Starting /dee2/code/volunteer_pipeline.sh SRR5030934
    current disk space = 160620003328
    free memory = 1048250188 
SRR5030934 SRAfilesize
c5fa687fffd505e279d35e47611b891f  SRR5030934.sra
SRR5030934.sra file validated
SRR5030934 is single end
SRR5030934 is conventional basespace
SRR5030934 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030934_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	32.35225	33.0	31.0	34.0	31.0	34.0
2	32.7145	34.0	31.0	34.0	31.0	34.0
3	32.79025	34.0	31.0	34.0	31.0	34.0
4	36.21025	37.0	37.0	37.0	35.0	37.0
5	36.1385	37.0	37.0	37.0	35.0	37.0
6	36.055	37.0	35.0	37.0	35.0	37.0
7	36.14325	37.0	35.0	37.0	35.0	37.0
8	36.09625	37.0	35.0	37.0	35.0	37.0
9	37.8225	39.0	38.0	39.0	35.0	39.0
10	37.76875	39.0	38.0	39.0	35.0	39.0
11	37.8065	39.0	38.0	39.0	35.0	39.0
12	37.90125	39.0	38.0	39.0	35.0	39.0
13	37.78575	39.0	38.0	39.0	35.0	39.0
14	39.21375	41.0	39.0	41.0	36.0	41.0
15	39.25575	41.0	39.0	41.0	36.0	41.0
16	39.14275	40.0	39.0	41.0	36.0	41.0
17	39.267	41.0	39.0	41.0	36.0	41.0
18	39.2115	41.0	39.0	41.0	36.0	41.0
19	39.0245	40.0	38.0	41.0	35.0	41.0
20	39.1125	40.0	39.0	41.0	35.0	41.0
21	39.082	40.0	39.0	41.0	35.0	41.0
22	39.05075	40.0	39.0	41.0	36.0	41.0
23	39.01025	40.0	39.0	41.0	36.0	41.0
24	38.4165	40.0	38.0	41.0	34.0	41.0
25	38.6185	40.0	38.0	41.0	34.0	41.0
26	38.6285	40.0	38.0	41.0	34.0	41.0
27	38.61575	40.0	38.0	41.0	34.0	41.0
28	38.601	40.0	38.0	41.0	34.0	41.0
29	38.38075	40.0	38.0	41.0	34.0	41.0
30	38.14775	40.0	38.0	41.0	33.0	41.0
31	38.5115	40.0	38.0	41.0	34.0	41.0
32	38.723	40.0	38.0	41.0	35.0	41.0
33	37.1255	40.0	37.0	41.0	31.0	41.0
34	36.52925	40.0	36.0	41.0	30.0	41.0
35	32.68825	38.0	31.0	40.0	15.0	41.0
36	29.944	37.0	23.0	40.0	8.0	41.0
37	30.486	37.0	25.0	40.0	7.0	41.0
38	32.58075	37.0	30.0	40.0	16.0	41.0
39	32.196	37.0	31.0	40.0	9.0	41.0
40	33.065	38.0	33.0	40.0	9.0	41.0
41	30.87325	37.0	28.0	40.0	2.0	41.0
42	32.26575	37.0	31.0	40.0	2.0	41.0
43	30.52575	37.0	26.0	40.0	2.0	41.0
44	31.5525	37.0	31.0	40.0	2.0	41.0
45	29.45925	37.0	26.0	40.0	2.0	41.0
46	27.4285	35.0	15.0	40.0	2.0	41.0
47	27.4235	35.0	15.0	39.0	2.0	41.0
48	28.02475	35.0	21.0	39.0	2.0	41.0
49	26.542	35.0	2.0	39.0	2.0	41.0
50	23.05925	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
13	1.0
14	0.0
15	1.0
16	2.0
17	5.0
18	2.0
19	9.0
20	8.0
21	13.0
22	24.0
23	33.0
24	44.0
25	54.0
26	75.0
27	134.0
28	66.0
29	111.0
30	159.0
31	190.0
32	162.0
33	176.0
34	231.0
35	263.0
36	319.0
37	409.0
38	673.0
39	836.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	12.769153730595894	25.363044566850274	46.619929894842265	15.247871807711565
2	24.775	29.375	19.45	26.400000000000002
3	23.200000000000003	19.225	23.400000000000002	34.175
4	30.0	29.95	15.75	24.3
5	22.75	36.3	26.974999999999998	13.975000000000001
6	28.799999999999997	18.15	39.675	13.375
7	20.625	20.4	23.875	35.099999999999994
8	23.5	32.85	15.725	27.925
9	20.275000000000002	34.0	29.775000000000002	15.950000000000001
10	24.474999999999998	18.275	28.775000000000002	28.475
11	34.8	16.025	15.25	33.925
12	16.775000000000002	23.400000000000002	29.2	30.625000000000004
13	26.400000000000002	19.225	33.050000000000004	21.325
14	30.45	27.175	23.150000000000002	19.225
15	33.375	22.975	25.95	17.7
16	17.150000000000002	22.425	22.45	37.974999999999994
17	25.55	23.25	34.275	16.925
18	25.7	18.575	32.9	22.825
19	31.1	17.724999999999998	32.4	18.775
20	41.075	16.400000000000002	25.575	16.950000000000003
21	24.224999999999998	23.724999999999998	25.35	26.700000000000003
22	29.549999999999997	15.675	41.949999999999996	12.825000000000001
23	25.2	15.125	42.449999999999996	17.224999999999998
24	46.2	14.374999999999998	27.425	12.0
25	48.0	21.525	17.5	12.975
26	28.849999999999998	42.3	15.024999999999999	13.825000000000001
