Starting /dee2/code/volunteer_pipeline.sh SRR5030938
    current disk space = 160615563264
    free memory = 73924864 
SRR5030938 SRAfilesize
ed65f463538dee6fc6f18333732bbf4b  SRR5030938.sra
SRR5030938.sra file validated
SRR5030938 is single end
SRR5030938 is conventional basespace
SRR5030938 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030938_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	32.3025	33.0	31.0	34.0	31.0	34.0
2	32.625	34.0	31.0	34.0	31.0	34.0
3	32.7175	34.0	31.0	34.0	31.0	34.0
4	36.21025	37.0	37.0	37.0	35.0	37.0
5	36.1535	37.0	37.0	37.0	35.0	37.0
6	35.89825	37.0	35.0	37.0	35.0	37.0
7	35.97425	37.0	35.0	37.0	35.0	37.0
8	36.067	37.0	35.0	37.0	35.0	37.0
9	37.7425	39.0	38.0	39.0	35.0	39.0
10	37.75625	39.0	38.0	39.0	35.0	39.0
11	37.702	39.0	37.0	39.0	35.0	39.0
12	37.69525	39.0	37.0	39.0	35.0	39.0
13	37.71075	39.0	37.0	39.0	35.0	39.0
14	39.01575	41.0	38.0	41.0	35.0	41.0
15	39.11975	40.0	38.0	41.0	36.0	41.0
16	38.98775	40.0	38.0	41.0	35.0	41.0
17	39.09225	40.0	38.0	41.0	35.0	41.0
18	39.06	40.0	38.0	41.0	35.0	41.0
19	38.80225	40.0	38.0	41.0	35.0	41.0
20	38.96475	40.0	38.0	41.0	35.0	41.0
21	38.9865	40.0	38.0	41.0	35.0	41.0
22	39.05875	40.0	39.0	41.0	36.0	41.0
23	38.97825	40.0	39.0	41.0	36.0	41.0
24	38.31825	40.0	38.0	41.0	34.0	41.0
25	38.5145	40.0	38.0	41.0	34.0	41.0
26	38.43275	40.0	38.0	41.0	34.0	41.0
27	38.6115	40.0	38.0	41.0	34.0	41.0
28	38.42825	40.0	38.0	41.0	34.0	41.0
29	38.12175	40.0	38.0	41.0	33.0	41.0
30	37.987	40.0	38.0	41.0	33.0	41.0
31	38.28825	40.0	38.0	41.0	34.0	41.0
32	38.58525	40.0	38.0	41.0	34.0	41.0
33	36.947	40.0	37.0	41.0	30.0	41.0
34	36.5295	40.0	36.0	41.0	30.0	41.0
35	32.6125	38.0	31.0	40.0	15.0	41.0
36	29.41125	37.0	18.0	40.0	8.0	41.0
37	30.058	36.0	24.0	40.0	6.0	41.0
38	32.435	37.0	30.0	40.0	15.0	41.0
39	32.037	37.0	30.0	40.0	8.0	41.0
40	32.732	38.0	32.0	40.0	7.0	41.0
41	30.50875	36.0	27.0	40.0	2.0	41.0
42	31.92475	37.0	31.0	40.0	2.0	41.0
43	30.2025	36.0	26.0	40.0	2.0	41.0
44	31.07225	37.0	30.0	40.0	2.0	41.0
45	29.213	36.0	26.0	40.0	2.0	41.0
46	27.1335	34.0	15.0	39.0	2.0	41.0
47	27.208	34.0	15.0	39.0	2.0	41.0
48	27.821	35.0	15.0	39.0	2.0	41.0
49	26.01275	34.0	2.0	39.0	2.0	41.0
50	22.726	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
3	1.0
4	0.0
5	1.0
6	0.0
7	0.0
8	0.0
9	0.0
10	0.0
11	1.0
12	1.0
13	1.0
14	0.0
15	1.0
16	0.0
17	0.0
18	5.0
19	4.0
20	8.0
21	16.0
22	22.0
23	32.0
24	50.0
25	57.0
26	124.0
27	133.0
28	82.0
29	107.0
30	169.0
31	157.0
32	158.0
33	172.0
34	223.0
35	297.0
36	302.0
37	464.0
38	633.0
39	779.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	12.337337337337337	26.351351351351347	46.846846846846844	14.464464464464463
2	25.85	27.975	19.975	26.200000000000003
3	23.75	18.875	22.675	34.699999999999996
4	31.65	30.275000000000002	14.399999999999999	23.674999999999997
5	23.724999999999998	35.25	27.800000000000004	13.225000000000001
6	28.925	17.375	40.525	13.175
7	20.974999999999998	20.275000000000002	22.275	36.475
8	23.974999999999998	30.975	16.775000000000002	28.275
9	19.85	34.65	30.225	15.275
10	24.85	18.35	28.225	28.575
11	36.199999999999996	15.425	14.774999999999999	33.6
12	16.900000000000002	23.724999999999998	28.999999999999996	30.375000000000004
13	27.875	18.075	32.875	21.175
14	28.525	27.55	25.374999999999996	18.55
15	33.175	22.575	26.0	18.25
16	18.025	20.125	23.05	38.800000000000004
17	25.825	24.3	34.0	15.875
18	25.95	17.575	32.324999999999996	24.15
19	31.0	15.775	34.825	18.4
20	41.075	17.275	26.825	14.825
21	24.675	23.625	24.15	27.55
22	29.599999999999998	14.45	43.824999999999996	12.125
23	25.124999999999996	15.1	43.55	16.225
24	48.25	13.125	26.125	12.5
25	50.1	21.825	16.025	12.049999999999999
26	28.275	43.275000000000006	13.675	14.774999999999999
