Starting /dee2/code/volunteer_pipeline.sh SRR5030857
    current disk space = 160669974528
    free memory = 1049401372 
SRR5030857 SRAfilesize
ab1f6a8bb8340cdf8c2d6d411865ad8b  SRR5030857.sra
SRR5030857.sra file validated
SRR5030857 is single end
SRR5030857 is conventional basespace
SRR5030857 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030857_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	fail
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	32.3775	33.0	31.0	34.0	31.0	34.0
2	32.713	34.0	31.0	34.0	31.0	34.0
3	32.80125	34.0	31.0	34.0	31.0	34.0
4	36.23675	37.0	37.0	37.0	35.0	37.0
5	36.20375	37.0	37.0	37.0	35.0	37.0
6	36.009	37.0	35.0	37.0	35.0	37.0
7	36.0605	37.0	35.0	37.0	35.0	37.0
8	36.15225	37.0	36.0	37.0	35.0	37.0
9	37.93525	39.0	38.0	39.0	35.0	39.0
10	37.94225	39.0	38.0	39.0	35.0	39.0
11	37.91	39.0	38.0	39.0	35.0	39.0
12	37.82575	39.0	38.0	39.0	35.0	39.0
13	37.8565	39.0	38.0	39.0	35.0	39.0
14	39.28175	41.0	39.0	41.0	36.0	41.0
15	39.229	41.0	39.0	41.0	36.0	41.0
16	39.20425	41.0	39.0	41.0	36.0	41.0
17	39.31925	41.0	39.0	41.0	36.0	41.0
18	39.27225	41.0	39.0	41.0	36.0	41.0
19	39.09225	40.0	39.0	41.0	36.0	41.0
20	39.224	41.0	39.0	41.0	36.0	41.0
21	39.1965	40.0	39.0	41.0	36.0	41.0
22	39.2145	41.0	39.0	41.0	36.0	41.0
23	39.17775	40.0	39.0	41.0	36.0	41.0
24	38.4895	40.0	38.0	41.0	34.0	41.0
25	38.7655	40.0	38.0	41.0	34.0	41.0
26	38.72375	40.0	38.0	41.0	35.0	41.0
27	38.79825	40.0	38.0	41.0	35.0	41.0
28	38.72925	40.0	38.0	41.0	35.0	41.0
29	38.595	40.0	38.0	41.0	34.0	41.0
30	38.33475	40.0	38.0	41.0	33.0	41.0
31	38.77425	40.0	38.0	41.0	34.0	41.0
32	38.999	41.0	39.0	41.0	35.0	41.0
33	37.66	40.0	38.0	41.0	32.0	41.0
34	36.71725	40.0	37.0	41.0	30.0	41.0
35	32.43875	38.0	30.0	40.0	9.0	41.0
36	29.40575	37.0	19.0	40.0	8.0	41.0
37	29.609	36.0	23.0	39.0	6.0	41.0
38	32.15675	37.0	30.0	40.0	9.0	41.0
39	31.52925	37.0	30.0	40.0	5.0	41.0
40	32.374	38.0	31.0	40.0	2.0	41.0
41	30.079	36.0	26.0	40.0	2.0	41.0
42	31.76775	37.0	30.0	40.0	2.0	41.0
43	29.96175	37.0	26.0	40.0	2.0	41.0
44	30.848	37.0	30.0	40.0	2.0	41.0
45	28.4625	36.0	22.0	40.0	2.0	41.0
46	26.43225	34.0	7.0	39.0	2.0	41.0
47	26.573	34.0	2.0	39.0	2.0	41.0
48	27.304	35.0	2.0	40.0	2.0	41.0
49	25.7485	35.0	2.0	40.0	2.0	41.0
50	22.511	30.0	2.0	38.0	2.0	40.0
>>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
11	1.0
12	0.0
13	1.0
14	1.0
15	0.0
16	0.0
17	3.0
18	7.0
19	6.0
20	10.0
21	17.0
22	25.0
23	27.0
24	38.0
25	56.0
26	104.0
27	167.0
28	86.0
29	103.0
30	160.0
31	165.0
32	174.0
33	172.0
34	218.0
35	231.0
36	337.0
37	443.0
38	609.0
39	839.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	10.275689223057643	27.092731829573935	47.4937343358396	15.137844611528822
2	23.674999999999997	29.049999999999997	18.825	28.449999999999996
3	23.849999999999998	22.25	22.15	31.75
4	28.499999999999996	28.449999999999996	16.175	26.875
5	21.224999999999998	40.25	26.5	12.025
6	32.725	17.65	35.325	14.299999999999999
7	17.4	19.425	26.424999999999997	36.75
8	26.700000000000003	31.474999999999998	14.2	27.625
9	18.575	36.1	30.825000000000003	14.499999999999998
10	24.2	22.35	27.1	26.35
11	33.550000000000004	13.075000000000001	17.65	35.725
12	16.575	19.625	29.799999999999997	34.0
13	31.125000000000004	20.025000000000002	30.875000000000004	17.974999999999998
14	31.125000000000004	30.225	20.849999999999998	17.8
15	30.2	26.1	28.125	15.575
16	17.724999999999998	21.75	21.224999999999998	39.300000000000004
17	23.025000000000002	22.675	38.475	15.825
18	24.2	18.425	29.049999999999997	28.325
19	31.55	14.7	33.75	20.0
20	39.300000000000004	16.25	28.299999999999997	16.150000000000002
21	23.95	22.025	28.625	25.4
22	30.725	12.875	44.375	12.025
23	26.625	14.674999999999999	42.15	16.55
24	50.275000000000006	14.224999999999998	24.8	10.7
25	48.375	23.45	15.525	12.65
26	28.675	43.95	13.750000000000002	13.625000000000002