27	18.475	44.55	22.175	14.799999999999999
28	14.649999999999999	26.950000000000003	43.8	14.6
29	12.35	14.75	53.349999999999994	19.55
30	11.95	8.1	37.375	42.575
31	14.85	7.35	43.1	34.699999999999996
32	27.275	7.6499999999999995	23.925	41.15
33	49.3	9.9	16.1	24.7
34	57.375	9.25	15.775	17.599999999999998
35	55.225	10.674999999999999	21.15	12.950000000000001
36	58.62500000000001	10.625	16.25	14.499999999999998
37	37.375	12.8	23.25	26.575
38	27.224999999999998	14.124999999999998	15.35	43.3
39	19.275000000000002	24.85	10.375	45.5
40	17.275	43.65	13.575000000000001	25.5
41	27.675	42.225	12.5	17.599999999999998
42	46.175	30.95	11.975	10.9
43	42.925000000000004	35.475	10.45	11.15
44	32.025	44.425	9.575	13.975000000000001
45	19.725	44.5	12.35	23.425
46	14.224999999999998	29.775000000000002	25.2	30.8
47	10.8	18.7	31.075000000000003	39.425
48	12.6	13.4	22.3	51.7
49	15.024999999999999	25.074999999999996	15.575	44.324999999999996
50	30.775000000000002	24.099999999999998	11.125	34.0
>>END_MODULE
>>Per sequence GC content	warn
#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	1.0
12	1.0
13	0.5
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	0.5
26	1.0
27	0.5
28	0.0
29	2.0
30	4.0
31	11.0
32	18.0
33	22.5
34	27.0
35	38.5
36	50.0
37	63.5
38	77.0
39	75.0
40	73.0
41	79.0
42	85.0
43	101.0
44	117.0
45	167.0
46	217.0
47	273.5
48	330.0
49	423.0
50	516.0
51	663.0
52	810.0
53	649.5
54	489.0
55	446.0
56	403.0
57	357.5
58	312.0
59	231.5
60	151.0
61	119.0
62	87.0
63	98.5
64	110.0
65	72.0
66	34.0
67	23.0
68	12.0
69	13.5
70	15.0
71	28.0
72	41.0
73	24.5
74	8.0
75	5.5
76	3.0
77	2.5
78	2.0
79	2.5
80	3.0
81	2.5
82	2.0
83	1.5
84	1.0
85	0.5
86	0.0
87	0.0
88	0.0
89	0.0
90	0.0
91	0.0
92	0.0
93	0.0
94	0.0
95	0.0
96	0.0
97	0.0
98	0.0
99	0.0
100	0.0
>>END_MODULE
>>Per base N content	pass
#Base	N-Count
1	0.15
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	warn
#Total Deduplicated Percentage	53.27499999999999
#Duplication Level	Percentage of deduplicated	Percentage of total
1	80.76020647583294	43.025000000000006
2	8.587517597372125	9.15
3	2.9094321914594086	4.65
4	1.923979352416706	4.1000000000000005
5	1.0323791647114031	2.75
6	0.656968559361802	2.1
7	0.656968559361802	2.45
8	0.6100422336931018	2.6
9	0.14077897700610043	0.675
>10	2.674800563115908	24.8
>50	0.0	0.0
>100	0.04692632566870014	3.6999999999999997
>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	148	3.6999999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	38	0.95	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	37	0.9249999999999999	RNA PCR Primer, Index 1 (100% over 26bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	33	0.8250000000000001	No Hit
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTACAGCATCTCGTATGC	32	0.8	RNA PCR Primer, Index 43 (100% over 50bp)
GGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	29	0.7250000000000001	No Hit
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	26	0.65	RNA PCR Primer, Index 1 (100% over 26bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTA	25	0.625	RNA PCR Primer, Index 7 (97% over 35bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	25	0.625	RNA PCR Primer, Index 1 (100% over 30bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	24	0.6	RNA PCR Primer, Index 1 (96% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	24	0.6	RNA PCR Primer, Index 1 (96% over 28bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	23	0.575	RNA PCR Primer, Index 1 (100% over 27bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	21	0.525	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	21	0.525	RNA PCR Primer, Index 1 (100% over 27bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	20	0.5	RNA PCR Primer, Index 1 (100% over 33bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	20	0.5	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	19	0.475	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	19	0.475	RNA PCR Primer, Index 1 (100% over 26bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (96% over 28bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	17	0.42500000000000004	No Hit