27	18.224999999999998	45.425	22.400000000000002	13.950000000000001
28	15.725	26.25	44.175	13.850000000000001
29	12.45	14.224999999999998	54.25	19.075
30	10.95	8.450000000000001	36.449999999999996	44.15
31	14.025000000000002	7.85	43.35	34.775
32	27.1	7.074999999999999	23.974999999999998	41.85
33	49.9	10.825	14.274999999999999	25.0
34	58.9	8.6	14.45	18.05
35	55.45	10.8	20.65	13.100000000000001
36	59.824999999999996	10.025	16.825000000000003	13.325000000000001
37	39.475	11.475	22.900000000000002	26.150000000000002
38	26.35	13.925	14.099999999999998	45.625
39	19.15	23.0	10.875	46.975
40	17.025000000000002	44.175	12.85	25.95
41	25.85	44.074999999999996	12.2	17.875
42	49.275000000000006	28.625	11.375	10.725
43	46.225	32.725	10.375	10.674999999999999
44	31.05	45.975	8.674999999999999	14.299999999999999
45	19.650000000000002	46.6	12.025	21.725
46	14.2	28.95	24.224999999999998	32.625
47	11.0	16.85	32.175	39.975
48	11.600000000000001	12.675	22.425	53.300000000000004
49	15.225	24.525	13.700000000000001	46.550000000000004
50	30.375000000000004	26.6	10.424999999999999	32.6
>>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	0.0
10	0.0
11	0.0
12	0.0
13	0.0
14	0.0
15	0.5
16	1.0
17	0.5
18	0.0
19	0.0
20	0.0
21	0.5
22	1.0
23	2.0
24	3.0
25	1.5
26	0.0
27	2.5
28	5.0
29	4.5
30	4.0
31	9.0
32	14.0
33	21.5
34	29.0
35	39.0
36	49.0
37	70.0
38	91.0
39	79.5
40	68.0
41	70.5
42	73.0
43	90.5
44	108.0
45	161.0
46	214.0
47	264.0
48	314.0
49	386.0
50	458.0
51	620.5
52	783.0
53	617.5
54	452.0
55	428.5
56	405.0
57	372.5
58	340.0
59	266.5
60	193.0
61	154.0
62	115.0
63	127.0
64	139.0
65	83.5
66	28.0
67	22.5
68	17.0
69	18.5
70	20.0
71	37.5
72	55.0
73	32.5
74	10.0
75	7.5
76	5.0
77	4.0
78	3.0
79	2.5
80	2.0
81	1.5
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	0.1
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	51.125
#Duplication Level	Percentage of deduplicated	Percentage of total
1	80.39119804400978	41.099999999999994
2	8.166259168704157	8.35
3	3.5696821515892423	5.475
4	1.9559902200488997	4.0
5	1.1246943765281174	2.875
6	0.6845965770171148	2.1
7	0.4400977995110024	1.575
8	0.4889975550122249	2.0
9	0.293398533007335	1.35
>10	2.787286063569682	26.0
>50	0.04889975550122249	1.325
>100	0.04889975550122249	3.85
>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	154	3.85	RNA PCR Primer, Index 1 (100% over 27bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	53	1.325	No Hit
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	37	0.9249999999999999	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	36	0.8999999999999999	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	36	0.8999999999999999	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	36	0.8999999999999999	RNA PCR Primer, Index 1 (96% over 28bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	35	0.8750000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGGCGATCTCGTATGC	34	0.8500000000000001	RNA PCR Primer, Index 33 (100% over 50bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
GGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	31	0.775	No Hit
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	30	0.75	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	28	0.7000000000000001	No Hit
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	27	0.675	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	26	0.65	RNA PCR Primer, Index 1 (100% over 26bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	23	0.575	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	21	0.525	RNA PCR Primer, Index 1 (96% over 28bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGAAATCAAA	21	0.525	No Hit
