Starting /dee2/code/volunteer_pipeline.sh SRR5030980
    current disk space = 160584351744
    free memory = 73949020 
SRR5030980 SRAfilesize
de9bffe90abee7141b5fd17e5f162d81  SRR5030980.sra
SRR5030980.sra file validated
SRR5030980 is single end
SRR5030980 is conventional basespace
SRR5030980 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030980_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	32.465	34.0	31.0	34.0	31.0	34.0
2	32.73725	34.0	31.0	34.0	31.0	34.0
3	32.768	34.0	31.0	34.0	31.0	34.0
4	36.2445	37.0	37.0	37.0	35.0	37.0
5	36.08475	37.0	35.0	37.0	35.0	37.0
6	35.912	37.0	35.0	37.0	35.0	37.0
7	35.97175	37.0	35.0	37.0	35.0	37.0
8	36.04375	37.0	35.0	37.0	35.0	37.0
9	37.72825	39.0	38.0	39.0	35.0	39.0
10	37.86475	39.0	38.0	39.0	35.0	39.0
11	37.676	39.0	37.0	39.0	35.0	39.0
12	37.70725	39.0	37.0	39.0	35.0	39.0
13	37.73375	39.0	37.0	39.0	35.0	39.0
14	38.9395	41.0	38.0	41.0	35.0	41.0
15	39.0465	41.0	38.0	41.0	35.0	41.0
16	39.10075	40.0	39.0	41.0	35.0	41.0
17	39.14925	41.0	39.0	41.0	35.0	41.0
18	39.149	41.0	38.0	41.0	36.0	41.0
19	38.872	40.0	38.0	41.0	35.0	41.0
20	38.84125	40.0	38.0	41.0	35.0	41.0
21	38.76725	40.0	38.0	41.0	34.0	41.0
22	38.79675	40.0	38.0	41.0	35.0	41.0
23	38.7095	40.0	38.0	41.0	35.0	41.0
24	38.86225	40.0	38.0	41.0	35.0	41.0
25	38.90625	40.0	38.0	41.0	35.0	41.0
26	38.7105	40.0	38.0	41.0	34.0	41.0
27	38.73425	40.0	38.0	41.0	34.0	41.0
28	38.2925	40.0	38.0	41.0	34.0	41.0
29	37.63025	40.0	37.0	41.0	31.0	41.0
30	37.83875	40.0	38.0	41.0	32.0	41.0
31	38.05825	40.0	38.0	41.0	33.0	41.0
32	38.08175	40.0	38.0	41.0	33.0	41.0
33	38.12475	40.0	38.0	41.0	33.0	41.0
34	38.1375	40.0	38.0	41.0	33.0	41.0
35	37.9095	40.0	38.0	41.0	33.0	41.0
36	37.41925	40.0	37.0	41.0	31.0	41.0
37	36.85625	39.0	36.0	41.0	30.0	41.0
38	37.0715	39.0	36.0	41.0	31.0	41.0
39	37.43775	39.0	37.0	40.0	33.0	41.0
40	37.56725	40.0	37.0	41.0	33.0	41.0
41	37.452	40.0	37.0	41.0	32.0	41.0
42	37.51875	40.0	37.0	41.0	33.0	41.0
43	37.5875	40.0	37.0	41.0	33.0	41.0
44	37.33775	39.0	37.0	41.0	33.0	41.0
45	37.03425	39.0	36.0	40.0	31.0	41.0
46	36.50975	39.0	36.0	40.0	30.0	41.0
47	35.79525	39.0	34.0	40.0	28.0	41.0
48	35.45275	38.0	34.0	40.0	28.0	41.0
49	35.71475	39.0	34.0	41.0	28.0	41.0
50	35.0735	38.0	34.0	40.0	27.0	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
4	1.0
5	0.0
6	0.0
7	1.0
8	0.0
9	0.0
10	0.0
11	0.0
12	0.0
13	0.0
14	1.0
15	2.0
16	1.0
17	0.0
18	1.0
19	3.0
20	6.0
21	4.0
22	4.0
23	5.0
24	7.0
25	7.0
26	18.0
27	31.0
28	29.0
29	38.0
30	59.0
31	67.0
32	76.0
33	122.0
34	163.0
35	196.0
36	272.0
37	500.0
38	867.0
39	1519.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	10.908181135851889	24.768576432324245	47.96097072804603	16.362271703777832
2	24.95	27.725	19.35	27.975
3	24.675	16.6	24.125	34.599999999999994
4	36.975	28.65	14.075	20.3
5	21.10527631907977	38.18454613653413	27.506876719179797	13.203300825206302
6	28.575	16.275000000000002	37.2	17.95
7	18.0	20.5	20.125	41.375
8	20.599999999999998	27.900000000000002	19.85	31.65
9	24.75	30.3	24.95	20.0
10	23.849999999999998	19.425	28.65	28.075
11	31.65	12.950000000000001	17.65	37.75
12	16.5	21.525	32.05	29.925
13	29.049999999999997	16.725	33.375	20.849999999999998
14	30.3	28.325	20.200000000000003	21.175
15	35.975	22.15	26.35	15.525
16	21.275	17.424999999999997	23.9	37.4
17	28.125	23.1	35.275	13.5
18	28.125	16.725	29.425	25.724999999999998
19	37.475	14.000000000000002	30.3	18.224999999999998
20	43.05	16.075	26.724999999999998	14.149999999999999
21	25.55	21.675	23.95	28.825
