Starting /dee2/code/volunteer_pipeline.sh SRR5030894
    current disk space = 160666763264
    free memory = 56711056 
SRR5030894 SRAfilesize
f07c9b62064050d7513cad0979a4fb08  SRR5030894.sra
SRR5030894.sra file validated
SRR5030894 is single end
SRR5030894 is conventional basespace
SRR5030894 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030894_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	32.4195	33.0	31.0	34.0	31.0	34.0
2	32.744	34.0	31.0	34.0	31.0	34.0
3	32.82675	34.0	31.0	34.0	31.0	34.0
4	36.2615	37.0	37.0	37.0	35.0	37.0
5	36.2315	37.0	37.0	37.0	35.0	37.0
6	36.022	37.0	35.0	37.0	35.0	37.0
7	36.14	37.0	35.0	37.0	35.0	37.0
8	36.193	37.0	36.0	37.0	35.0	37.0
9	37.9245	39.0	38.0	39.0	35.0	39.0
10	37.97925	39.0	38.0	39.0	35.0	39.0
11	37.9435	39.0	38.0	39.0	35.0	39.0
12	37.95275	39.0	38.0	39.0	35.0	39.0
13	37.993	39.0	38.0	39.0	35.0	39.0
14	39.341	41.0	39.0	41.0	36.0	41.0
15	39.30625	41.0	39.0	41.0	36.0	41.0
16	39.188	40.0	39.0	41.0	36.0	41.0
17	39.26425	41.0	39.0	41.0	36.0	41.0
18	39.283	41.0	39.0	41.0	36.0	41.0
19	39.06025	40.0	39.0	41.0	36.0	41.0
20	39.172	40.0	39.0	41.0	36.0	41.0
21	39.241	40.0	39.0	41.0	36.0	41.0
22	39.19225	41.0	39.0	41.0	36.0	41.0
23	39.20225	40.0	39.0	41.0	36.0	41.0
24	38.4425	40.0	38.0	41.0	34.0	41.0
25	38.68075	40.0	38.0	41.0	35.0	41.0
26	38.654	40.0	38.0	41.0	34.0	41.0
27	38.72875	40.0	38.0	41.0	35.0	41.0
28	38.59825	40.0	38.0	41.0	34.0	41.0
29	38.53375	40.0	38.0	41.0	34.0	41.0
30	38.27675	40.0	38.0	41.0	34.0	41.0
31	38.6255	40.0	38.0	41.0	34.0	41.0
32	38.85375	40.0	38.0	41.0	35.0	41.0
33	37.29475	40.0	37.0	41.0	31.0	41.0
34	36.605	40.0	37.0	41.0	30.0	41.0
35	33.3425	38.0	32.0	40.0	15.0	41.0
36	29.94525	37.0	22.0	40.0	8.0	41.0
37	30.5805	37.0	25.0	40.0	8.0	41.0
38	32.90325	37.0	31.0	40.0	20.0	41.0
39	32.57075	38.0	31.0	40.0	12.0	41.0
40	33.1245	38.0	33.0	40.0	9.0	41.0
41	31.24425	37.0	28.0	40.0	7.0	41.0
42	32.635	38.0	32.0	40.0	2.0	41.0
43	31.32025	37.0	30.0	40.0	2.0	41.0
44	32.09925	38.0	32.0	40.0	2.0	41.0
45	29.811	37.0	26.0	40.0	2.0	41.0
46	27.94	35.0	21.0	39.0	2.0	41.0
47	28.11575	35.0	22.0	39.0	2.0	41.0
48	28.674	36.0	26.0	40.0	2.0	41.0
49	27.09525	35.0	2.0	39.0	2.0	41.0
50	23.189	31.0	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
14	1.0
15	1.0
16	2.0
17	3.0
18	4.0
19	4.0
20	8.0
21	17.0
22	19.0
23	17.0
24	44.0
25	81.0
26	82.0
27	113.0
28	69.0
29	94.0
30	136.0
31	147.0
32	144.0
33	165.0
34	218.0
35	292.0
36	336.0
37	501.0
38	660.0
39	842.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	12.912912912912914	25.425425425425423	43.61861861861862	18.043043043043046
2	25.1	25.575	21.099999999999998	28.225
3	22.725	20.599999999999998	21.675	35.0
4	30.075000000000003	27.85	16.275000000000002	25.8
5	23.65	38.725	25.7	11.924999999999999
6	31.275	16.325	36.275	16.125
7	20.175	20.575	25.124999999999996	34.125
8	26.224999999999998	30.675	17.150000000000002	25.95
9	18.7	34.5	31.8	15.0
10	25.074999999999996	20.925	28.975	25.025
11	35.15	15.024999999999999	15.575	34.25
12	17.175	22.3	29.075	31.45
13	27.150000000000002	18.975	31.85	22.025
14	27.825	29.7	22.8	19.675
15	31.65	25.2	26.825	16.325
16	19.900000000000002	20.925	23.599999999999998	35.575
17	25.25	23.474999999999998	34.925	16.35
18	24.175	20.275000000000002	29.7	25.85
19	34.225	16.425	30.15	19.2
20	39.45	16.8	29.075	14.674999999999999
21	25.174999999999997	21.725	26.6	26.5
22	29.375	14.149999999999999	43.15	13.325000000000001
23	25.674999999999997	15.174999999999999	41.675000000000004	17.474999999999998
24	47.675	14.274999999999999	25.825	12.225
25	46.825	23.200000000000003	16.175	13.8
26	28.675	41.349999999999994	13.975000000000001	16.0
27	17.675	44.375	22.175	15.775
28	14.549999999999999	25.674999999999997	43.5	16.275000000000002