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCA	20	0.5	RNA PCR Primer, Index 7 (100% over 35bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	19	0.475	RNA PCR Primer, Index 1 (96% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	19	0.475	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	19	0.475	RNA PCR Primer, Index 1 (100% over 29bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCG	19	0.475	No Hit
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (96% over 28bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 27bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	16	0.4	No Hit
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGC	16	0.4	RNA PCR Primer, Index 1 (96% over 29bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	15	0.375	RNA PCR Primer, Index 1 (100% over 27bp)
TGCTGTGATGAGATGACTAAGTAGGAAGTGCCGTCAGAGTCGATAACTGA	15	0.375	No Hit
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	15	0.375	No Hit
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 26bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 33bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (96% over 28bp)
GACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGCT	13	0.325	No Hit
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	13	0.325	No Hit
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	12	0.3	RNA PCR Primer, Index 1 (100% over 25bp)
TGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	12	0.3	No Hit
GTAAATGATGAGATTCCATTGGTCCGTGTTTCTGAACTACATGATTTTCC	12	0.3	No Hit
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	12	0.3	RNA PCR Primer, Index 1 (100% over 26bp)
CGACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGC	11	0.27499999999999997	No Hit
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	11	0.27499999999999997	No Hit
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	11	0.27499999999999997	No Hit
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TTGCAATGATGACTTATATATCTGTCAATCCCCTGAGAGATCACTGACGA	11	0.27499999999999997	No Hit
TGCGGGGCTAGGGCTAACAGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGGGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (96% over 28bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCG	10	0.25	RNA PCR Primer, Index 1 (96% over 27bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCG	10	0.25	RNA PCR Primer, Index 1 (96% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCG	10	0.25	RNA PCR Primer, Index 1 (96% over 27bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	10	0.25	No Hit
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGGCGATCTC	9	0.22499999999999998	RNA PCR Primer, Index 33 (100% over 44bp)
TGAACTGATGATATCATTTCTTTCCCCGTCAGATCGACCCTGTTGATCTC	9	0.22499999999999998	No Hit
ACGGATGATGACACCTGGGTATGCTGCACACTCCCGACTGCGTCGTGGGG	9	0.22499999999999998	No Hit
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCGG	9	0.22499999999999998	No Hit
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCG	8	0.2	RNA PCR Primer, Index 1 (96% over 27bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	8	0.2	No Hit
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCG	8	0.2	RNA PCR Primer, Index 1 (96% over 27bp)
AACCCGTAGATCCGAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
GGTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCG	7	0.17500000000000002	No Hit
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAA	7	0.17500000000000002	No Hit
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAATTCCG	7	0.17500000000000002	RNA PCR Primer, Index 1 (95% over 23bp)
CTGCATGATGACGAACAAATACTGACTACCTGAAGATCTTATTAGCTCTA	7	0.17500000000000002	No Hit
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TACCCTGTAGAACCGAATTTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	7	0.17500000000000002	No Hit