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (96% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCG	17	0.42500000000000004	RNA PCR Primer, Index 1 (96% over 27bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	16	0.4	RNA PCR Primer, Index 1 (100% over 27bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTACAGCATCTC	16	0.4	RNA PCR Primer, Index 43 (100% over 44bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGAAATCAAA	16	0.4	No Hit
GACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGCT	15	0.375	No Hit
TGCGGGGCTAGGGCTAACAGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCG	15	0.375	No Hit
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	15	0.375	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	14	0.35000000000000003	No Hit
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 27bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
GGTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCG	13	0.325	No Hit
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (96% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCG	12	0.3	RNA PCR Primer, Index 1 (96% over 27bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGC	12	0.3	RNA PCR Primer, Index 1 (96% over 29bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	12	0.3	No Hit
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCG	11	0.27499999999999997	RNA PCR Primer, Index 1 (96% over 27bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
CGACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGC	10	0.25	No Hit
TGCTGTGATGAGATGACTAAGTAGGAAGTGCCGTCAGAGTCGATAACTGA	10	0.25	No Hit
CATTATTACTTTTGGTACGCGTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	10	0.25	RNA PCR Primer, Index 1 (100% over 25bp)
TTGCAATGATGACTTATATATCTGTCAATCCCCTGAGAGATCACTGACGA	10	0.25	No Hit
ATACATGATGATCTCACACAACTTGAACTCTCTCACTGATTACTTGATGA	10	0.25	No Hit
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGGGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (96% over 28bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	9	0.22499999999999998	No Hit
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	8	0.2	No Hit
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCG	8	0.2	RNA PCR Primer, Index 1 (96% over 27bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	8	0.2	No Hit
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCG	8	0.2	RNA PCR Primer, Index 1 (96% over 27bp)
TCCTGTACTGAGCTGCCCCGATGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (96% over 28bp)
GTAAATGATGAGATTCCATTGGTCCGTGTTTCTGAACTACATGATTTTCC	8	0.2	No Hit
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCGG	8	0.2	No Hit
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	8	0.2	No Hit
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
GCATGTGATGACATTATTTAGCGACCAAAGTCTGATAAAGATGATTGTGA	7	0.17500000000000002	No Hit
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	7	0.17500000000000002	No Hit
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAA	7	0.17500000000000002	No Hit
TGAACTGATGATATCATTTCTTTCCCCGTCAGATCGACCCTGTTGATCTC	7	0.17500000000000002	No Hit
TGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	7	0.17500000000000002	No Hit
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	7	0.17500000000000002	No Hit
GCGGATGATGACACCTGGGTATGCTGCACACTCCCGACTGCGTCGTGGGG	7	0.17500000000000002	No Hit
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