27	15.625	46.050000000000004	23.849999999999998	14.475
28	12.7	26.075	46.425	14.799999999999999
29	10.225	14.825	56.925000000000004	18.025
30	10.225	8.450000000000001	37.2	44.125
31	15.25	6.275	45.225	33.25
32	28.925	6.225	22.175	42.675000000000004
33	51.37500000000001	8.649999999999999	15.049999999999999	24.925
34	60.099999999999994	7.074999999999999	15.65	17.175
35	58.550000000000004	6.9750000000000005	21.9	12.575
36	63.14999999999999	9.15	14.475	13.225000000000001
37	38.175	11.25	21.15	29.425
38	25.074999999999996	14.549999999999999	13.950000000000001	46.425
39	18.224999999999998	26.424999999999997	10.325	45.025
40	17.25	45.324999999999996	12.174999999999999	25.25
41	29.799999999999997	42.4	11.525	16.275000000000002
42	48.525	30.3	10.925	10.25
43	44.425	35.675000000000004	9.75	10.15
44	30.9	47.85	7.8	13.450000000000001
45	20.375	43.6	11.3	24.725
46	12.8	28.999999999999996	27.175	31.025000000000002
47	9.475	17.75	31.324999999999996	41.449999999999996
48	10.7	13.0	22.15	54.15
49	13.075000000000001	25.174999999999997	15.575	46.175
50	32.00800200050013	23.330832708177045	11.77794448612153	32.883220805201304
>>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	0.0
18	0.0
19	0.0
20	0.0
21	1.0
22	2.0
23	1.0
24	0.0
25	2.0
26	4.0
27	4.5
28	5.0
29	3.0
30	1.0
31	7.5
32	14.0
33	21.5
34	29.0
35	37.5
36	46.0
37	64.0
38	82.0
39	72.0
40	62.0
41	68.0
42	74.0
43	98.5
44	123.0
45	151.5
46	180.0
47	248.5
48	317.0
49	425.0
50	533.0
51	686.0
52	839.0
53	683.5
54	528.0
55	454.5
56	381.0
57	345.0
58	309.0
59	225.0
60	141.0
61	109.5
62	78.0
63	92.0
64	106.0
65	65.5
66	25.0
67	19.5
68	14.0
69	20.0
70	26.0
71	40.0
72	54.0
73	32.0
74	10.0
75	7.0
76	4.0
77	5.0
78	6.0
79	5.5
80	5.0
81	3.0
82	1.0
83	0.5
84	0.0
85	0.0
86	0.0
87	0.0
88	0.0
89	0.0
90	0.0
91	0.0
92	0.0
93	0.0
94	0.0
95	0.0
96	0.0
97	0.0
98	0.0
99	0.0
100	0.0
>>END_MODULE
>>Per base N content	pass
#Base	N-Count
1	0.25
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	0.025
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
50	4000.0
>>END_MODULE
>>Sequence Duplication Levels	warn
#Total Deduplicated Percentage	52.625
#Duplication Level	Percentage of deduplicated	Percentage of total
1	80.33254156769596	42.275
2	8.883610451306414	9.35
3	3.040380047505938	4.8
4	1.9002375296912115	4.0
5	1.0926365795724466	2.875
6	0.9976247030878859	3.15
7	0.9501187648456058	3.5000000000000004
8	0.14251781472684086	0.6
9	0.38004750593824227	1.7999999999999998
>10	2.137767220902613	20.925
>50	0.09501187648456057	3.75
>100	0.047505938242280284	2.9749999999999996
>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
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	119	2.9749999999999996	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	96	2.4	RNA PCR Primer, Index 1 (100% over 29bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	54	1.35	No Hit
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	39	0.975	RNA PCR Primer, Index 1 (96% over 28bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	38	0.95	RNA PCR Primer, Index 1 (100% over 26bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	36	0.8999999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	32	0.8	RNA PCR Primer, Index 1 (96% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	32	0.8	RNA PCR Primer, Index 1 (96% over 28bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	31	0.775	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 30bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	27	0.675	RNA PCR Primer, Index 1 (100% over 27bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	27	0.675	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	24	0.6	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 29bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	22	0.5499999999999999	No Hit