22	31.775	15.0	42.0	11.225
23	25.525	13.200000000000001	43.824999999999996	17.45
24	48.725	15.174999999999999	26.85	9.25
25	47.575	24.7	16.325	11.4
26	27.55	42.85	15.55	14.05
27	17.8	43.575	22.475	16.150000000000002
28	15.049999999999999	22.525000000000002	44.574999999999996	17.849999999999998
29	16.1	13.475000000000001	52.0	18.425
30	12.7	7.249999999999999	32.775	47.275
31	15.975	5.575	45.7	32.75
32	28.050000000000004	6.75	22.25	42.95
33	51.2	11.225	14.475	23.1
34	56.49999999999999	8.799999999999999	18.9	15.8
35	63.9	8.200000000000001	17.075000000000003	10.825
36	42.475	8.674999999999999	35.699999999999996	13.15
37	43.525000000000006	14.124999999999998	19.2	23.150000000000002
38	23.200000000000003	20.925	12.925	42.95
39	17.1	23.025000000000002	12.425	47.449999999999996
40	16.325	44.975	14.85	23.849999999999998
41	23.575	45.375	9.5	21.55
42	45.725	28.249999999999996	13.925	12.1
43	48.825	28.675	8.025	14.475
44	32.35	44.4	8.275	14.975
45	21.125	46.150000000000006	14.825	17.9
46	17.775	24.175	16.55	41.5
47	10.424999999999999	15.65	39.45	34.475
48	13.825000000000001	12.65	19.6	53.925
49	13.65	19.025	15.950000000000001	51.37500000000001
50	17.45	35.949999999999996	13.175	33.425
>>END_MODULE
>>Per sequence GC content	fail
#GC Content	Count
0	0.0
1	0.5
2	1.0
3	0.5
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	0.5
22	1.0
23	1.5
24	2.0
25	2.0
26	2.0
27	1.5
28	1.0
29	1.5
30	2.0
31	6.0
32	10.0
33	8.5
34	7.0
35	11.0
36	15.0
37	24.0
38	33.0
39	30.0
40	27.0
41	37.5
42	48.0
43	73.5
44	99.0
45	118.5
46	138.0
47	273.5
48	409.0
49	525.0
50	641.0
51	736.0
52	831.0
53	619.0
54	407.0
55	480.0
56	553.0
57	420.0
58	287.0
59	182.0
60	77.0
61	67.0
62	57.0
63	122.0
64	187.0
65	111.0
66	35.0
67	25.0
68	15.0
69	24.5
70	34.0
71	56.0
72	78.0
73	40.5
74	3.0
75	1.5
76	0.0
77	0.0
78	0.0
79	0.0
80	0.0
81	0.0
82	0.0
83	0.0
84	0.0
85	0.0
86	0.0
87	0.0
88	0.0
89	0.0
90	0.0
91	0.0
92	0.0
93	0.0
94	0.0
95	0.0
96	0.0
97	0.0
98	0.0
99	0.0
100	0.0
>>END_MODULE
>>Per base N content	pass
#Base	N-Count
1	0.075
2	0.0
3	0.0
4	0.0
5	0.025
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	38.65
#Duplication Level	Percentage of deduplicated	Percentage of total
1	75.09702457956016	29.025000000000002
2	10.34928848641656	8.0
3	4.3984476067270375	5.1
4	2.393272962483829	3.6999999999999997
5	1.2289780077619665	2.375
6	1.3583441138421735	3.15
7	0.646830530401035	1.7500000000000002
8	0.7761966364812419	2.4
9	0.38809831824062097	1.35
>10	2.78137128072445	20.225
>50	0.3234152652005175	10.674999999999999
>100	0.258732212160414	12.25
>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	128	3.2	No Hit
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	125	3.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	121	3.025	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	116	2.9000000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	99	2.475	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	99	2.475	RNA PCR Primer, Index 1 (100% over 30bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	91	2.275	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	84	2.1	RNA PCR Primer, Index 1 (100% over 28bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTC	54	1.35	RNA PCR Primer, Index 5 (97% over 35bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	41	1.0250000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	41	1.0250000000000001	No Hit