29	13.900000000000002	14.099999999999998	53.25	18.75
30	11.05	8.825	35.5	44.625
31	14.924999999999999	8.0	44.95	32.125
32	27.224999999999998	8.450000000000001	22.85	41.475
33	47.775	11.924999999999999	15.575	24.725
34	55.7	8.924999999999999	17.150000000000002	18.224999999999998
35	58.15	9.45	19.0	13.4
36	57.9	10.375	17.849999999999998	13.875000000000002
37	39.1	13.425	22.85	24.625
38	26.200000000000003	16.0	15.299999999999999	42.5
39	18.45	23.974999999999998	13.600000000000001	43.974999999999994
40	16.625	43.2	15.049999999999999	25.124999999999996
41	25.324999999999996	43.025000000000006	13.325000000000001	18.325
42	45.7	28.875	14.85	10.575
43	45.75	30.049999999999997	12.5	11.700000000000001
44	30.625000000000004	44.6	10.475	14.299999999999999
45	20.825	44.4	13.325000000000001	21.45
46	14.575	29.075	23.549999999999997	32.800000000000004
47	11.799999999999999	17.175	35.65	35.375
48	13.450000000000001	13.200000000000001	22.975	50.375
49	14.899999999999999	22.325	15.475	47.3
50	28.325	25.124999999999996	13.375	33.175
>>END_MODULE
>>Per sequence GC content	fail
#GC Content	Count
0	0.0
1	0.0
2	0.0
3	0.0
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.0
10	0.0
11	0.0
12	0.0
13	0.0
14	0.0
15	0.0
16	0.0
17	0.0
18	0.0
19	0.0
20	0.0
21	0.0
22	0.0
23	0.5
24	1.0
25	1.5
26	2.0
27	1.0
28	0.0
29	2.0
30	4.0
31	8.5
32	13.0
33	27.5
34	42.0
35	54.0
36	66.0
37	87.5
38	109.0
39	91.5
40	74.0
41	74.5
42	75.0
43	103.0
44	131.0
45	161.5
46	192.0
47	238.5
48	285.0
49	399.0
50	513.0
51	624.5
52	736.0
53	637.0
54	538.0
55	465.5
56	393.0
57	337.0
58	281.0
59	228.5
60	176.0
61	129.0
62	82.0
63	124.0
64	166.0
65	100.0
66	34.0
67	23.5
68	13.0
69	15.5
70	18.0
71	29.5
72	41.0
73	22.5
74	4.0
75	3.5
76	3.0
77	3.0
78	3.0
79	2.0
80	1.0
81	2.0
82	3.0
83	2.0
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	0.1
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	51.675000000000004
#Duplication Level	Percentage of deduplicated	Percentage of total
1	79.29366231253023	40.975
2	9.433962264150944	9.75
3	3.483309143686502	5.4
4	1.741654571843251	3.5999999999999996
5	1.0643444605708756	2.75
6	0.628930817610063	1.95
7	0.43541364296081275	1.575
8	0.48379293662312534	2.0
9	0.5805515239477503	2.7
>10	2.7092404450895016	23.275000000000002
>50	0.14513788098693758	6.0249999999999995
>100	0.0	0.0
>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	98	2.45	RNA PCR Primer, Index 1 (100% over 27bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	90	2.25	No Hit
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	53	1.325	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	35	0.8750000000000001	RNA PCR Primer, Index 1 (96% over 28bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	34	0.8500000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	30	0.75	RNA PCR Primer, Index 1 (96% over 28bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	27	0.675	RNA PCR Primer, Index 1 (100% over 26bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	26	0.65	RNA PCR Primer, Index 1 (100% over 27bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	26	0.65	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	24	0.6	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	24	0.6	RNA PCR Primer, Index 1 (96% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	24	0.6	RNA PCR Primer, Index 1 (100% over 30bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	23	0.575	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	23	0.575	RNA PCR Primer, Index 1 (100% over 26bp)
GCGGATGATGACACCTGGGTATGCTGCACACTCCCGACTGCGTCGTGGGG	22	0.5499999999999999	No Hit