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	21	0.525	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	20	0.5	RNA PCR Primer, Index 1 (100% over 26bp)
TGAACTGATGATATCATTTCTTTCCCCGTCAGATCGACCCTGTTGATCTC	19	0.475	No Hit
GACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGCT	19	0.475	No Hit
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTG	19	0.475	RNA PCR Primer, Index 2 (97% over 35bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 33bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	18	0.44999999999999996	No Hit
GTAAATGATGAGATTCCATTGGTCCGTGTTTCTGAACTACATGATTTTCC	18	0.44999999999999996	No Hit
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 29bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	17	0.42500000000000004	No Hit
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGC	17	0.42500000000000004	RNA PCR Primer, Index 1 (96% over 29bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTGACCAATCTC	15	0.375	RNA PCR Primer, Index 4 (100% over 44bp)
GCGGATGATGACACCTGGGTATGCTGCACACTCCCGACTGCGTCGTGGGG	15	0.375	No Hit
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (96% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCG	14	0.35000000000000003	RNA PCR Primer, Index 1 (96% over 27bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTGACCAATCTCGTATGC	14	0.35000000000000003	RNA PCR Primer, Index 4 (100% over 50bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCGG	14	0.35000000000000003	No Hit
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	13	0.325	No Hit
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	13	0.325	RNA PCR Primer, Index 1 (100% over 26bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	12	0.3	RNA PCR Primer, Index 1 (100% over 26bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	12	0.3	No Hit
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCG	11	0.27499999999999997	No Hit
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
CGACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGC	10	0.25	No Hit
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TGCTGTGATGAGATGACTAAGTAGGAAGTGCCGTCAGAGTCGATAACTGA	9	0.22499999999999998	No Hit
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAC	9	0.22499999999999998	No Hit
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	9	0.22499999999999998	No Hit
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGGGCCAAGGAACTCCG	9	0.22499999999999998	RNA PCR Primer, Index 1 (96% over 27bp)
CTAGACTGAGGCTCCTTGAGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	8	0.2	No Hit
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGATTGTATAGTTATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
GCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 32bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (96% over 28bp)
AAGGGATTCTGATGTTGGTCACATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
CACCCTGATGAACTGAATACCGCCCCAGTCTGATAGCTGTGGAGAAAGGT	7	0.17500000000000002	No Hit
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (96% over 28bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCG	7	0.17500000000000002	RNA PCR Primer, Index 1 (96% over 27bp)
TTGCAATGATGACTTATATATCTGTCAATCCCCTGAGAGATCACTGACGA	7	0.17500000000000002	No Hit
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	7	0.17500000000000002	No Hit
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGAAATCAAA	7	0.17500000000000002	No Hit
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCG	7	0.17500000000000002	RNA PCR Primer, Index 1 (96% over 27bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGGGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (96% over 28bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	7	0.17500000000000002	No Hit
AAGGGATTCTGATGTTGGTCACACTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGGGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (96% over 28bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
GGTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCG	6	0.15	No Hit
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCG	6	0.15	RNA PCR Primer, Index 1 (96% over 27bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	6	0.15	No Hit
TCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCC	6	0.15	No Hit
ATATATGATGACTTTCATAGAATCTCGTTCGGCTGATGATTGCTGTTGAG	6	0.15	No Hit
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAATTCCG	6	0.15	RNA PCR Primer, Index 1 (95% over 23bp)
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	6	0.15	No Hit
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGGGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (96% over 28bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGGAATTCTCGGGTGCCAA	6	0.15	No Hit
CTGCAGTGATGACTATCTTAGGACACCTTTGGATTTACCGTGAAAAGAAG	6	0.15	No Hit
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
GTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCGG	6	0.15	No Hit
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTC	6	0.15	No Hit
GTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATACT	6	0.15	No Hit
GTGAAATGATGGCAAATCATCTTTCGGGACTGACCTGAAATGAAGAGAAT	6	0.15	No Hit
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGTGCCCAGGAACTCCAG	5	0.125	No Hit
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GCATGTGATGACATTATTTAGCGACCAAAGTCTGATAAAGATGATTGTGA	5	0.125	No Hit
GCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAATTC	5	0.125	No Hit
CATTATTACTTTTGGTACGCGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAA	5	0.125	No Hit
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AGCCCATGATGGTATGAGAGTAGTGGACAGAAGGGATTTCTGAAAAACAC	5	0.125	No Hit
TTCAAGTAATCCAGGATAGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGTGCCAAGGAACTCCAG	5	0.125	No Hit
AACATTCAACGCTGTCGGTGAGTTTTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
TTGTGCTTGATCTAACCATGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATT	5	0.125	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGGAATTCTCGGGTGCCAA	5	0.125	No Hit
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGGGCCAAGGAACTCCAGC	5	0.125	RNA PCR Primer, Index 1 (96% over 29bp)
TGCGGGGCTAGGGCTAACAGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
ACTAATCCTAGCCCTAGCCCTACACAAATATAATTATACTATTATTGGAA	5	0.125	No Hit
GTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAAT	5	0.125	No Hit
AACATTCAACCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
>>END_MODULE
>>Adapter Content	fail
#Position	Illumina Universal Adapter	Illumina Small RNA 3' Adapter	Illumina Small RNA 5' Adapter	Nextera Transposase Sequence	SOLID Small RNA Adapter
1	0.0	0.4	0.0	0.0	0.0
2	0.0	0.4	0.0	0.0	0.0
3	0.0	0.525	0.0	0.0	0.0
4	0.0	0.55	0.0	0.0	0.0
5	0.0	0.575	0.0	0.0	0.0
6	0.0	0.675	0.0	0.0	0.0
7	0.0	1.15	0.0	0.0	0.0
8	0.0	1.25	0.0	0.0	0.0
9	0.0	1.35	0.0	0.0	0.0
10	0.0	1.475	0.0	0.0	0.0
11	0.0	1.65	0.0	0.0	0.0
12	0.0	1.825	0.0	0.0	0.0
13	0.0	2.0	0.0	0.0	0.0
14	0.0	2.2	0.0	0.0	0.0
15	0.0	2.35	0.0	0.0	0.0
16	0.0	3.125	0.0	0.0	0.0
17	0.0	3.725	0.0	0.0	0.0
18	0.0	4.425	0.0	0.0	0.0
19	0.0	4.775	0.0	0.0	0.0
20	0.0	5.725	0.0	0.0	0.0
21	0.0	10.3	0.0	0.0	0.0
22	0.0	20.925	0.0	0.0	0.0
23	0.0	48.05	0.0	0.0	0.0
24	0.0	60.7	0.0	0.0	0.0
25	0.0	66.9	0.0	0.0	0.0
26	0.0	68.525	0.0	0.0	0.0
27	0.0	69.225	0.0	0.0	0.0
28	0.0	69.7	0.0	0.0	0.0
29	0.0	69.875	0.0	0.0	0.0
30	0.0	70.275	0.0	0.0	0.0
31	0.0	70.75	0.0	0.0	0.0
32	0.0	71.725	0.0	0.0	0.0
33	0.0	72.475	0.0	0.0	0.0
34	0.0	74.675	0.0	0.0	0.0
35	0.0	75.4	0.0	0.0	0.0
36	0.0	75.7	0.0	0.0	0.0
37	0.0	75.95	0.0	0.0	0.0
38	0.0	76.25	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TTCAAGT	30	1.7904422E-6	44.531647	1
TCGGATC	25	3.4343255E-5	44.531647	1
TGAGGTA	30	1.7904422E-6	44.531647	1