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	39	0.975	RNA PCR Primer, Index 1 (100% over 33bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	32	0.8	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	31	0.775	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCGAAGATCTC	28	0.7000000000000001	RNA PCR Primer, Index 47 (100% over 44bp)
GGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	28	0.7000000000000001	No Hit
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	27	0.675	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	26	0.65	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	24	0.6	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	23	0.575	RNA PCR Primer, Index 1 (100% over 27bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	21	0.525	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	21	0.525	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	20	0.5	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	19	0.475	RNA PCR Primer, Index 1 (100% over 28bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 29bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	16	0.4	No Hit
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCGAAGATCTCGTATGC	15	0.375	RNA PCR Primer, Index 47 (100% over 50bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	15	0.375	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	15	0.375	RNA PCR Primer, Index 1 (100% over 27bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	15	0.375	No Hit
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	14	0.35000000000000003	No Hit
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TACCCTGTAGAACCGAATTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	12	0.3	RNA PCR Primer, Index 1 (100% over 31bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	12	0.3	RNA PCR Primer, Index 1 (100% over 26bp)
CATTATTACTTTTGGTACGCGTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TACCCTGTAGATCCGAATTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	10	0.25	No Hit
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGATGAAGCACTGTAGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	10	0.25	RNA PCR Primer, Index 1 (100% over 30bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGT	9	0.22499999999999998	No Hit
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TACGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
AGAAATGCGGATATGGGACTGAGATGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (100% over 30bp)
TGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	8	0.2	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATGGAATTCTCGGGTGCCAAG	8	0.2	No Hit
TTCAAGTAATTCAGGATAGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGATGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	8	0.2	RNA PCR Primer, Index 1 (100% over 33bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TCTCCCAACCCTTGTACCAGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCTGGAATTCTCGGGTG	7	0.17500000000000002	No Hit
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 25bp)
AAGGGATTCTGATGTTGGTCACATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGCATTCTCGGGTGCC	7	0.17500000000000002	No Hit
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTC	7	0.17500000000000002	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCTGGAATTCTCGGGTGC	7	0.17500000000000002	No Hit
CATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCGAAGATCTCGTAT	6	0.15	RNA PCR Primer, Index 47 (100% over 48bp)
TCCTGTACTGAGCTGCCCCGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
CGACACAAGGGTTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACT	6	0.15	RNA PCR Primer, Index 3 (100% over 34bp)
TATTGCACTCGTCCCGGCCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTTTTGGAATTCTCGGGTGCCAAGGAACT	6	0.15	RNA PCR Primer, Index 1 (100% over 25bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGACTGGAATTCTCGGGT	6	0.15	No Hit
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCGTACCGTGAGTAATAATGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	6	0.15	No Hit
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	6	0.15	No Hit
ACTAATCCTAGCCCTAGCCCTATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TATTGCACTCGTCCCGGCCTCATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TTCCCTTTGTCATCCTATGCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AACCCGTAGATCCGAACTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TAGCTTATCAGACTGATGTTGATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
GTCTCTACGGAGACTGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACT	5	0.125	RNA PCR Primer, Index 3 (100% over 34bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTTGGAATTCTCGGGTGCCA	5	0.125	No Hit
ACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTC	5	0.125	RNA PCR Primer, Index 5 (97% over 35bp)
GCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAATTC	5	0.125	No Hit
GCATTGGTAGTTCAATGGTAGAATTCTCGCCTCCCTGGAATTCTCGGGTG	5	0.125	No Hit
AGTAAGGTCAGCTAATTAAGCTATCGGGCCCTGGAATTCTCGGGTGCCAA	5	0.125	No Hit
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TATGCAAGGGCAAGCTCTCTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TGTAAACATCCTACACTCAGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTCTCTGGAATTCTCGGGT	5	0.125	No Hit
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGTGGTCTAGTGGTTAGGATTCGGCGCTCTTGGAATTCTCGGGTGC	5	0.125	No Hit
ATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCTGGAATTCTCGGGTGCC	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	0.55	0.0	0.0	0.0
2	0.0	0.575	0.0	0.0	0.0
3	0.0	0.775	0.0	0.0	0.0
4	0.0	0.8	0.0	0.0	0.0
5	0.0	0.85	0.0	0.0	0.0
6	0.0	1.0	0.0	0.0	0.0
7	0.0	1.925	0.0	0.0	0.0
8	0.0	2.25	0.0	0.0	0.0
9	0.0	2.4	0.0	0.0	0.0
10	0.0	2.625	0.0	0.0	0.0
11	0.0	2.975	0.0	0.0	0.0
12	0.0	3.275	0.0	0.0	0.0
13	0.0	3.425	0.0	0.0	0.0
14	0.0	3.675	0.0	0.0	0.0
15	0.0	4.05	0.0	0.0	0.0
16	0.0	6.025	0.0	0.0	0.0
17	0.0	6.875	0.0	0.0	0.0
18	0.0	8.55	0.0	0.0	0.0
19	0.0	9.225	0.0	0.0	0.0
20	0.0	10.475	0.0	0.0	0.0
21	0.0	16.075	0.0	0.0	0.0
22	0.0	25.725	0.0	0.0	0.0
23	0.0	52.925	0.0	0.0	0.0
24	0.0	64.575	0.0	0.0	0.0
25	0.0	70.225	0.0	0.0	0.0
26	0.0	71.85	0.0	0.0	0.0
27	0.0	72.65	0.0	0.0	0.0
28	0.0	73.675	0.0	0.0	0.0
29	0.0	74.475	0.0	0.0	0.0
30	0.0	74.95	0.0	0.0	0.0
31	0.0	75.85	0.0	0.0	0.0
32	0.0	77.65	0.0	0.0	0.0
33	0.0	78.875	0.0	0.0	0.0
34	0.0	83.825	0.0	0.0	0.0
35	0.0	85.075	0.0	0.0	0.0
36	0.0	86.15	0.0	0.0	0.0
37	0.0	87.175	0.0	0.0	0.0
38	0.0	87.725	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TTTGAAC	25	3.451688E-5	44.49367	1
TTCAACG	30	1.8010014E-6	44.49367	5
GGATCCG	45	2.4374458E-10	44.49367	3
ATGAAGC	25	3.451688E-5	44.49367	5
TCGGATC	45	2.4374458E-10	44.49367	1
CATTCAA	30	1.8010014E-6	44.49367	3
CGGATCC	45	2.4374458E-10	44.49367	2
GATGAAG	25	3.451688E-5	44.49367	4
ACATTCA	30	1.8010014E-6	44.49367	2
AACCATC	25	3.451688E-5	44.49367	5
GAACCAT	25	3.451688E-5	44.49367	4
GATCCGT	45	2.4374458E-10	44.49367	4
AGATGAA	25	3.451688E-5	44.49367	3
TTGAACC	25	3.451688E-5	44.49367	2
ATCCGTC	45	2.4374458E-10	44.49367	5
TGAACCA	25	3.451688E-5	44.49367	3
ATTCAAC	30	1.8010014E-6	44.49367	4
AACATTC	30	1.8010014E-6	44.49367	1