CCTGCATGATGACGAACAAATACTGACTACCTGAAGATCTTATTAGCTCT	7	0.17500000000000002	No Hit
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	7	0.17500000000000002	No Hit
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TATTGCACTCGTCCCGGCCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
CACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGT	6	0.15	No Hit
GCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAATTC	6	0.15	No Hit
CTTCTCACTACTGCACTTGACTAGTCTTGGAATTCTCGGGTGCCAAGGAA	6	0.15	RNA PCR Primer, Index 1 (100% over 23bp)
TATTGCACTCGTCCCGGCCTCCATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
AAGGGATTCTGATGTTGGTCACATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
ACGGATGATGACACCTGGGTATGCTGCACACTCCCGACTGCGTCGTGGGG	6	0.15	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGGAATTCTCGGGTGCCAA	6	0.15	No Hit
TCTGGCTCCGTGTCTTCACTCCCTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
GTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCGG	6	0.15	No Hit
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTACAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATTCAGGATAGGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGCTGGAATTCTCGGGTGCC	5	0.125	No Hit
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAATTCCG	5	0.125	RNA PCR Primer, Index 1 (95% over 23bp)
ATATATGATGACTTTCATAGAATCTCGTTCGGCTGATGATTGCTGTTGAG	5	0.125	No Hit
TTTGGCAATGGTAGAACTCACACCTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TATTGCACTCGTCCCGGCCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGT	5	0.125	No Hit
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCG	5	0.125	RNA PCR Primer, Index 1 (96% over 27bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGGGCCAAGGAATTCCG	5	0.125	RNA PCR Primer, Index 1 (95% over 23bp)
GTCCATGATGAGCAACACTCACCATCTTTCGTTTGAGTCTCACGACTGTG	5	0.125	No Hit
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	5	0.125	No Hit
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCAATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAATTCCG	5	0.125	RNA PCR Primer, Index 1 (95% over 23bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTTGGAATTCTCGGGTGCCA	5	0.125	No Hit
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
CAAGGGTTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTACAGC	5	0.125	RNA PCR Primer, Index 43 (100% over 39bp)
TGTAAACATCCTCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	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	0.875	0.0	0.0	0.0
2	0.0	0.9	0.0	0.0	0.0
3	0.0	1.025	0.0	0.0	0.0
4	0.0	1.05	0.0	0.0	0.0
5	0.0	1.1	0.0	0.0	0.0
6	0.0	1.15	0.0	0.0	0.0
7	0.0	1.675	0.0	0.0	0.0
8	0.0	1.85	0.0	0.0	0.0
9	0.0	1.975	0.0	0.0	0.0
10	0.0	2.125	0.0	0.0	0.0
11	0.0	2.2	0.0	0.0	0.0
12	0.0	2.525	0.0	0.0	0.0
13	0.0	2.825	0.0	0.0	0.0
14	0.0	3.0	0.0	0.0	0.0
15	0.0	3.4	0.0	0.0	0.0
16	0.0	4.55	0.0	0.0	0.0
17	0.0	5.0	0.0	0.0	0.0
18	0.0	6.025	0.0	0.0	0.0
19	0.0	6.45	0.0	0.0	0.0
20	0.0	7.325	0.0	0.0	0.0
21	0.0	11.425	0.0	0.0	0.0
22	0.0	21.275	0.0	0.0	0.0
23	0.0	45.525	0.0	0.0	0.0
24	0.0	58.125	0.0	0.0	0.0
25	0.0	64.375	0.0	0.0	0.0
26	0.0	65.75	0.0	0.0	0.0
27	0.0	66.5	0.0	0.0	0.0
28	0.0	67.175	0.0	0.0	0.0
29	0.0	67.5	0.0	0.0	0.0
30	0.0	67.975	0.0	0.0	0.0
31	0.0	68.975	0.0	0.0	0.0
32	0.0	70.625	0.0	0.0	0.0
33	0.0	71.35	0.0	0.0	0.0
34	0.0	73.525	0.0	0.0	0.0
35	0.0	74.275	0.0	0.0	0.0
36	0.0	75.15	0.0	0.0	0.0
37	0.0	75.875	0.0	0.0	0.0
38	0.0	76.5	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
GTAGATT	20	6.952051E-4	44.000004	8
ACTGTTG	20	6.952051E-4	44.000004	18
GAGGTAG	45	2.728484E-10	44.000004	2
GGTTGTA	20	6.952051E-4	44.000004	11
GTTTGGA	40	5.315087E-9	44.000004	20
GTTGAAG	20	6.952051E-4	44.000004	10
ATCCAGG	20	6.952051E-4	44.000004	9
AACTGTT	20	6.952051E-4	44.000004	17
