Starting /dee2/code/volunteer_pipeline.sh SRR5030974
    current disk space = 160576094208
    free memory = 73924416 
SRR5030974 SRAfilesize
a64e0bf6d3e7d7d92bb6253461d2f678  SRR5030974.sra
SRR5030974.sra file validated
SRR5030974 is single end
SRR5030974 is conventional basespace
SRR5030974 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030974_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	32.45	33.0	31.0	34.0	31.0	34.0
2	32.74725	34.0	31.0	34.0	31.0	34.0
3	32.675	34.0	31.0	34.0	31.0	34.0
4	36.2535	37.0	37.0	37.0	35.0	37.0
5	36.17025	37.0	37.0	37.0	35.0	37.0
6	35.81475	37.0	35.0	37.0	33.0	37.0
7	35.9725	37.0	35.0	37.0	35.0	37.0
8	36.075	37.0	35.0	37.0	35.0	37.0
9	37.78325	39.0	38.0	39.0	35.0	39.0
10	37.90125	39.0	38.0	39.0	35.0	39.0
11	37.82875	39.0	38.0	39.0	35.0	39.0
12	37.74625	39.0	38.0	39.0	35.0	39.0
13	37.73875	39.0	37.0	39.0	35.0	39.0
14	38.988	41.0	38.0	41.0	35.0	41.0
15	39.168	41.0	39.0	41.0	36.0	41.0
16	39.17025	40.0	39.0	41.0	36.0	41.0
17	39.13725	41.0	39.0	41.0	36.0	41.0
18	39.22575	41.0	39.0	41.0	36.0	41.0
19	38.883	40.0	38.0	41.0	34.0	41.0
20	38.99275	40.0	39.0	41.0	35.0	41.0
21	39.00525	40.0	38.0	41.0	35.0	41.0
22	39.07025	40.0	39.0	41.0	36.0	41.0
23	38.8365	40.0	38.0	41.0	35.0	41.0
24	38.93575	40.0	38.0	41.0	35.0	41.0
25	38.998	40.0	39.0	41.0	35.0	41.0
26	38.7425	40.0	38.0	41.0	34.0	41.0
27	38.84475	40.0	38.0	41.0	35.0	41.0
28	38.63475	40.0	38.0	41.0	34.0	41.0
29	38.05375	40.0	38.0	41.0	32.0	41.0
30	38.29825	40.0	38.0	41.0	33.0	41.0
31	38.49125	40.0	38.0	41.0	34.0	41.0
32	38.17725	40.0	38.0	41.0	34.0	41.0
33	38.09625	40.0	38.0	41.0	33.0	41.0
34	37.9595	40.0	38.0	41.0	33.0	41.0
35	37.74325	39.0	37.0	40.0	33.0	41.0
36	37.527	39.0	37.0	41.0	32.0	41.0
37	37.351	40.0	37.0	41.0	31.0	41.0
38	37.5165	40.0	37.0	41.0	32.0	41.0
39	37.78	40.0	37.0	41.0	33.0	41.0
40	37.835	40.0	38.0	41.0	33.0	41.0
41	37.80775	40.0	38.0	41.0	33.0	41.0
42	38.0735	40.0	38.0	41.0	33.0	41.0
43	38.29275	40.0	38.0	41.0	33.0	41.0
44	38.17575	40.0	38.0	41.0	33.0	41.0
45	37.87225	40.0	38.0	41.0	33.0	41.0
46	37.098	40.0	37.0	41.0	31.0	41.0
47	36.55575	40.0	36.0	41.0	30.0	41.0
48	36.0915	39.0	35.0	41.0	29.0	41.0
49	36.35475	39.0	35.0	41.0	30.0	41.0
50	35.841	39.0	35.0	41.0	29.0	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	0.0
16	0.0
17	1.0
18	0.0
19	2.0
20	1.0
21	7.0
22	1.0
23	3.0
24	13.0
25	2.0
26	9.0
27	14.0
28	38.0
29	39.0
30	40.0
31	59.0
32	113.0
33	107.0
34	139.0
35	186.0
36	281.0
37	449.0
38	753.0
39	1742.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	7.630723042281712	22.742056542406804	57.29296972729547	12.334250688016011
2	26.775	25.974999999999998	21.3	25.95
3	16.225	19.425	22.1	42.25
4	28.175	38.0	12.6	21.224999999999998
5	22.25	38.3	29.025000000000002	10.424999999999999
6	33.300000000000004	15.875	38.175	12.65
7	12.475	23.95	23.65	39.925
8	23.7	40.475	15.275	20.549999999999997
9	17.7	38.5	30.775000000000002	13.025
10	18.075	20.974999999999998	26.625	34.325
11	33.550000000000004	8.85	13.975000000000001	43.625
12	14.274999999999999	17.25	24.875	43.6
13	21.099999999999998	20.175	40.2	18.525
14	40.275	21.275	24.474999999999998	13.975000000000001
15	38.425	20.175	28.975	12.425
16	13.0	23.35	23.474999999999998	40.175
17	27.35	23.225	38.725	10.7
18	31.6	18.025	25.4	24.975
19	37.724999999999994	13.875000000000002	32.4	16.0
20	49.5	17.275	21.45	11.774999999999999
21	19.85	26.825	26.625	26.700000000000003
22	33.475	10.6	48.65	7.2749999999999995
23	27.200000000000003	11.025	48.375	13.4
24	51.575	13.025	30.2	5.2
25	54.15	24.25	14.424999999999999	7.175
26	31.225	47.85	12.75	8.175
27	14.499999999999998	51.949999999999996	25.1	8.450000000000001
28	8.649999999999999	27.325	49.95	14.075
29	9.75	10.674999999999999	60.575	19.0
30	8.75	4.3	41.125	45.824999999999996
31	12.950000000000001	3.8	44.85	38.4
32	27.800000000000004	3.85	24.099999999999998	44.25
33	56.525000000000006	6.5	12.475	24.5
34	68.125	5.675	13.25	12.950000000000001
35	69.77499999999999	5.775	17.474999999999998	6.9750000000000005
36	45.9	5.675	36.199999999999996	12.225
37	44.875	8.85	23.0	23.275000000000002
38	24.525	15.475	10.9	49.1
39	13.450000000000001	23.674999999999997	8.025	54.85
40	13.325000000000001	49.175000000000004	8.0	29.5
41	24.5	54.449999999999996	5.7250000000000005	15.325
42	49.325	34.050000000000004	8.425	8.200000000000001
43	56.325	29.975	5.0	8.7
44	33.525	48.699999999999996	5.949999999999999	11.825
45	15.6	53.6	11.575000000000001	19.225
46	9.700000000000001	28.599999999999998	17.325	44.375
47	7.025	13.475000000000001	37.9	41.6
48	8.4	11.275	21.825	58.5
49	12.45	18.875	11.774999999999999	56.89999999999999
50	18.025	38.324999999999996	10.975	32.675
>>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	0.0
14	0.0
15	0.0
16	0.0
17	0.5
18	1.0
19	0.5
20	0.0
21	0.0
22	0.0
23	0.0
24	0.0
25	0.0
26	0.0
27	0.5
28	1.0
29	1.0
30	1.0
31	2.5
32	4.0
33	5.0
34	6.0
35	6.0
36	6.0
37	10.5
38	15.0
39	18.0
40	21.0
41	27.5
42	34.0
43	95.0
44	156.0
45	190.5
46	225.0
47	416.0
48	607.0
49	603.0
50	599.0
51	821.0
52	1043.0
53	694.5
54	346.0
55	367.0
56	388.0
57	309.0
58	230.0
59	162.0
60	94.0
61	68.0
62	42.0
