20745	  0.83%
 41	  26306	  1.05%
 42	  30158	  1.20%
 43	  20224	  0.81%
 44	  15377	  0.61%
 45	  20241	  0.81%
 46	  14647	  0.58%
 47	  11414	  0.46%
 48	    937	  0.04%
 49	   1326	  0.05%
 50	  86168	  3.44%


criterion=sequence-density
sequence-density=6.18
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=0.02
sequence-density-rank=38
fanout-score=132.99
fanout-score-rank=1
prefix-density=2.05
prefix-fanout=1.0
sequence=ATTGTATAGTTTAACAGTCTACAGCCATGGTCGT
                                 Started job on |	Mar 04 07:18:48
                             Started mapping on |	Mar 04 07:18:48
                                    Finished on |	Mar 04 07:19:13
       Mapping speed, Million of reads per hour |	369.70

                          Number of input reads |	2567379
                      Average input read length |	26
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1372857
                        Uniquely mapped reads % |	53.47%
                          Average mapped length |	24.51
                       Number of splices: Total |	1885
            Number of splices: Annotated (sjdb) |	635
                       Number of splices: GT/AG |	1774
                       Number of splices: GC/AG |	24
                       Number of splices: AT/AC |	2
               Number of splices: Non-canonical |	85
                      Mismatch rate per base, % |	0.19%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.79
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.08
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	872890
             % of reads mapped to multiple loci |	34.00%
        Number of reads mapped to too many loci |	55389
             % of reads mapped to too many loci |	2.16%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	9.81%
                     % of reads unmapped: other |	0.56%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	321632	321632	321632
N_multimapping	872890	872890	872890
N_noFeature	65209	81252	987912
N_ambiguous	748283	421322	11116
UnstrandedReadsAssigned:559365 PositiveStrandReadsAssigned:870283 NegativeStrandReadsAssigned:373829
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=22 echo kmer=19
SRR5031073 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: SRR5031073-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,567,379 reads, 639,823 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,138 rounds

 109283 SRR5031073.ke.tsv
  52636 SRR5031073.se.tsv
 161919 total
==> SRR5031073.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

==> SRR5031073.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	1
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031073 completed mapping pipeline successfully
