Starting /dee2/code/volunteer_pipeline.sh SRR5031021
    current disk space = 160542310400
    free memory = 56712232 
SRR5031021 SRAfilesize
c893da839d71c0aaff0239f0e905ce99  SRR5031021.sra
SRR5031021.sra file validated
SRR5031021 is single end
SRR5031021 is conventional basespace
SRR5031021 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031021_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	32.334	33.0	31.0	34.0	31.0	34.0
2	32.5385	34.0	31.0	34.0	31.0	34.0
3	32.55125	34.0	31.0	34.0	31.0	34.0
4	36.1915	37.0	35.0	37.0	35.0	37.0
5	36.07275	37.0	35.0	37.0	35.0	37.0
6	35.88	37.0	35.0	37.0	33.0	37.0
7	35.7465	37.0	35.0	37.0	35.0	37.0
8	35.91525	37.0	35.0	37.0	35.0	37.0
9	37.48075	39.0	37.0	39.0	34.0	39.0
10	37.3835	39.0	37.0	39.0	34.0	39.0
11	37.24425	39.0	37.0	39.0	33.0	39.0
12	37.57175	39.0	37.0	39.0	35.0	39.0
13	37.51775	39.0	37.0	39.0	34.0	39.0
14	38.9005	40.0	38.0	41.0	34.0	41.0
15	38.79625	40.0	38.0	41.0	35.0	41.0
16	38.80525	40.0	38.0	41.0	34.0	41.0
17	39.07775	40.0	38.0	41.0	35.0	41.0
18	39.02525	41.0	38.0	41.0	35.0	41.0
19	38.839	40.0	38.0	41.0	35.0	41.0
20	38.76925	40.0	38.0	41.0	34.0	41.0
21	38.84975	40.0	38.0	41.0	35.0	41.0
22	38.884	40.0	39.0	41.0	35.0	41.0
23	38.55375	40.0	38.0	41.0	34.0	41.0
24	38.83075	40.0	38.0	41.0	35.0	41.0
25	38.94225	40.0	38.0	41.0	35.0	41.0
26	38.727	40.0	38.0	41.0	34.0	41.0
27	38.88	40.0	38.0	41.0	35.0	41.0
28	38.57025	40.0	38.0	41.0	34.0	41.0
29	38.2685	40.0	38.0	41.0	33.0	41.0
30	38.267	40.0	38.0	41.0	33.0	41.0
31	38.49175	40.0	38.0	41.0	34.0	41.0
32	38.3285	40.0	38.0	41.0	33.0	41.0
33	37.81525	40.0	38.0	41.0	33.0	41.0
34	37.82425	40.0	37.0	41.0	33.0	41.0
35	37.70175	40.0	37.0	41.0	33.0	41.0
36	37.731	40.0	37.0	41.0	33.0	41.0
37	37.0375	39.0	37.0	41.0	31.0	41.0
38	37.14175	39.0	36.0	41.0	31.0	41.0
39	37.57175	40.0	37.0	41.0	33.0	41.0
40	37.76875	40.0	37.0	41.0	33.0	41.0
41	37.8825	40.0	37.0	41.0	33.0	41.0
42	37.8605	40.0	37.0	41.0	33.0	41.0
43	37.7815	40.0	37.0	41.0	33.0	41.0
44	37.765	40.0	37.0	41.0	33.0	41.0
45	37.687	40.0	37.0	41.0	33.0	41.0
46	37.43825	40.0	37.0	41.0	32.0	41.0
47	36.76025	40.0	36.0	41.0	30.0	41.0
48	36.532	39.0	35.0	41.0	30.0	41.0
49	36.68	39.0	35.0	41.0	31.0	41.0
50	36.04675	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
17	2.0
18	1.0
19	6.0
20	6.0
21	2.0
22	3.0
23	10.0
24	6.0
25	15.0
26	13.0
27	17.0
28	34.0
29	41.0
30	56.0
31	63.0
32	85.0
33	120.0
34	154.0
35	175.0
36	254.0
37	460.0
38	807.0
39	1670.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	9.625	22.575	50.0	17.8
2	26.303911735205617	24.874623871614844	18.480441323971917	30.341023069207623
3	24.425	20.525	23.225	31.825
4	37.7	26.400000000000002	14.2	21.7
5	22.15	41.925000000000004	25.124999999999996	10.8
6	33.550000000000004	16.175	33.525	16.75
7	16.475	21.275	22.725	39.525
8	24.8	26.6	18.25	30.349999999999998
9	21.625	31.474999999999998	26.875	20.025000000000002
10	20.025000000000002	25.124999999999996	28.050000000000004	26.8
11	32.475	10.45	16.5	40.575
12	16.400000000000002	20.4	30.475	32.725
13	32.300000000000004	16.75	35.025	15.925
14	30.599999999999998	28.975	20.25	20.175
15	35.55	24.975	26.674999999999997	12.8
16	19.875	18.675	22.55	38.9
17	24.0	22.975	39.925	13.100000000000001
18	24.7	16.225	29.45	29.625
19	38.05	14.899999999999999	30.175	16.875
20	41.875	15.950000000000001	28.4	13.775
21	25.5	20.075000000000003	27.675	26.75
22	31.1	13.575000000000001	44.55	10.775
23	27.85	12.875	40.699999999999996	18.575
24	51.24999999999999	14.975	24.825	8.95
25	47.0	27.625	14.875	10.5
26	27.675	44.125	15.125	13.075000000000001