AGTAGAT	20	6.952051E-4	44.000004	7
CGGGGGC	90	0.0	44.000004	32
TCGGTGA	20	6.952051E-4	44.000004	15
ATAGGCT	20	6.952051E-4	44.000004	16
AGTGGAA	20	6.952051E-4	44.000004	21
GATTGTA	20	6.952051E-4	44.000004	11
GAAGAAC	20	6.952051E-4	44.000004	13
AGAACTG	20	6.952051E-4	44.000004	15
TCCAGGA	20	6.952051E-4	44.000004	10
TAGTAGA	20	6.952051E-4	44.000004	6
TCTCGGT	20	6.952051E-4	44.000004	29
AGTAATC	20	6.952051E-4	44.000004	5
>>END_MODULE
Read 56205 spots for SRR5030934.sra
Written 56205 spots for SRR5030934.sra
Read 56205 spots for SRR5030934.sra
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Read 56205 spots for SRR5030934.sra
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Read 56205 spots for SRR5030934.sra
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Read 56205 spots for SRR5030934.sra
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SRR ids: ['SRR5030934.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_shl3eazs
SRR5030934.sra spots: 2697870
blocks: [[1, 56205], [56206, 112410], [112411, 168615], [168616, 224820], [224821, 281025], [281026, 337230], [337231, 393435], [393436, 449640], [449641, 505845], [505846, 562050], [562051, 618255], [618256, 674460], [674461, 730665], [730666, 786870], [786871, 843075], [843076, 899280], [899281, 955485], [955486, 1011690], [1011691, 1067895], [1067896, 1124100], [1124101, 1180305], [1180306, 1236510], [1236511, 1292715], [1292716, 1348920], [1348921, 1405125], [1405126, 1461330], [1461331, 1517535], [1517536, 1573740], [1573741, 1629945], [1629946, 1686150], [1686151, 1742355], [1742356, 1798560], [1798561, 1854765], [1854766, 1910970], [1910971, 1967175], [1967176, 2023380], [2023381, 2079585], [2079586, 2135790], [2135791, 2191995], [2191996, 2248200], [2248201, 2304405], [2304406, 2360610], [2360611, 2416815], [2416816, 2473020], [2473021, 2529225], [2529226, 2585430], [2585431, 2641635], [2641636, 2697870]]
SRR5030934 file size 466524
SRR5030934 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 48 -o SRR5030934 SRR5030934_1.fastq
Input file:	SRR5030934_1.fastq
trimmed:	SRR5030934-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 06:48:27 2020 >> started

Wed Mar  4 06:48:29 2020 >> done (1.673s)
2697870 reads processed; of these:
    187 ( 0.01%) short reads filtered out after trimming by size control
     10 ( 0.00%) empty reads filtered out after trimming by size control
2697673 (99.99%) reads available; of these:
 317295 (11.76%) trimmed reads available after processing
2380378 (88.24%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     57	  0.00%
 19	     69	  0.00%
 20	    144	  0.01%
 21	    167	  0.01%
 22	    312	  0.01%
 23	    420	  0.02%
 24	    405	  0.02%
 25	    538	  0.02%
 26	    455	  0.02%
 27	    580	  0.02%
 28	    671	  0.02%
 29	   1304	  0.05%
 30	    872	  0.03%
 31	   1235	  0.05%
 32	   3110	  0.12%
 33	   8247	  0.31%
 34	  20676	  0.77%
 35	   4441	  0.16%
 36	   4942	  0.18%
 37	   2956	  0.11%
 38	   5496	  0.20%
 39	   5574	  0.21%
 40	  10875	  0.40%
 41	   6057	  0.22%
 42	  17376	  0.64%
 43	   7005	  0.26%
 44	  31161	  1.16%
 45	  19438	  0.72%
 46	  17204	  0.64%
 47	  20380	  0.76%
 48	  55356	  2.05%
 49	  69772	  2.59%
 50	2380378	 88.24%
2697673 reads passed initial QC


criterion=sequence-density
sequence-density=75.88
sequence-density-rank=1
fanout-score=22.04
fanout-score-rank=3
prefix-density=78.68
prefix-fanout=21.3
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTACAGCATCTCGTATGCC


criterion=fanout-score
sequence-density=1.78
sequence-density-rank=4
fanout-score=422.86
fanout-score-rank=1
prefix-density=77.75
prefix-fanout=9.7
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTACAGCATCTCGTATGCC -o SRR5030934 -