GTGAAATGATGGCAAATCATCTTTCGGGACTGACCTGAAATGAAGAGAAT	7	0.17500000000000002	No Hit
ACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCA	6	0.15	RNA PCR Primer, Index 7 (100% over 35bp)
CACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGT	6	0.15	No Hit
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCGGG	6	0.15	No Hit
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	6	0.15	No Hit
CACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCC	6	0.15	No Hit
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGGGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (96% over 28bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCTGGCTCCGTGTCTTCACTCCCTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAATTCCG	6	0.15	RNA PCR Primer, Index 1 (95% over 23bp)
ATACATGATGATCTCACACAACTTGAACTCTCTCACTGATTACTTGATGA	6	0.15	No Hit
CCTGCATGATGACGAACAAATACTGACTACCTGAAGATCTTATTAGCTCT	6	0.15	No Hit
GTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCGG	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)
TCGGATCCGTCTGAGCTTGGCTAATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TATTGCACTTGTCCCGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTCACTGGAATTCTCGGGT	5	0.125	No Hit
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAC	5	0.125	No Hit
TCCTGTACTGAGCTGCCCCGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
CACCCTGATGAACTGAATACCGCCCCAGTCTGATAGCTGTGGAGAAAGGT	5	0.125	No Hit
GCGGATGATGACACCTGGGTATGCTGCACACTCCCGACTGCGTCGTGGGG	5	0.125	No Hit
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
TACCCTGTAGAACCGAATTTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
CTGCAGTGATGACTATCTTAGGACACCTTTGGATTTACCGTGAAAAGAAG	5	0.125	No Hit
TCGGATCCGTCTGAGCTTGGCAATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAATTCCA	5	0.125	RNA PCR Primer, Index 1 (95% over 23bp)
CGCACGGGGTCGGCGGCGATGTCGGCTGGAATTCTCGGGTGCCAAGGAAC	5	0.125	RNA PCR Primer, Index 1 (100% over 24bp)
CACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGG	5	0.125	RNA PCR Primer, Index 31 (97% over 37bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTGCTGTTATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	5	0.125	No Hit
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGGGCCAAGGAACTCCG	5	0.125	RNA PCR Primer, Index 1 (96% 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	0.9	0.0	0.0	0.0
2	0.0	0.925	0.0	0.0	0.0
3	0.0	1.0	0.0	0.0	0.0
4	0.0	1.025	0.0	0.0	0.0
5	0.0	1.05	0.0	0.0	0.0
6	0.0	1.15	0.0	0.0	0.0
7	0.0	1.575	0.0	0.0	0.0
8	0.0	1.7	0.0	0.0	0.0
9	0.0	1.7	0.0	0.0	0.0
10	0.0	1.825	0.0	0.0	0.0
11	0.0	1.95	0.0	0.0	0.0
12	0.0	2.275	0.0	0.0	0.0
13	0.0	2.45	0.0	0.0	0.0
14	0.0	2.875	0.0	0.0	0.0
15	0.0	3.3	0.0	0.0	0.0
16	0.0	4.525	0.0	0.0	0.0
17	0.0	5.35	0.0	0.0	0.0
18	0.0	6.15	0.0	0.0	0.0
19	0.0	6.475	0.0	0.0	0.0
20	0.0	7.125	0.0	0.0	0.0
21	0.0	10.95	0.0	0.0	0.0
22	0.0	20.55	0.0	0.0	0.0
23	0.0	46.475	0.0	0.0	0.0
24	0.0	59.35	0.0	0.0	0.0
25	0.0	64.875	0.0	0.0	0.0
26	0.0	66.3	0.0	0.0	0.0
27	0.0	67.175	0.0	0.0	0.0
28	0.0	67.75	0.0	0.0	0.0
29	0.0	68.0	0.0	0.0	0.0
30	0.0	68.525	0.0	0.0	0.0
31	0.0	69.225	0.0	0.0	0.0
32	0.0	70.925	0.0	0.0	0.0
33	0.0	71.525	0.0	0.0	0.0
34	0.0	73.675	0.0	0.0	0.0
35	0.0	74.275	0.0	0.0	0.0
36	0.0	74.825	0.0	0.0	0.0
37	0.0	75.675	0.0	0.0	0.0
38	0.0	76.05	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
ACATTCA	40	5.315087E-9	44.000004	2
TTGGCTT	20	6.952051E-4	44.000004	17
GTCGGTG	40	5.315087E-9	44.000004	14
TGGCTTG	20	6.952051E-4	44.000004	18
AACATTC	40	5.315087E-9	44.000004	1
TGTCGGT	40	5.315087E-9	44.000004	13
TGAGACC	25	3.6958358E-5	44.0	5
AACGCTG	35	1.02281774E-7	44.0	8
GAGGTAG	25	3.6958358E-5	44.0	2