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (100% over 28bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCATTTTATCTCGTATGC	20	0.5	RNA PCR Primer, Index 35 (100% over 50bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCATTTTATCTC	19	0.475	RNA PCR Primer, Index 35 (100% over 44bp)
GTAAATGATGAGATTCCATTGGTCCGTGTTTCTGAACTACATGATTTTCC	18	0.44999999999999996	No Hit
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	17	0.42500000000000004	No Hit
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCG	17	0.42500000000000004	RNA PCR Primer, Index 1 (96% over 27bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 29bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCA	17	0.42500000000000004	RNA PCR Primer, Index 7 (100% over 35bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (96% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCG	14	0.35000000000000003	RNA PCR Primer, Index 1 (96% over 27bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 26bp)
TTGCAATGATGACTTATATATCTGTCAATCCCCTGAGAGATCACTGACGA	14	0.35000000000000003	No Hit
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	13	0.325	No Hit
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	13	0.325	No Hit
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGC	13	0.325	RNA PCR Primer, Index 1 (96% over 29bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCG	13	0.325	RNA PCR Primer, Index 1 (96% over 27bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	12	0.3	RNA PCR Primer, Index 1 (100% over 33bp)
TGCTGTGATGAGATGACTAAGTAGGAAGTGCCGTCAGAGTCGATAACTGA	12	0.3	No Hit
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (96% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 26bp)
CACCCTGATGAACTGAATACCGCCCCAGTCTGATAGCTGTGGAGAAAGGT	11	0.27499999999999997	No Hit
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCG	11	0.27499999999999997	RNA PCR Primer, Index 1 (96% over 27bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	11	0.27499999999999997	No Hit
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGAAATCAAA	11	0.27499999999999997	No Hit
GTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCGG	11	0.27499999999999997	No Hit
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAA	10	0.25	No Hit
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (96% over 28bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
CTGCAGTGATGACTATCTTAGGACACCTTTGGATTTACCGTGAAAAGAAG	10	0.25	No Hit
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
ATACATGATGATCTCACACAACTTGAACTCTCTCACTGATTACTTGATGA	10	0.25	No Hit
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	10	0.25	No Hit
CGACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGC	9	0.22499999999999998	No Hit
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	9	0.22499999999999998	No Hit
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TGAACTGATGATATCATTTCTTTCCCCGTCAGATCGACCCTGTTGATCTC	9	0.22499999999999998	No Hit
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
AGCCCATGATGGTATGAGAGTAGTGGACAGAAGGGATTTCTGAAAAACAC	9	0.22499999999999998	No Hit
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
GTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAAT	9	0.22499999999999998	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCTGGAATTCTCGGGTGC	9	0.22499999999999998	No Hit
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (96% over 28bp)
GGTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCG	8	0.2	No Hit
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	8	0.2	No Hit
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
GACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGCT	8	0.2	No Hit
CTGCATGATGACGAACAAATACTGACTACCTGAAGATCTTATTAGCTCTA	8	0.2	No Hit
TGCGGGGCTAGGGCTAACAGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCG	8	0.2	No Hit