27	16.8	43.65	23.9	15.65
28	13.825000000000001	22.35	45.574999999999996	18.25
29	14.725	12.875	52.800000000000004	19.6
30	10.25	7.324999999999999	34.9	47.525
31	15.2	5.35	46.7	32.75
32	32.225	5.4	20.775	41.6
33	51.925	10.8	13.950000000000001	23.325000000000003
34	58.550000000000004	7.9750000000000005	18.5	14.975
35	63.87500000000001	7.449999999999999	18.6	10.075000000000001
36	43.45	8.3	34.0	14.249999999999998
37	43.225	13.025	19.15	24.6
38	23.549999999999997	19.825	11.95	44.675
39	15.575	24.075	12.8	47.55
40	17.175	45.275	13.750000000000002	23.799999999999997
41	25.4	45.375	8.924999999999999	20.3
42	45.15	28.7	14.224999999999998	11.924999999999999
43	48.949999999999996	29.475	7.9750000000000005	13.600000000000001
44	32.725	46.45	7.6	13.225000000000001
45	20.75	46.35	13.950000000000001	18.95
46	17.375	24.55	17.575	40.5
47	9.775	15.65	38.775	35.8
48	13.025	13.8	19.35	53.825
49	14.2	19.775000000000002	14.075	51.949999999999996
50	18.525	35.25	13.675	32.550000000000004
>>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	0.0
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	1.5
28	3.0
29	2.5
30	2.0
31	9.5
32	17.0
33	17.5
34	18.0
35	19.5
36	21.0
37	26.0
38	31.0
39	30.0
40	29.0
41	35.5
42	42.0
43	74.0
44	106.0
45	145.5
46	185.0
47	306.5
48	428.0
49	517.0
50	606.0
51	715.5
52	825.0
53	610.0
54	395.0
55	471.5
56	548.0
57	391.0
58	234.0
59	154.5
60	75.0
61	59.5
62	44.0
63	132.5
64	221.0
65	134.0
66	47.0
67	34.5
68	22.0
69	19.5
70	17.0
71	45.5
72	74.0
73	38.5
74	3.0
75	2.5
76	2.0
77	2.5
78	3.0
79	1.5
80	0.0
81	0.5
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	0.5
92	1.0
93	0.5
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	0.3
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	35.85
#Duplication Level	Percentage of deduplicated	Percentage of total
1	76.35983263598327	27.375
2	8.786610878661087	6.3
3	3.695955369595537	3.975
4	2.580195258019526	3.6999999999999997
5	2.092050209205021	3.75
6	0.5578800557880056	1.2
7	1.0460251046025104	2.625
8	0.3486750348675035	1.0
9	0.5578800557880056	1.7999999999999998
>10	3.2775453277545328	23.875
>50	0.3486750348675035	9.45
>100	0.3486750348675035	14.95
>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
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	152	3.8	No Hit
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	119	2.9749999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	112	2.8000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	111	2.775	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	104	2.6	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	100	2.5	RNA PCR Primer, Index 1 (100% over 30bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	91	2.275	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	83	2.075	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	53	1.325	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	51	1.275	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	49	1.225	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	41	1.0250000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	41	1.0250000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGA	38	0.95	RNA PCR Primer, Index 7 (97% over 35bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	37	0.9249999999999999	No Hit
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	36	0.8999999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 33bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	32	0.8	RNA PCR Primer, Index 1 (100% over 26bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	31	0.775	RNA PCR Primer, Index 1 (100% over 27bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	30	0.75	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	24	0.6	RNA PCR Primer, Index 1 (100% over 27bp)