GGTGAGT	25	3.6958358E-5	44.0	17
ACGCTGT	35	1.02281774E-7	44.0	9
CTGAGCT	35	1.02281774E-7	44.0	11
CTGAGAC	25	3.6958358E-5	44.0	4
TTCAACG	35	1.02281774E-7	44.0	5
TCGGTGA	30	1.9515464E-6	44.0	15
GAGCTTG	35	1.02281774E-7	44.0	13
GGATCCG	35	1.02281774E-7	44.0	3
CCGTCTG	35	1.02281774E-7	44.0	7
CCTGAGA	25	3.6958358E-5	44.0	3
TCGGATC	35	1.02281774E-7	44.0	1
>>END_MODULE
Read 169932 spots for SRR5030938.sra
Written 169932 spots for SRR5030938.sra
Read 169932 spots for SRR5030938.sra
Written 169932 spots for SRR5030938.sra
Read 169932 spots for SRR5030938.sra
Written 169932 spots for SRR5030938.sra
Read 169932 spots for SRR5030938.sra
Written 169932 spots for SRR5030938.sra
Read 169932 spots for SRR5030938.sra
Written 169932 spots for SRR5030938.sra
Read 169932 spots for SRR5030938.sra
Written 169932 spots for SRR5030938.sra
Read 169932 spots for SRR5030938.sra
Written 169932 spots for SRR5030938.sra
Read 169932 spots for SRR5030938.sra
Written 169932 spots for SRR5030938.sra
Read 169932 spots for SRR5030938.sra
Written 169932 spots for SRR5030938.sra
Read 169932 spots for SRR5030938.sra
Written 169932 spots for SRR5030938.sra
Read 169940 spots for SRR5030938.sra
Written 169940 spots for SRR5030938.sra
Read 169932 spots for SRR5030938.sra
Written 169932 spots for SRR5030938.sra
SRR ids: ['SRR5030938.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_jcy0dn1k
SRR5030938.sra spots: 2039192
blocks: [[1, 169932], [169933, 339864], [339865, 509796], [509797, 679728], [679729, 849660], [849661, 1019592], [1019593, 1189524], [1189525, 1359456], [1359457, 1529388], [1529389, 1699320], [1699321, 1869252], [1869253, 2039192]]
SRR5030938 file size 352355
SRR5030938 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030938 SRR5030938_1.fastq
Input file:	SRR5030938_1.fastq
trimmed:	SRR5030938-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 06:49:26 2020 >> started

Wed Mar  4 06:49:27 2020 >> done (1.369s)
2039192 reads processed; of these:
    201 ( 0.01%) short reads filtered out after trimming by size control
      7 ( 0.00%) empty reads filtered out after trimming by size control
2038984 (99.99%) reads available; of these:
 243738 (11.95%) trimmed reads available after processing
1795246 (88.05%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     53	  0.00%
 19	     69	  0.00%
 20	    112	  0.01%
 21	    149	  0.01%
 22	    219	  0.01%
 23	    321	  0.02%
 24	    307	  0.02%
 25	    411	  0.02%
 26	    416	  0.02%
 27	    520	  0.03%
 28	    571	  0.03%
 29	    919	  0.05%
 30	    698	  0.03%
 31	    952	  0.05%
 32	   2447	  0.12%
 33	   6782	  0.33%
 34	  16275	  0.80%
 35	   3712	  0.18%
 36	   4084	  0.20%
 37	   2480	  0.12%
 38	   4764	  0.23%
 39	   4738	  0.23%
 40	   8855	  0.43%
 41	   4842	  0.24%
 42	  13104	  0.64%
 43	   5542	  0.27%
 44	  23573	  1.16%
 45	  15387	  0.75%
 46	  13716	  0.67%
 47	  15905	  0.78%
 48	  43143	  2.12%
 49	  48672	  2.39%
 50	1795246	 88.05%
2038984 reads passed initial QC


criterion=sequence-density
sequence-density=74.93
sequence-density-rank=1
fanout-score=22.06
fanout-score-rank=3
prefix-density=77.40
prefix-fanout=21.4
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGGCGATCTCGTATGCC


criterion=fanout-score
sequence-density=1.23
sequence-density-rank=6
fanout-score=595.12
fanout-score-rank=1
prefix-density=76.49
prefix-fanout=9.6
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 12 -x TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGGCGATCTCGTATGCC -o SRR5030938 -
Input file:	STDIN
trimmed:	SRR5030938-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGGCGATCTCGTATGCC
-- 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 06:49:40 2020 >> started