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
CACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGT	7	0.17500000000000002	No Hit
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 25bp)
GTGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCA	7	0.17500000000000002	No Hit
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTATGG	7	0.17500000000000002	No Hit
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
CCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAT	7	0.17500000000000002	RNA PCR Primer, Index 9 (97% over 36bp)
CTTAATGATGAACAATGTAAATGACAAGCATATGGCTGAGTTGCAATGAT	7	0.17500000000000002	No Hit
GTGAAATGATGGCAAATCATCTTTCGGGACTGACCTGAAATGAAGAGAAT	7	0.17500000000000002	No Hit
GCATGTGATGACATTATTTAGCGACCAAAGTCTGATAAAGATGATTGTGA	6	0.15	No Hit
TCTTAGATCGATGTGGTGCTCCGGAGTTCTCTTCGGGCCAGGGCCTAAGC	6	0.15	No Hit
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
ACCAGTGATGTGATGATTCTGCCAAATGATACAAAGTGATATCACCTTTA	6	0.15	No Hit
ATATATGATGACTTTCATAGAATCTCGTTCGGCTGATGATTGCTGTTGAG	6	0.15	No Hit
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCG	6	0.15	RNA PCR Primer, Index 1 (96% over 27bp)
TGACTTGATGAAAGTACTTTTGAACCCTTTTCCATCTGATGTGGAATTCT	6	0.15	No Hit
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCGG	6	0.15	No Hit
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	6	0.15	No Hit
TGTAAACATCCTCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAATTCCG	5	0.125	RNA PCR Primer, Index 1 (95% over 23bp)
TATTGCACTTGTCCCGGCCTGTATTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCC	5	0.125	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCTGGAATTCTCGGGTG	5	0.125	No Hit
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGACTGGAATTCTCGGGT	5	0.125	No Hit
TGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	5	0.125	No Hit
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCG	5	0.125	RNA PCR Primer, Index 1 (96% over 27bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGGAATTCTCGGGTGCCA	5	0.125	No Hit
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTA	5	0.125	No Hit
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGGGCCAAGGAACTCCAGC	5	0.125	RNA PCR Primer, Index 1 (96% over 29bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GAGCAATGATGACCCCAACATGCCATCTGAGTGGCTTTGCTGAAATCCAG	5	0.125	No Hit
CTAGACTGAGGCTCCTTGAGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCATTTTATCTCGTAT	5	0.125	RNA PCR Primer, Index 35 (100% over 48bp)
>>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	0.575	0.0	0.0	0.0
2	0.0	0.575	0.0	0.0	0.0
3	0.0	0.775	0.0	0.0	0.0
4	0.0	0.85	0.0	0.0	0.0
5	0.0	0.9	0.0	0.0	0.0
6	0.0	0.925	0.0	0.0	0.0
7	0.0	1.5	0.0	0.0	0.0
8	0.0	1.7	0.0	0.0	0.0
9	0.0	1.875	0.0	0.0	0.0
10	0.0	2.075	0.0	0.0	0.0
11	0.0	2.225	0.0	0.0	0.0
12	0.0	2.45	0.0	0.0	0.0
13	0.0	2.625	0.0	0.0	0.0
14	0.0	2.875	0.0	0.0	0.0
15	0.0	3.45	0.0	0.0	0.0
16	0.0	4.275	0.0	0.0	0.0
17	0.0	4.7	0.0	0.0	0.0
18	0.0	5.575	0.0	0.0	0.0
19	0.0	5.95	0.0	0.0	0.0
20	0.0	6.55	0.0	0.0	0.0
21	0.0	10.625	0.0	0.0	0.0
22	0.0	19.35	0.0	0.0	0.0
23	0.0	44.425	0.0	0.0	0.0
24	0.0	56.4	0.0	0.0	0.0
25	0.0	61.775	0.0	0.0	0.0
26	0.0	63.175	0.0	0.0	0.0
27	0.0	63.95	0.0	0.0	0.0
28	0.0	64.525	0.0	0.0	0.0
29	0.0	64.75	0.0	0.0	0.0
30	0.0	65.15	0.0	0.0	0.0
31	0.0	65.775	0.0	0.0	0.0
32	0.0	66.65	0.0	0.0	0.0
33	0.0	67.65	0.0	0.0	0.0
34	0.0	71.3	0.0	0.0	0.0
35	0.0	72.225	0.0	0.0	0.0
36	0.0	72.925	0.0	0.0	0.0
37	0.0	73.925	0.0	0.0	0.0
38	0.0	74.35	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TGAGACC	20	6.952051E-4	44.000004	5
ACTGTTG	20	6.952051E-4	44.000004	18
GGTGAGT	20	6.952051E-4	44.000004	17
GTTGAAG	20	6.952051E-4	44.000004	10
AAGTAAT	20	6.952051E-4	44.000004	4
TCAAGTA	20	6.952051E-4	44.000004	2