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	23	0.575	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	23	0.575	RNA PCR Primer, Index 1 (100% over 26bp)
GGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	23	0.575	No Hit
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGACGACATCTC	23	0.575	RNA PCR Primer, Index 41 (100% over 44bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	23	0.575	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	21	0.525	RNA PCR Primer, Index 1 (100% over 26bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	20	0.5	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	19	0.475	RNA PCR Primer, Index 1 (100% over 28bp)
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	19	0.475	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	17	0.42500000000000004	No Hit
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 29bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 30bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	16	0.4	No Hit
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	15	0.375	No Hit
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 27bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	14	0.35000000000000003	No Hit
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	13	0.325	RNA PCR Primer, Index 1 (100% over 30bp)
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	13	0.325	RNA PCR Primer, Index 1 (100% over 25bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	12	0.3	RNA PCR Primer, Index 1 (100% over 26bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGACGACATCTCGTATGC	12	0.3	RNA PCR Primer, Index 41 (100% over 50bp)
CGCACGGGGTCGGCGGCGATGTCGGCTGGAATTCTCGGGTGCCAAGGAAC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 24bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	11	0.27499999999999997	No Hit
TCACAGTGAACCGGTCTCTTTATGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	11	0.27499999999999997	No Hit
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGCTGGAATTCTCGGGTGCC	10	0.25	No Hit
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	10	0.25	No Hit
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 30bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	9	0.22499999999999998	No Hit
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	8	0.2	No Hit
CAAGGGTTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGACGAC	8	0.2	RNA PCR Primer, Index 41 (100% over 39bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
GAAGGATCATTATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGACGA	7	0.17500000000000002	RNA PCR Primer, Index 31 (97% over 38bp)
TCGGATCCGTCTGAGCTTGGCAATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 31bp)
CATTATTACTTTTGGTACGCGTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	7	0.17500000000000002	No Hit
TATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAATTCTCGGGTGCC	7	0.17500000000000002	No Hit
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TAAGGCACGCGGTGAATGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	6	0.15	RNA PCR Primer, Index 1 (100% over 31bp)
TGGGGGGCCCAAGTCCTTCTGATCGAGGCCTGGAATTCTCGGGTGCCAAG	6	0.15	No Hit
GCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAATTC	6	0.15	No Hit
TGAGGTAGGAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
CTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACG	6	0.15	RNA PCR Primer, Index 6 (100% over 34bp)