GAGATGA	25	3.451688E-5	44.49367	2
TGAGATG	25	3.451688E-5	44.49367	1
>>END_MODULE
Read 211051 spots for SRR5030980.sra
Written 211051 spots for SRR5030980.sra
Read 211051 spots for SRR5030980.sra
Written 211051 spots for SRR5030980.sra
Read 211051 spots for SRR5030980.sra
Written 211051 spots for SRR5030980.sra
Read 211051 spots for SRR5030980.sra
Written 211051 spots for SRR5030980.sra
Read 211051 spots for SRR5030980.sra
Written 211051 spots for SRR5030980.sra
Read 211051 spots for SRR5030980.sra
Written 211051 spots for SRR5030980.sra
Read 211051 spots for SRR5030980.sra
Written 211051 spots for SRR5030980.sra
Read 211051 spots for SRR5030980.sra
Written 211051 spots for SRR5030980.sra
Read 211051 spots for SRR5030980.sra
Written 211051 spots for SRR5030980.sra
Read 211057 spots for SRR5030980.sra
Written 211057 spots for SRR5030980.sra
Read 211051 spots for SRR5030980.sra
Written 211051 spots for SRR5030980.sra
Read 211051 spots for SRR5030980.sra
Written 211051 spots for SRR5030980.sra
SRR ids: ['SRR5030980.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_fmpqn_am
SRR5030980.sra spots: 2532618
blocks: [[1, 211051], [211052, 422102], [422103, 633153], [633154, 844204], [844205, 1055255], [1055256, 1266306], [1266307, 1477357], [1477358, 1688408], [1688409, 1899459], [1899460, 2110510], [2110511, 2321561], [2321562, 2532618]]
SRR5030980 file size 437886
SRR5030980 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030980 SRR5030980_1.fastq
Input file:	SRR5030980_1.fastq
trimmed:	SRR5030980-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 06:59:06 2020 >> started

Wed Mar  4 06:59:07 2020 >> done (1.541s)
2532618 reads processed; of these:
    286 ( 0.01%) short reads filtered out after trimming by size control
     10 ( 0.00%) empty reads filtered out after trimming by size control
2532322 (99.99%) reads available; of these:
 181568 ( 7.17%) trimmed reads available after processing
2350754 (92.83%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     65	  0.00%
 19	     66	  0.00%
 20	    155	  0.01%
 21	    207	  0.01%
 22	    296	  0.01%
 23	    360	  0.01%
 24	    376	  0.01%
 25	    530	  0.02%
 26	    476	  0.02%
 27	    566	  0.02%
 28	    703	  0.03%
 29	    856	  0.03%
 30	    643	  0.03%
 31	    719	  0.03%
 32	    792	  0.03%
 33	   1200	  0.05%
 34	   1405	  0.06%
 35	   2835	  0.11%
 36	   2571	  0.10%
 37	   2630	  0.10%
 38	   2716	  0.11%
 39	   2987	  0.12%
 40	   3409	  0.13%
 41	   3648	  0.14%
 42	   5087	  0.20%
 43	   7177	  0.28%
 44	   9778	  0.39%
 45	  12973	  0.51%
 46	  20000	  0.79%
 47	  19478	  0.77%
 48	  30887	  1.22%
 49	  45977	  1.82%
 50	2350754	 92.83%
2532322 reads passed initial QC


criterion=sequence-density
sequence-density=87.88
sequence-density-rank=1
fanout-score=20.52
fanout-score-rank=1
prefix-density=89.91
prefix-fanout=20.1
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCGAAGATCTCGTATGCC


criterion=fanout-score
sequence-density=87.88
sequence-density-rank=1
fanout-score=20.52
fanout-score-rank=1
prefix-density=89.91
prefix-fanout=20.1
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCGAAGATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCGAAGATCTCGTATGCC -o SRR5030980 -
Input file:	STDIN
trimmed:	SRR5030980-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCGAAGATCTCGTATGCC
-- 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 06:59:20 2020 >> started

Wed Mar  4 06:59:23 2020 >> done (2.993s)