AACATTC	30	1.7904422E-6	44.531647	1
TCACAGT	20	6.54202E-4	44.531643	1
AACGCTG	30	1.9592044E-6	43.975002	8
GGTGAGT	25	3.7082697E-5	43.975002	17
AAGTAAT	30	1.9592044E-6	43.975002	4
TCAAGTA	30	1.9592044E-6	43.975002	2
ACGCTGT	30	1.9592044E-6	43.975002	9
AATCCAG	30	1.9592044E-6	43.975002	8
CTGAGCT	25	3.7082697E-5	43.975002	11
ATCCAGG	30	1.9592044E-6	43.975002	9
TTCAACG	30	1.9592044E-6	43.975002	5
AGGATAG	30	1.9592044E-6	43.975002	13
TCGGTGA	30	1.9592044E-6	43.975002	15
ATAGGCT	25	3.7082697E-5	43.975002	16
GAGCTTG	25	3.7082697E-5	43.975002	13
GGATCCG	25	3.7082697E-5	43.975002	3
CCGTCTG	25	3.7082697E-5	43.975002	7
>>END_MODULE
Read 60920 spots for SRR5030857.sra
Written 60920 spots for SRR5030857.sra
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Read 60920 spots for SRR5030857.sra
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Read 60920 spots for SRR5030857.sra
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SRR ids: ['SRR5030857.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_s0aa4h0w
SRR5030857.sra spots: 2924179
blocks: [[1, 60920], [60921, 121840], [121841, 182760], [182761, 243680], [243681, 304600], [304601, 365520], [365521, 426440], [426441, 487360], [487361, 548280], [548281, 609200], [609201, 670120], [670121, 731040], [731041, 791960], [791961, 852880], [852881, 913800], [913801, 974720], [974721, 1035640], [1035641, 1096560], [1096561, 1157480], [1157481, 1218400], [1218401, 1279320], [1279321, 1340240], [1340241, 1401160], [1401161, 1462080], [1462081, 1523000], [1523001, 1583920], [1583921, 1644840], [1644841, 1705760], [1705761, 1766680], [1766681, 1827600], [1827601, 1888520], [1888521, 1949440], [1949441, 2010360], [2010361, 2071280], [2071281, 2132200], [2132201, 2193120], [2193121, 2254040], [2254041, 2314960], [2314961, 2375880], [2375881, 2436800], [2436801, 2497720], [2497721, 2558640], [2558641, 2619560], [2619561, 2680480], [2680481, 2741400], [2741401, 2802320], [2802321, 2863240], [2863241, 2924179]]
SRR5030857 file size 505748
SRR5030857 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 48 -o SRR5030857 SRR5030857_1.fastq
Input file:	SRR5030857_1.fastq
trimmed:	SRR5030857-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):	32
Wed Mar  4 06:29:23 2020 >> started

Wed Mar  4 06:29:25 2020 >> done (1.704s)
2924179 reads processed; of these:
    150 ( 0.01%) short reads filtered out after trimming by size control
      6 ( 0.00%) empty reads filtered out after trimming by size control
2924023 (99.99%) reads available; of these:
 346063 (11.84%) trimmed reads available after processing
2577960 (88.16%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     44	  0.00%
 19	     60	  0.00%
 20	    132	  0.00%
 21	    174	  0.01%
 22	    330	  0.01%
 23	    402	  0.01%
 24	    375	  0.01%
 25	    540	  0.02%
 26	    521	  0.02%
 27	    627	  0.02%
 28	    841	  0.03%
 29	   1279	  0.04%
 30	    944	  0.03%
 31	   1279	  0.04%
 32	   3374	  0.12%
 33	  10441	  0.36%
 34	  24490	  0.84%
 35	   5707	  0.20%
 36	   6261	  0.21%
 37	   3541	  0.12%
 38	   7082	  0.24%
 39	   6472	  0.22%
 40	  12723	  0.44%
 41	   7004	  0.24%
 42	  17260	  0.59%
 43	   8011	  0.27%
 44	  36029	  1.23%
 45	  20529	  0.70%
 46	  18834	  0.64%
 47	  20820	  0.71%
 48	  60669	  2.07%
 49	  69268	  2.37%
 50	2577960	 88.16%
2924023 reads passed initial QC


criterion=sequence-density
sequence-density=76.05
sequence-density-rank=1
fanout-score=20.32
fanout-score-rank=3
prefix-density=78.43
prefix-fanout=19.7
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTGACCAATCTCGTATGCC


criterion=fanout-score
sequence-density=1.62
sequence-density-rank=5
fanout-score=440.31
fanout-score-rank=1
prefix-density=77.61
prefix-fanout=9.2
sequence=GGAATTCTCGGTGCCAAGGA