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
ACTAATCCTAGCCCTAGCCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCTGGCTCCGTGTCTTCACTCCCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TTTAGCTGTTAACTAAATTTTCGTAGGTTTAATTCCTGCCAATCTAGCCA	5	0.125	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTTGGAATTCTCGGGTGCCA	5	0.125	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGCATTCTCGGGTGCC	5	0.125	No Hit
CATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGACGACATCTCGTAT	5	0.125	RNA PCR Primer, Index 41 (100% over 48bp)
TCGGATCCGTCTGAGCTTGGCTAAATGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGGAATTCTCGGGTGCCAA	5	0.125	No Hit
CGCACGGGGTCGGCGGCGATGTCGGTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
GTGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCA	5	0.125	No Hit
TCGGATCCGTCTGAGCTTGGCTTTTTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGATGAAGCACTGTAGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
CGCGACCTCAGATCAGATGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	5	0.125	RNA PCR Primer, Index 1 (100% over 33bp)
AAGGGATTCTGATGTTGGTCACACTCTGGAATTCTCGGGTGCCAAGGAAC	5	0.125	RNA PCR Primer, Index 1 (100% over 24bp)
TCAGTGCACTACAGAACTTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGGCAATGGTAGAACTCACATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTC	5	0.125	No Hit
TTTGGCAATGGTAGAACTCACACCTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
AAGGGATTCTGATGTTGGTCACATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	5	0.125	No Hit
AGAGGTAGTAGGTTGCATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TAAGGCACGCGGTGAATGCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGT	5	0.125	No Hit
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CTGGGCTACACATTTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGA	5	0.125	RNA PCR Primer, Index 7 (97% over 35bp)
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	5	0.125	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCTGGAATTCTCGGGTGC	5	0.125	No Hit
>>END_MODULE
>>Adapter Content	fail
#Position	Illumina Universal Adapter	Illumina Small RNA 3' Adapter	Illumina Small RNA 5' Adapter	Nextera Transposase Sequence	SOLID Small RNA Adapter
1	0.0	0.35	0.0	0.0	0.0
2	0.0	0.45	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	0.7	0.0	0.0	0.0
6	0.0	0.8	0.0	0.0	0.0
7	0.0	1.425	0.0	0.0	0.0
8	0.0	1.525	0.0	0.0	0.0
9	0.0	1.6	0.0	0.0	0.0
10	0.0	1.7	0.0	0.0	0.0
11	0.0	1.875	0.0	0.0	0.0
12	0.0	2.15	0.0	0.0	0.0
13	0.0	2.6	0.0	0.0	0.0
14	0.0	2.85	0.0	0.0	0.0
15	0.0	3.275	0.0	0.0	0.0
16	0.0	4.875	0.0	0.0	0.0
17	0.0	5.625	0.0	0.0	0.0
18	0.0	6.925	0.0	0.0	0.0
19	0.0	7.35	0.0	0.0	0.0
20	0.0	8.525	0.0	0.0	0.0
21	0.0	14.5	0.0	0.0	0.0
22	0.0	25.9	0.0	0.0	0.0
23	0.0	52.6	0.0	0.0	0.0
24	0.0	64.675	0.0	0.0	0.0
25	0.0	70.5	0.0	0.0	0.0
26	0.0	72.4	0.0	0.0	0.0
27	0.0	73.525	0.0	0.0	0.0
28	0.0	73.975	0.0	0.0	0.0
29	0.0	74.375	0.0	0.0	0.0
30	0.0	74.85	0.0	0.0	0.0
31	0.0	75.675	0.0	0.0	0.0
32	0.0	76.85	0.0	0.0	0.0
33	0.0	77.975	0.0	0.0	0.0
34	0.0	83.15	0.0	0.0	0.0
35	0.0	84.225	0.0	0.0	0.0
36	0.0	85.05	0.0	0.0	0.0
37	0.0	85.975	0.0	0.0	0.0
38	0.0	86.35	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
CTGAGCT	45	2.728484E-10	44.000004	11
TAAACAT	20	6.952051E-4	44.000004	3
AAACATC	20	6.952051E-4	44.000004	4
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
ACATCCT	20	6.952051E-4	44.000004	6
GATCCGT	45	2.728484E-10	44.000004	4
TCCGTCT	45	2.728484E-10	44.000004	6
ATCCGTC	45	2.728484E-10	44.000004	5
TGAGCTT	45	2.728484E-10	44.000004	12