63	66.0
64	90.0
65	51.5
66	13.0
67	11.0
68	9.0
69	16.5
70	24.0
71	30.0
72	36.0
73	20.5
74	5.0
75	3.0
76	1.0
77	0.5
78	0.0
79	1.0
80	2.0
81	1.0
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	0.0
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	33.5
#Duplication Level	Percentage of deduplicated	Percentage of total
1	75.0	25.124999999999996
2	9.701492537313433	6.5
3	4.253731343283582	4.275
4	2.014925373134328	2.7
5	1.791044776119403	3.0
6	0.8955223880597015	1.7999999999999998
7	0.3731343283582089	0.8750000000000001
8	0.5223880597014926	1.4000000000000001
9	0.7462686567164178	2.25
>10	4.104477611940299	28.449999999999996
>50	0.3731343283582089	8.85
>100	0.22388059701492538	14.774999999999999
>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
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	248	6.2	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	228	5.7	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	115	2.875	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	96	2.4	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	80	2.0	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	67	1.675	RNA PCR Primer, Index 1 (100% over 30bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	57	1.425	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	54	1.35	No Hit
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	48	1.2	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	47	1.175	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	47	1.175	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	46	1.15	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	38	0.95	RNA PCR Primer, Index 1 (100% over 27bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	37	0.9249999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	36	0.8999999999999999	RNA PCR Primer, Index 1 (100% over 26bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	31	0.775	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	31	0.775	RNA PCR Primer, Index 1 (100% over 26bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGA	30	0.75	RNA PCR Primer, Index 7 (97% over 35bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	27	0.675	RNA PCR Primer, Index 1 (100% over 29bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	25	0.625	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	24	0.6	RNA PCR Primer, Index 1 (100% over 30bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	24	0.6	RNA PCR Primer, Index 1 (100% over 30bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	24	0.6	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	23	0.575	RNA PCR Primer, Index 1 (100% over 29bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	23	0.575	RNA PCR Primer, Index 1 (100% over 28bp)
TTCCCTTTGTCATCCTATGCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	21	0.525	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	20	0.5	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	19	0.475	RNA PCR Primer, Index 1 (100% over 30bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	19	0.475	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 26bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	16	0.4	No Hit
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	15	0.375	RNA PCR Primer, Index 1 (100% over 33bp)
TCCTGTACTGAGCTGCCCCGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	13	0.325	No Hit
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	12	0.3	No Hit
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
TCCTGTACTGAGCTGCCCCGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	12	0.3	RNA PCR Primer, Index 1 (100% over 31bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	12	0.3	No Hit
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGACGACATCTCGTATGC	12	0.3	RNA PCR Primer, Index 41 (100% over 50bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGTTTGTACAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TCCTGTACTGAGCTGCCCCGATGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGACGACATCTC	11	0.27499999999999997	RNA PCR Primer, Index 41 (100% over 44bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTATGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TCTTTGGTTATCTAGCTGTATGTTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATTCAGGATAGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAATGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAGTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
CCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGAC	9	0.22499999999999998	RNA PCR Primer, Index 6 (97% over 36bp)
TGTAAACATCCTCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGATGAAGCACTGTAGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	8	0.2	No Hit
TGTAAACATCCTCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TAAGGCACGCGGTGAATGCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (100% over 30bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGGAATTCTCGGGTGCCA	8	0.2	No Hit
AACATTCAACGCTGTCGGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
CATTATTACTTTTGGTACGCGTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	7	0.17500000000000002	No Hit