Input file:	STDIN
trimmed:	SRR5030934-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTACAGCATCTCGTATGCC
-- 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 06:48:44 2020 >> started

Wed Mar  4 06:48:48 2020 >> done (3.839s)
2626682 reads processed; of these:
 134511 ( 5.12%) short reads filtered out after trimming by size control
  19276 ( 0.73%) empty reads filtered out after trimming by size control
2472895 (94.15%) reads available; of these:
2087533 (84.42%) trimmed reads available after processing
 385362 (15.58%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  15190	  0.61%
 19	  20316	  0.82%
 20	 107153	  4.33%
 21	 249797	 10.10%
 22	 667714	 27.00%
 23	 333845	 13.50%
 24	 159343	  6.44%
 25	  43490	  1.76%
 26	  22682	  0.92%
 27	  18485	  0.75%
 28	  19342	  0.78%
 29	  16386	  0.66%
 30	  21676	  0.88%
 31	  41568	  1.68%
 32	  26634	  1.08%
 33	  57430	  2.32%
 34	  28561	  1.15%
 35	  23481	  0.95%
 36	  29264	  1.18%
 37	  14399	  0.58%
 38	  16002	  0.65%
 39	  15373	  0.62%
 40	  24360	  0.99%
 41	  26804	  1.08%
 42	  33967	  1.37%
 43	  22235	  0.90%
 44	  22601	  0.91%
 45	  24036	  0.97%
 46	  19682	  0.80%
 47	  15247	  0.62%
 48	   6283	  0.25%
 49	  11367	  0.46%
 50	 318182	 12.87%


criterion=sequence-density
sequence-density=8.69
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=17
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.47
sequence-density-rank=31
fanout-score=13.87
fanout-score-rank=1
prefix-density=6.53
prefix-fanout=1.0
sequence=TGAGCTTGGCTT
                                 Started job on |	Mar 04 06:49:27
                             Started mapping on |	Mar 04 06:49:28
                                    Finished on |	Mar 04 06:49:59
       Mapping speed, Million of reads per hour |	295.42

                          Number of input reads |	2543886
                      Average input read length |	29
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1394098
                        Uniquely mapped reads % |	54.80%
                          Average mapped length |	28.26
                       Number of splices: Total |	1559
            Number of splices: Annotated (sjdb) |	213
                       Number of splices: GT/AG |	1426
                       Number of splices: GC/AG |	18
                       Number of splices: AT/AC |	2
               Number of splices: Non-canonical |	113
                      Mismatch rate per base, % |	0.23%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.28
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.04
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	791043
             % of reads mapped to multiple loci |	31.10%
        Number of reads mapped to too many loci |	54443
             % of reads mapped to too many loci |	2.14%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	11.11%
                     % of reads unmapped: other |	0.85%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	358745	358745	358745
N_multimapping	791043	791043	791043
N_noFeature	85987	103894	1015964
N_ambiguous	732986	402632	12182
UnstrandedReadsAssigned:575125 PositiveStrandReadsAssigned:887572 NegativeStrandReadsAssigned:365952
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5030934 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: SRR5030934-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,543,886 reads, 576,393 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,107 rounds

 109283 SRR5030934.ke.tsv
  52636 SRR5030934.se.tsv
 161919 total
==> SRR5030934.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

==> SRR5030934.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030934 completed mapping pipeline successfully