CGTCTGA	45	2.728484E-10	44.000004	8
TGTAAAC	20	6.952051E-4	44.000004	1
GTAAACA	20	6.952051E-4	44.000004	2
AACATCC	20	6.952051E-4	44.000004	5
AACGCTG	30	1.9515464E-6	44.0	8
ACGCTGT	30	1.9515464E-6	44.0	9
GAGTGGA	25	3.6958358E-5	44.0	20
>>END_MODULE
Read 236030 spots for SRR5031021.sra
Written 236030 spots for SRR5031021.sra
Read 236030 spots for SRR5031021.sra
Written 236030 spots for SRR5031021.sra
Read 236030 spots for SRR5031021.sra
Written 236030 spots for SRR5031021.sra
Read 236030 spots for SRR5031021.sra
Written 236030 spots for SRR5031021.sra
Read 236030 spots for SRR5031021.sra
Written 236030 spots for SRR5031021.sra
Read 236030 spots for SRR5031021.sra
Written 236030 spots for SRR5031021.sra
Read 236030 spots for SRR5031021.sra
Written 236030 spots for SRR5031021.sra
Read 236030 spots for SRR5031021.sra
Written 236030 spots for SRR5031021.sra
Read 236030 spots for SRR5031021.sra
Written 236030 spots for SRR5031021.sra
Read 236030 spots for SRR5031021.sra
Written 236030 spots for SRR5031021.sra
Read 236030 spots for SRR5031021.sra
Written 236030 spots for SRR5031021.sra
Read 236041 spots for SRR5031021.sra
Written 236041 spots for SRR5031021.sra
SRR ids: ['SRR5031021.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_tl4abi76
SRR5031021.sra spots: 2832371
blocks: [[1, 236030], [236031, 472060], [472061, 708090], [708091, 944120], [944121, 1180150], [1180151, 1416180], [1416181, 1652210], [1652211, 1888240], [1888241, 2124270], [2124271, 2360300], [2360301, 2596330], [2596331, 2832371]]
SRR5031021 file size 489840
SRR5031021 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031021 SRR5031021_1.fastq
Input file:	SRR5031021_1.fastq
trimmed:	SRR5031021-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 07:08:11 2020 >> started

Wed Mar  4 07:08:13 2020 >> done (1.827s)
2832371 reads processed; of these:
    318 ( 0.01%) short reads filtered out after trimming by size control
     16 ( 0.00%) empty reads filtered out after trimming by size control
2832037 (99.99%) reads available; of these:
 169623 ( 5.99%) trimmed reads available after processing
2662414 (94.01%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     77	  0.00%
 19	     88	  0.00%
 20	    156	  0.01%
 21	    206	  0.01%
 22	    375	  0.01%
 23	    405	  0.01%
 24	    450	  0.02%
 25	    641	  0.02%
 26	    532	  0.02%
 27	    662	  0.02%
 28	    763	  0.03%
 29	   1087	  0.04%
 30	    790	  0.03%
 31	    874	  0.03%
 32	   1068	  0.04%
 33	   1121	  0.04%
 34	   1368	  0.05%
 35	   2160	  0.08%
 36	   2255	  0.08%
 37	   2641	  0.09%
 38	   2688	  0.09%
 39	   3083	  0.11%
 40	   3431	  0.12%
 41	   3583	  0.13%
 42	   4638	  0.16%
 43	   7023	  0.25%
 44	   9652	  0.34%
 45	  12243	  0.43%
 46	  17446	  0.62%
 47	  19963	  0.70%
 48	  29642	  1.05%
 49	  38512	  1.36%
 50	2662414	 94.01%
2832037 reads passed initial QC


criterion=sequence-density
sequence-density=85.38
sequence-density-rank=1
fanout-score=21.04
fanout-score-rank=1
prefix-density=87.43
prefix-fanout=20.6
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGACGACATCTCGTATGCC


criterion=fanout-score
sequence-density=85.38
sequence-density-rank=1
fanout-score=21.04
fanout-score-rank=1
prefix-density=87.43
prefix-fanout=20.6
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGACGACATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGACGACATCTCGTATGCC -o SRR5031021 -
Input file:	STDIN
trimmed:	SRR5031021-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGACGACATCTCGTATGCC
-- 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 07:08:27 2020 >> started

Wed Mar  4 07:08:32 2020 >> done (4.461s)
2766176 reads processed; of these:
 170979 ( 6.18%) short reads filtered out after trimming by size control
  13262 ( 0.48%) empty reads filtered out after trimming by size control
2581935 (93.34%) reads available; of these:
2447008 (94.77%) trimmed reads available after processing
 134927 ( 5.23%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  12597	  0.49%
 19	  28973	  1.12%
 20	 148220	  5.74%
 21	 311485	 12.06%
 22	 756286	 29.29%
 23	 357863	 13.86%
 24	 173011	  6.70%
 25	  46235	  1.79%
 26	  23546	  0.91%
 27	  17993	  0.70%
 28	  18217	  0.71%
 29	  14215	  0.55%
 30	  23575	  0.91%
 31	  43018	  1.67%
 32	  29275	  1.13%
 33	 132538	  5.13%
 34	  31510	  1.22%
 35	  24404	  0.95%
 36	  29732	  1.15%
 37	  14088	  0.55%
 38	  16158	  0.63%
 39	  14467	  0.56%
 40	  21521	  0.83%
 41	  29612	  1.15%
 42	  36468	  1.41%
 43	  25694	  1.00%
 44	  19390	  0.75%
 45	  27805	  1.08%
 46	  20353	  0.79%
 47	  15233	  0.59%
 48	   1248	  0.05%
 49	   2249	  0.09%
 50	 114956	  4.45%


criterion=sequence-density
sequence-density=6.62
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=19
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.01
sequence-density-rank=40
fanout-score=116.20
fanout-score-rank=1
prefix-density=1.70
prefix-fanout=1.0
sequence=ATTGTATAGTTTAACAGTCTACAGCCATGGTCGT
                                 Started job on |	Mar 04 07:08:53
                             Started mapping on |	Mar 04 07:08:53
                                    Finished on |	Mar 04 07:09:18
       Mapping speed, Million of reads per hour |	381.28

                          Number of input reads |	2647796
                      Average input read length |	27
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1357480
                        Uniquely mapped reads % |	51.27%
                          Average mapped length |	24.57
                       Number of splices: Total |	1507
            Number of splices: Annotated (sjdb) |	253
                       Number of splices: GT/AG |	1408
                       Number of splices: GC/AG |	26
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	73
                      Mismatch rate per base, % |	0.20%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.75
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.02
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	860470
             % of reads mapped to multiple loci |	32.50%
        Number of reads mapped to too many loci |	67696
             % of reads mapped to too many loci |	2.56%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	12.99%
                     % of reads unmapped: other |	0.69%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	429846	429846	429846
N_multimapping	860470	860470	860470
N_noFeature	83048	98463	923671
N_ambiguous	745702	366992	13633
UnstrandedReadsAssigned:528730 PositiveStrandReadsAssigned:892025 NegativeStrandReadsAssigned:420176
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5031021 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: SRR5031021-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,647,796 reads, 648,506 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 762 rounds

 109283 SRR5031021.ke.tsv
  52636 SRR5031021.se.tsv
 161919 total
==> SRR5031021.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

==> SRR5031021.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031021 completed mapping pipeline successfully