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 48 -x TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTGACCAATCTCGTATGCC -o SRR5030857 -
Input file:	STDIN
trimmed:	SRR5030857-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTGACCAATCTCGTATGCC
-- 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):	32
Wed Mar  4 06:29:41 2020 >> started

Wed Mar  4 06:29:46 2020 >> done (4.384s)
2848074 reads processed; of these:
 126432 ( 4.44%) short reads filtered out after trimming by size control
  14130 ( 0.50%) empty reads filtered out after trimming by size control
2707512 (95.06%) reads available; of these:
2278017 (84.14%) trimmed reads available after processing
 429495 (15.86%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  17856	  0.66%
 19	  26185	  0.97%
 20	 129436	  4.78%
 21	 315370	 11.65%
 22	 751295	 27.75%
 23	 362136	 13.38%
 24	 179763	  6.64%
 25	  45081	  1.67%
 26	  23518	  0.87%
 27	  17732	  0.65%
 28	  19200	  0.71%
 29	  15142	  0.56%
 30	  18640	  0.69%
 31	  21242	  0.78%
 32	  23781	  0.88%
 33	  63965	  2.36%
 34	  19666	  0.73%
 35	  14269	  0.53%
 36	  18320	  0.68%
 37	  12348	  0.46%
 38	  14233	  0.53%
 39	  15096	  0.56%
 40	  24405	  0.90%
 41	  29845	  1.10%
 42	  38690	  1.43%
 43	  25682	  0.95%
 44	  23664	  0.87%
 45	  27694	  1.02%
 46	  22282	  0.82%
 47	  17203	  0.64%
 48	   6859	  0.25%
 49	  12426	  0.46%
 50	 354488	 13.09%


criterion=sequence-density
sequence-density=5.96
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=16
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.01
sequence-density-rank=41
fanout-score=274.28
fanout-score-rank=1
prefix-density=2.15
prefix-fanout=1.8
sequence=TTGTATAGTTTAACAGTCTACAGCCATGGTCGT
                                 Started job on |	Mar 04 06:30:27
                             Started mapping on |	Mar 04 06:30:27
                                    Finished on |	Mar 04 06:30:55
       Mapping speed, Million of reads per hour |	357.87

                          Number of input reads |	2783461
                      Average input read length |	29
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1517741
                        Uniquely mapped reads % |	54.53%
                          Average mapped length |	27.97
                       Number of splices: Total |	1430
            Number of splices: Annotated (sjdb) |	190
                       Number of splices: GT/AG |	1299
                       Number of splices: GC/AG |	18
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	113
                      Mismatch rate per base, % |	0.21%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.24
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.04
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	863531
             % of reads mapped to multiple loci |	31.02%
        Number of reads mapped to too many loci |	48524
             % of reads mapped to too many loci |	1.74%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	12.15%
                     % of reads unmapped: other |	0.55%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	402189	402189	402189
N_multimapping	863531	863531	863531
N_noFeature	67777	84790	1125956
N_ambiguous	827256	489017	15954
UnstrandedReadsAssigned:622708 PositiveStrandReadsAssigned:943934 NegativeStrandReadsAssigned:375831
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5030857 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: SRR5030857-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,783,461 reads, 668,793 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,046 rounds

 109283 SRR5030857.ke.tsv
  52636 SRR5030857.se.tsv
 161919 total
==> SRR5030857.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

==> SRR5030857.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030857 completed mapping pipeline successfully