Wed Mar  4 06:49:43 2020 >> done (2.973s)
1984611 reads processed; of these:
  93421 ( 4.71%) short reads filtered out after trimming by size control
  14406 ( 0.73%) empty reads filtered out after trimming by size control
1876784 (94.57%) reads available; of these:
1560556 (83.15%) trimmed reads available after processing
 316228 (16.85%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  11752	  0.63%
 19	  15952	  0.85%
 20	  77933	  4.15%
 21	 188918	 10.07%
 22	 502847	 26.79%
 23	 249972	 13.32%
 24	 118343	  6.31%
 25	  31838	  1.70%
 26	  16552	  0.88%
 27	  13047	  0.70%
 28	  13802	  0.74%
 29	  12551	  0.67%
 30	  16138	  0.86%
 31	  32037	  1.71%
 32	  19687	  1.05%
 33	  50785	  2.71%
 34	  19448	  1.04%
 35	  15600	  0.83%
 36	  19094	  1.02%
 37	   9955	  0.53%
 38	  11954	  0.64%
 39	  11151	  0.59%
 40	  17657	  0.94%
 41	  19072	  1.02%
 42	  25282	  1.35%
 43	  16588	  0.88%
 44	  16157	  0.86%
 45	  18697	  1.00%
 46	  15244	  0.81%
 47	  12593	  0.67%
 48	   5029	  0.27%
 49	   9066	  0.48%
 50	 262043	 13.96%


criterion=sequence-density
sequence-density=2.80
sequence-density-rank=1
fanout-score=18.40
fanout-score-rank=1
prefix-density=2.90
prefix-fanout=17.7
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGGCGATCTCGTATGC


criterion=fanout-score
sequence-density=2.80
sequence-density-rank=1
fanout-score=18.40
fanout-score-rank=1
prefix-density=2.90
prefix-fanout=17.7
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGGCGATCTCGTATGC
                                 Started job on |	Mar 04 06:50:04
                             Started mapping on |	Mar 04 06:50:04
                                    Finished on |	Mar 04 06:50:28
       Mapping speed, Million of reads per hour |	289.67

                          Number of input reads |	1931157
                      Average input read length |	29
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1039256
                        Uniquely mapped reads % |	53.82%
                          Average mapped length |	28.27
                       Number of splices: Total |	1235
            Number of splices: Annotated (sjdb) |	150
                       Number of splices: GT/AG |	1141
                       Number of splices: GC/AG |	23
                       Number of splices: AT/AC |	1
               Number of splices: Non-canonical |	70
                      Mismatch rate per base, % |	0.22%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.31
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.03
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	589760
             % of reads mapped to multiple loci |	30.54%
        Number of reads mapped to too many loci |	41857
             % of reads mapped to too many loci |	2.17%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	12.74%
                     % of reads unmapped: other |	0.73%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	302141	302141	302141
N_multimapping	589760	589760	589760
N_noFeature	65333	78057	758309
N_ambiguous	550357	303105	8782
UnstrandedReadsAssigned:423566 PositiveStrandReadsAssigned:658094 NegativeStrandReadsAssigned:272165
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5030938 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: SRR5030938-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 1,931,157 reads, 433,461 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,044 rounds

 109283 SRR5030938.ke.tsv
  52636 SRR5030938.se.tsv
 161919 total
==> SRR5030938.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

==> SRR5030938.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030938 completed mapping pipeline successfully