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTCTGGAATTCTCGGGTGC	6	0.15	No Hit
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
ACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGA	6	0.15	RNA PCR Primer, Index 7 (97% over 35bp)
TAGCACCATCTGAAATCGGTTATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCCTGTACTGAGCTGCCCCGATTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	6	0.15	No Hit
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
CACCCGTAGAACCGACCTTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	5	0.125	No Hit
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
ACTGGACTTGGAGTCAGAAGGCTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCTGGAATTCTCGGGTGCCAAG	5	0.125	No Hit
CACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGACG	5	0.125	RNA PCR Primer, Index 31 (97% over 37bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	5	0.125	No Hit
TACAGTACTGTGATAACTGAATTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GTACAGTACTGTGATAACTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
GTACAGTACTGTGATAACTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	5	0.125	RNA PCR Primer, Index 1 (100% over 31bp)
TGCGGGGCTAGGGCTAACAGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTTGGAATTCTCGGGTGCC	5	0.125	No Hit
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TTAAGGCACGCGGTGAATGCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AGAGGTAGTAGGTTGCATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTGTGGTTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	5	0.125	RNA PCR Primer, Index 1 (100% over 31bp)
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGAATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GTGGGGGGCCCAAGTCCTTCTGATCGAGGCCTGGAATTCTCGGGTGCCAA	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	0.3	0.0	0.0	0.0
2	0.0	0.3	0.0	0.0	0.0
3	0.0	0.375	0.0	0.0	0.0
4	0.0	0.475	0.0	0.0	0.0
5	0.0	0.5	0.0	0.0	0.0
6	0.0	0.55	0.0	0.0	0.0
7	0.0	0.95	0.0	0.0	0.0
8	0.0	1.1	0.0	0.0	0.0
9	0.0	1.175	0.0	0.0	0.0
10	0.0	1.325	0.0	0.0	0.0
11	0.0	1.475	0.0	0.0	0.0
12	0.0	1.65	0.0	0.0	0.0
13	0.0	1.95	0.0	0.0	0.0
14	0.0	2.3	0.0	0.0	0.0
15	0.0	2.75	0.0	0.0	0.0
16	0.0	4.225	0.0	0.0	0.0
17	0.0	4.875	0.0	0.0	0.0
18	0.0	5.725	0.0	0.0	0.0
19	0.0	6.325	0.0	0.0	0.0
20	0.0	7.525	0.0	0.0	0.0
21	0.0	13.5	0.0	0.0	0.0
22	0.0	26.25	0.0	0.0	0.0
23	0.0	57.175	0.0	0.0	0.0
24	0.0	74.7	0.0	0.0	0.0
25	0.0	81.25	0.0	0.0	0.0
26	0.0	82.075	0.0	0.0	0.0
27	0.0	82.6	0.0	0.0	0.0
28	0.0	82.925	0.0	0.0	0.0
29	0.0	83.525	0.0	0.0	0.0
30	0.0	83.9	0.0	0.0	0.0
31	0.0	84.825	0.0	0.0	0.0
32	0.0	85.65	0.0	0.0	0.0
33	0.0	86.625	0.0	0.0	0.0
34	0.0	88.95	0.0	0.0	0.0
35	0.0	89.6	0.0	0.0	0.0
36	0.0	90.2	0.0	0.0	0.0
37	0.0	90.925	0.0	0.0	0.0
38	0.0	91.1	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
AACGCTG	45	2.728484E-10	44.000004	8
GGTTGTA	20	6.952051E-4	44.000004	11
ACGCTGT	45	2.728484E-10	44.000004	9
TTGTATA	20	6.952051E-4	44.000004	13
TTCAACG	45	2.728484E-10	44.000004	5
TCGGTGA	45	2.728484E-10	44.000004	15
ATAGGCT	20	6.952051E-4	44.000004	16
CATTCAA	45	2.728484E-10	44.000004	3
TCAACGC	45	2.728484E-10	44.000004	6
ACATTCA	45	2.728484E-10	44.000004	2
GTATAGT	20	6.952051E-4	44.000004	15
ATAGTTT	20	6.952051E-4	44.000004	17
GCTGTCG	45	2.728484E-10	44.000004	11
ACCCTTT	20	6.952051E-4	44.000004	9
AGGTTGT	20	6.952051E-4	44.000004	10
GACCCTT	20	6.952051E-4	44.000004	8
CCCTTTA	20	6.952051E-4	44.000004	10
CTGTCGG	45	2.728484E-10	44.000004	12
TGTATAG	20	6.952051E-4	44.000004	14
AGTTTGG	20	6.952051E-4	44.000004	19
>>END_MODULE
Read 217459 spots for SRR5030974.sra
Written 217459 spots for SRR5030974.sra
Read 217459 spots for SRR5030974.sra
Written 217459 spots for SRR5030974.sra
Read 217459 spots for SRR5030974.sra
Written 217459 spots for SRR5030974.sra
Read 217459 spots for SRR5030974.sra
Written 217459 spots for SRR5030974.sra
Read 217470 spots for SRR5030974.sra
Written 217470 spots for SRR5030974.sra
Read 217459 spots for SRR5030974.sra
Written 217459 spots for SRR5030974.sra
Read 217459 spots for SRR5030974.sra
Written 217459 spots for SRR5030974.sra
Read 217459 spots for SRR5030974.sra
Written 217459 spots for SRR5030974.sra
Read 217459 spots for SRR5030974.sra
Written 217459 spots for SRR5030974.sra
Read 217459 spots for SRR5030974.sra
Written 217459 spots for SRR5030974.sra
Read 217459 spots for SRR5030974.sra
Written 217459 spots for SRR5030974.sra
Read 217459 spots for SRR5030974.sra
Written 217459 spots for SRR5030974.sra
SRR ids: ['SRR5030974.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_h80pt_6r
SRR5030974.sra spots: 2609519
blocks: [[1, 217459], [217460, 434918], [434919, 652377], [652378, 869836], [869837, 1087295], [1087296, 1304754], [1304755, 1522213], [1522214, 1739672], [1739673, 1957131], [1957132, 2174590], [2174591, 2392049], [2392050, 2609519]]
SRR5030974 file size 451217
SRR5030974 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030974 SRR5030974_1.fastq
Input file:	SRR5030974_1.fastq
trimmed:	SRR5030974-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 06:57:26 2020 >> started