AATCCAG	20	6.952051E-4	44.000004	8
CAGTTGA	20	6.952051E-4	44.000004	8
CTGAGCT	40	5.315087E-9	44.000004	11
CTGAGAC	20	6.952051E-4	44.000004	4
ATCCAGG	20	6.952051E-4	44.000004	9
CCAGTTG	20	6.952051E-4	44.000004	7
AACTGTT	20	6.952051E-4	44.000004	17
GGACTTC	20	6.952051E-4	44.000004	42
TTCAAGT	20	6.952051E-4	44.000004	1
CGGGGCC	20	6.952051E-4	44.000004	32
AGGATAG	20	6.952051E-4	44.000004	13
CATCCCC	20	6.952051E-4	44.000004	7
ATAGGCT	20	6.952051E-4	44.000004	16
GAGCTTG	40	5.315087E-9	44.000004	13
>>END_MODULE
Read 276079 spots for SRR5030894.sra
Written 276079 spots for SRR5030894.sra
Read 276079 spots for SRR5030894.sra
Written 276079 spots for SRR5030894.sra
Read 276079 spots for SRR5030894.sra
Written 276079 spots for SRR5030894.sra
Read 276079 spots for SRR5030894.sra
Written 276079 spots for SRR5030894.sra
Read 276079 spots for SRR5030894.sra
Written 276079 spots for SRR5030894.sra
Read 276079 spots for SRR5030894.sra
Written 276079 spots for SRR5030894.sra
Read 276079 spots for SRR5030894.sra
Written 276079 spots for SRR5030894.sra
Read 276079 spots for SRR5030894.sra
Written 276079 spots for SRR5030894.sra
Read 276079 spots for SRR5030894.sra
Written 276079 spots for SRR5030894.sra
Read 276079 spots for SRR5030894.sra
Written 276079 spots for SRR5030894.sra
Read 276079 spots for SRR5030894.sra
Written 276079 spots for SRR5030894.sra
Read 276086 spots for SRR5030894.sra
Written 276086 spots for SRR5030894.sra
SRR ids: ['SRR5030894.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_5culek_s
SRR5030894.sra spots: 3312955
blocks: [[1, 276079], [276080, 552158], [552159, 828237], [828238, 1104316], [1104317, 1380395], [1380396, 1656474], [1656475, 1932553], [1932554, 2208632], [2208633, 2484711], [2484712, 2760790], [2760791, 3036869], [3036870, 3312955]]
SRR5030894 file size 573137
SRR5030894 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030894 SRR5030894_1.fastq
Input file:	SRR5030894_1.fastq
trimmed:	SRR5030894-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 06:39:00 2020 >> started

Wed Mar  4 06:39:02 2020 >> done (1.998s)
3312955 reads processed; of these:
    189 ( 0.01%) short reads filtered out after trimming by size control
      7 ( 0.00%) empty reads filtered out after trimming by size control
3312759 (99.99%) reads available; of these:
 385822 (11.65%) trimmed reads available after processing
2926937 (88.35%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     62	  0.00%
 19	     76	  0.00%
 20	    168	  0.01%
 21	    212	  0.01%
 22	    378	  0.01%
 23	    456	  0.01%
 24	    517	  0.02%
 25	    675	  0.02%
 26	    547	  0.02%
 27	    706	  0.02%
 28	   1009	  0.03%
 29	   1536	  0.05%
 30	   1038	  0.03%
 31	   1506	  0.05%
 32	   3589	  0.11%
 33	  10634	  0.32%
 34	  24045	  0.73%
 35	   5829	  0.18%
 36	   6543	  0.20%
 37	   3782	  0.11%
 38	   7274	  0.22%
 39	   7118	  0.21%
 40	  13221	  0.40%
 41	   8091	  0.24%
 42	  18628	  0.56%
 43	   9284	  0.28%
 44	  38402	  1.16%
 45	  22021	  0.66%
 46	  22815	  0.69%
 47	  24296	  0.73%
 48	  65490	  1.98%
 49	  85874	  2.59%
 50	2926937	 88.35%
3312759 reads passed initial QC


criterion=sequence-density
sequence-density=72.84
sequence-density-rank=1
fanout-score=21.21
fanout-score-rank=2
prefix-density=75.17
prefix-fanout=20.6
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCATTTTATCTCGTATGCC


criterion=fanout-score
sequence-density=3.25
sequence-density-rank=3
fanout-score=71.28
fanout-score-rank=1
prefix-density=75.00
prefix-fanout=3.1
sequence=GAATTCTCGGGGGCCAAGGAACT
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCATTTTATCTCGTATGCC -o SRR5030894 -
Input file:	STDIN