2474769 reads processed; of these:
 206549 ( 8.35%) short reads filtered out after trimming by size control
   9916 ( 0.40%) empty reads filtered out after trimming by size control
2258304 (91.25%) reads available; of these:
2169126 (96.05%) trimmed reads available after processing
  89178 ( 3.95%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  15665	  0.69%
 19	  29944	  1.33%
 20	 144097	  6.38%
 21	 257452	 11.40%
 22	 667441	 29.55%
 23	 302813	 13.41%
 24	 148144	  6.56%
 25	  40951	  1.81%
 26	  21677	  0.96%
 27	  18180	  0.81%
 28	  18411	  0.82%
 29	  13846	  0.61%
 30	  23645	  1.05%
 31	  45663	  2.02%
 32	  29663	  1.31%
 33	 122178	  5.41%
 34	  37125	  1.64%
 35	  29782	  1.32%
 36	  31665	  1.40%
 37	  13694	  0.61%
 38	  15294	  0.68%
 39	  12664	  0.56%
 40	  17014	  0.75%
 41	  21827	  0.97%
 42	  25195	  1.12%
 43	  18000	  0.80%
 44	  13819	  0.61%
 45	  20041	  0.89%
 46	  15421	  0.68%
 47	  11093	  0.49%
 48	    918	  0.04%
 49	   1557	  0.07%
 50	  73425	  3.25%


criterion=sequence-density
sequence-density=8.55
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=14
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.67
sequence-density-rank=22
fanout-score=11.76
fanout-score-rank=1
prefix-density=7.89
prefix-fanout=1.0
sequence=TGAGCTTGGCTATT
                                 Started job on |	Mar 04 06:59:43
                             Started mapping on |	Mar 04 06:59:43
                                    Finished on |	Mar 04 07:00:08
       Mapping speed, Million of reads per hour |	333.48

                          Number of input reads |	2315857
                      Average input read length |	26
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1209485
                        Uniquely mapped reads % |	52.23%
                          Average mapped length |	24.07
                       Number of splices: Total |	1422
            Number of splices: Annotated (sjdb) |	283
                       Number of splices: GT/AG |	1353
                       Number of splices: GC/AG |	17
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	52
                      Mismatch rate per base, % |	0.18%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.80
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.01
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	740401
             % of reads mapped to multiple loci |	31.97%
        Number of reads mapped to too many loci |	65057
             % of reads mapped to too many loci |	2.81%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	11.85%
                     % of reads unmapped: other |	1.14%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	365971	365971	365971
N_multimapping	740401	740401	740401
N_noFeature	77164	91223	800358
N_ambiguous	658180	293980	9634
UnstrandedReadsAssigned:474141 PositiveStrandReadsAssigned:824282 NegativeStrandReadsAssigned:399493
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5030980 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: SRR5030980-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,315,857 reads, 572,755 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,145 rounds

 109283 SRR5030980.ke.tsv
  52636 SRR5030980.se.tsv
 161919 total
==> SRR5030980.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

==> SRR5030980.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	1
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030980 completed mapping pipeline successfully