Wed Mar  4 06:57:28 2020 >> done (1.676s)
2609519 reads processed; of these:
    113 ( 0.00%) short reads filtered out after trimming by size control
      1 ( 0.00%) empty reads filtered out after trimming by size control
2609405 (100.00%) reads available; of these:
 161751 ( 6.20%) trimmed reads available after processing
2447654 (93.80%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     30	  0.00%
 19	     65	  0.00%
 20	    115	  0.00%
 21	    157	  0.01%
 22	    273	  0.01%
 23	    299	  0.01%
 24	    312	  0.01%
 25	    456	  0.02%
 26	    385	  0.01%
 27	    466	  0.02%
 28	    648	  0.02%
 29	    965	  0.04%
 30	    575	  0.02%
 31	    587	  0.02%
 32	    713	  0.03%
 33	    866	  0.03%
 34	   1115	  0.04%
 35	   1953	  0.07%
 36	   1897	  0.07%
 37	   1898	  0.07%
 38	   1893	  0.07%
 39	   2280	  0.09%
 40	   2787	  0.11%
 41	   3120	  0.12%
 42	   4310	  0.17%
 43	   6230	  0.24%
 44	   8922	  0.34%
 45	  11476	  0.44%
 46	  15246	  0.58%
 47	  17852	  0.68%
 48	  30072	  1.15%
 49	  43788	  1.68%
 50	2447654	 93.80%
2609405 reads passed initial QC