trimmed:	SRR5030894-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCATTTTATCTCGTATGCC
-- 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 06:39:17 2020 >> started

Wed Mar  4 06:39:22 2020 >> done (5.224s)
3221999 reads processed; of these:
 147517 ( 4.58%) short reads filtered out after trimming by size control
  22188 ( 0.69%) empty reads filtered out after trimming by size control
3052294 (94.73%) reads available; of these:
2473874 (81.05%) trimmed reads available after processing
 578420 (18.95%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  18568	  0.61%
 19	  26438	  0.87%
 20	 130960	  4.29%
 21	 292370	  9.58%
 22	 784766	 25.71%
 23	 373668	 12.24%
 24	 169772	  5.56%
 25	  46499	  1.52%
 26	  24432	  0.80%
 27	  20478	  0.67%
 28	  22012	  0.72%
 29	  17323	  0.57%
 30	  23498	  0.77%
 31	  28147	  0.92%
 32	  31859	  1.04%
 33	 130539	  4.28%
 34	  37213	  1.22%
 35	  28070	  0.92%
 36	  38363	  1.26%
 37	  16304	  0.53%
 38	  18939	  0.62%
 39	  18575	  0.61%
 40	  28016	  0.92%
 41	  34548	  1.13%
 42	  43426	  1.42%
 43	  28876	  0.95%
 44	  26381	  0.86%
 45	  30522	  1.00%
 46	  25687	  0.84%
 47	  21526	  0.71%
 48	   9461	  0.31%
 49	  17319	  0.57%
 50	 487739	 15.98%


criterion=sequence-density
sequence-density=5.64
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=15
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.54
sequence-density-rank=23
fanout-score=11.31
fanout-score-rank=1
prefix-density=6.09
prefix-fanout=1.0
sequence=TGAGCTTGGCTATT
                                 Started job on |	Mar 04 06:39:44
                             Started mapping on |	Mar 04 06:39:44
                                    Finished on |	Mar 04 06:40:08
       Mapping speed, Million of reads per hour |	471.46

                          Number of input reads |	3143054
                      Average input read length |	30
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1691261
                        Uniquely mapped reads % |	53.81%
                          Average mapped length |	29.71
                       Number of splices: Total |	1872
            Number of splices: Annotated (sjdb) |	268
                       Number of splices: GT/AG |	1744
                       Number of splices: GC/AG |	28
                       Number of splices: AT/AC |	2
               Number of splices: Non-canonical |	98
                      Mismatch rate per base, % |	0.20%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.29
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.08
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	940900
             % of reads mapped to multiple loci |	29.94%
        Number of reads mapped to too many loci |	77855
             % of reads mapped to too many loci |	2.48%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	13.21%
                     % of reads unmapped: other |	0.57%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	510893	510893	510893
N_multimapping	940900	940900	940900
N_noFeature	76060	94895	1273544
N_ambiguous	927800	572993	16223
UnstrandedReadsAssigned:687401 PositiveStrandReadsAssigned:1023373 NegativeStrandReadsAssigned:401494
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5030894 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: SRR5030894-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,143,054 reads, 737,554 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 916 rounds

 109283 SRR5030894.ke.tsv
  52636 SRR5030894.se.tsv
 161919 total
==> SRR5030894.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

==> SRR5030894.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030894 completed mapping pipeline successfully