criterion=sequence-density
sequence-density=92.33
sequence-density-rank=1
fanout-score=18.34
fanout-score-rank=1
prefix-density=93.64
prefix-fanout=18.1
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGACGACATCTCGTATGCC


criterion=fanout-score
sequence-density=92.33
sequence-density-rank=1
fanout-score=18.34
fanout-score-rank=1
prefix-density=93.64
prefix-fanout=18.1
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 SRR5030974 -
Input file:	STDIN
trimmed:	SRR5030974-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 06:57:41 2020 >> started

Wed Mar  4 06:57:45 2020 >> done (3.484s)
2553289 reads processed; of these:
 140111 ( 5.49%) short reads filtered out after trimming by size control
  10347 ( 0.41%) empty reads filtered out after trimming by size control
2402831 (94.11%) reads available; of these:
2352013 (97.89%) trimmed reads available after processing
  50818 ( 2.11%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  14166	  0.59%
 19	  33947	  1.41%
 20	 132776	  5.53%
 21	 320910	 13.36%
 22	 863028	 35.92%
 23	 477498	 19.87%
 24	 157245	  6.54%
 25	  24190	  1.01%
 26	  12701	  0.53%
 27	  12034	  0.50%
 28	  13629	  0.57%
 29	  11135	  0.46%
 30	  18434	  0.77%
 31	  25479	  1.06%
 32	  27424	  1.14%
 33	  56687	  2.36%
 34	  21023	  0.87%
 35	  13163	  0.55%
 36	  13671	  0.57%
 37	   7818	  0.33%
 38	   8775	  0.37%
 39	   8123	  0.34%
 40	  10324	  0.43%
 41	  14200	  0.59%
 42	  15907	  0.66%
 43	  12689	  0.53%
 44	   9769	  0.41%
 45	  10162	  0.42%
 46	   7793	  0.32%
 47	   5863	  0.24%
 48	    549	  0.02%
 49	    820	  0.03%
 50	  40899	  1.70%


criterion=sequence-density
sequence-density=4.84
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=15
prefix-density=0.00
prefix-fanout=1.0
sequence=TCCCTGAGACCCTTTAACCTGTGAA


criterion=fanout-score
sequence-density=0.39
sequence-density-rank=30
fanout-score=8.25
fanout-score-rank=1
prefix-density=3.25
prefix-fanout=1.0
sequence=TAGTAGGTTGTGTGGTTTT
                                 Started job on |	Mar 04 06:58:04
                             Started mapping on |	Mar 04 06:58:05
                                    Finished on |	Mar 04 06:58:30
       Mapping speed, Million of reads per hour |	354.09

                          Number of input reads |	2458947
                      Average input read length |	24
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1123290
                        Uniquely mapped reads % |	45.68%
                          Average mapped length |	23.30
                       Number of splices: Total |	1059
            Number of splices: Annotated (sjdb) |	134
                       Number of splices: GT/AG |	984
                       Number of splices: GC/AG |	13
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	62
                      Mismatch rate per base, % |	0.12%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.78
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.18
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1109010
             % of reads mapped to multiple loci |	45.10%
        Number of reads mapped to too many loci |	47276
             % of reads mapped to too many loci |	1.92%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	6.60%
                     % of reads unmapped: other |	0.69%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	226647	226647	226647
N_multimapping	1109010	1109010	1109010
N_noFeature	46850	55640	851961
N_ambiguous	603255	366420	6956
UnstrandedReadsAssigned:473185 PositiveStrandReadsAssigned:701230 NegativeStrandReadsAssigned:264373
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=21 echo kmer=19
SRR5030974 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: SRR5030974-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,458,947 reads, 464,671 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,091 rounds

 109283 SRR5030974.ke.tsv
  52636 SRR5030974.se.tsv
 161919 total
==> SRR5030974.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

==> SRR5030974.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030974 completed mapping pipeline successfully
