Starting /dee2/code/volunteer_pipeline.sh SRR14127852
    current disk space = 672991860
    free memory = 195357252 
SRR14127852 SRAfilesize
c384aab26f6c7aa1f81e850e9d204bac  SRR14127852.sra
SRR14127852.sra file validated
SRR14127852 is single end
SRR14127852 is conventional basespace
SRR14127852 read1 length is 51 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR14127852_1.fastq
File type	Conventional base calls
Encoding	Sanger / Illumina 1.9
Total Sequences	4000
Sequences flagged as poor quality	0
Sequence length	51
%GC	49
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	31.2515	37.0	25.0	37.0	11.0	37.0
2	35.52925	37.0	37.0	37.0	37.0	37.0
3	35.528	37.0	37.0	37.0	25.0	37.0
4	36.1925	37.0	37.0	37.0	37.0	37.0
5	36.01	37.0	37.0	37.0	37.0	37.0
6	36.328	37.0	37.0	37.0	37.0	37.0
7	36.3345	37.0	37.0	37.0	37.0	37.0
8	36.4365	37.0	37.0	37.0	37.0	37.0
9	36.472	37.0	37.0	37.0	37.0	37.0
10	36.451	37.0	37.0	37.0	37.0	37.0
11	36.5305	37.0	37.0	37.0	37.0	37.0
12	36.6375	37.0	37.0	37.0	37.0	37.0
13	36.534	37.0	37.0	37.0	37.0	37.0
14	36.491	37.0	37.0	37.0	37.0	37.0
15	36.403	37.0	37.0	37.0	37.0	37.0
16	36.3855	37.0	37.0	37.0	37.0	37.0
17	36.505	37.0	37.0	37.0	37.0	37.0
18	36.3	37.0	37.0	37.0	37.0	37.0
19	36.463	37.0	37.0	37.0	37.0	37.0
20	36.446	37.0	37.0	37.0	37.0	37.0
21	36.419	37.0	37.0	37.0	37.0	37.0
22	36.585	37.0	37.0	37.0	37.0	37.0
23	36.5385	37.0	37.0	37.0	37.0	37.0
24	36.3995	37.0	37.0	37.0	37.0	37.0
25	36.5175	37.0	37.0	37.0	37.0	37.0
26	36.4545	37.0	37.0	37.0	37.0	37.0
27	36.4335	37.0	37.0	37.0	37.0	37.0
28	36.4245	37.0	37.0	37.0	37.0	37.0
29	36.514	37.0	37.0	37.0	37.0	37.0
30	36.6995	37.0	37.0	37.0	37.0	37.0
31	36.605	37.0	37.0	37.0	37.0	37.0
32	36.4885	37.0	37.0	37.0	37.0	37.0
33	36.541	37.0	37.0	37.0	37.0	37.0
34	36.4255	37.0	37.0	37.0	37.0	37.0
35	36.6245	37.0	37.0	37.0	37.0	37.0
36	36.695	37.0	37.0	37.0	37.0	37.0
37	36.658	37.0	37.0	37.0	37.0	37.0
38	36.6925	37.0	37.0	37.0	37.0	37.0
39	36.5105	37.0	37.0	37.0	37.0	37.0
40	36.438	37.0	37.0	37.0	37.0	37.0
41	36.3675	37.0	37.0	37.0	37.0	37.0
42	36.442	37.0	37.0	37.0	37.0	37.0
43	36.3175	37.0	37.0	37.0	37.0	37.0
44	36.4285	37.0	37.0	37.0	37.0	37.0
45	36.643	37.0	37.0	37.0	37.0	37.0
46	36.6775	37.0	37.0	37.0	37.0	37.0
47	36.516	37.0	37.0	37.0	37.0	37.0
48	36.5165	37.0	37.0	37.0	37.0	37.0
49	36.505	37.0	37.0	37.0	37.0	37.0
50	36.478	37.0	37.0	37.0	37.0	37.0
51	36.398	37.0	37.0	37.0	37.0	37.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
23	1.0
24	1.0
25	1.0
26	2.0
27	10.0
28	10.0
29	24.0
30	24.0
31	39.0
32	54.0
33	70.0
34	104.0
35	217.0
36	1754.0
37	1689.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	25.575	7.8	61.4	5.225
2	50.415303297256486	15.001258494840172	12.031210672036245	22.552227535867104
3	16.7	62.0	5.675	15.625
4	49.175000000000004	13.275	20.175	17.375
5	13.900000000000002	50.025	28.000000000000004	8.075000000000001
6	28.1	9.325	54.625	7.95
7	57.875	19.35	12.65	10.125
8	15.775	46.625	32.824999999999996	4.775
9	23.075000000000003	45.1	19.15	12.675
10	59.150000000000006	20.125	12.174999999999999	8.55
11	20.724999999999998	8.175	21.925	49.175000000000004
12	9.9	50.1	25.474999999999998	14.524999999999999
13	7.55	14.549999999999999	13.8	64.1
14	13.55	26.474999999999998	53.75	6.225
15	76.5	13.075000000000001	6.0	4.425
16	8.674999999999999	21.0	63.575	6.75
17	23.9	49.3	19.475	7.324999999999999
18	63.625	12.8	14.124999999999998	9.45
19	14.875	10.75	36.3	38.074999999999996
20	20.75	21.85	49.75	7.6499999999999995
21	31.075000000000003	16.125	15.6	37.2
22	16.225	44.675	31.075000000000003	8.025
23	22.075	62.25000000000001	8.95	6.7250000000000005
24	40.775	29.825000000000003	25.424999999999997	3.975
25	13.875000000000002	42.925000000000004	32.65	10.549999999999999
26	15.25	12.575	38.4	33.775
27	27.975	8.450000000000001	24.025	39.550000000000004
28	57.550000000000004	12.075	4.9750000000000005	25.4
29	62.050000000000004	28.575	2.25	7.124999999999999
30	22.675	57.475	2.3	17.549999999999997
31	24.4	57.175	3.6999999999999997	14.725
32	48.075	36.625	9.3	6.0
33	34.475	52.0	2.125	11.4
34	48.65	24.175	3.925	23.25
35	12.0	31.35	8.15	48.5
36	7.675	49.125	9.725	33.475
37	12.0	29.625	3.05	55.325
38	23.05	44.95	3.85	28.15
39	26.875	18.65	11.275	43.2
40	40.875	18.575	20.275000000000002	20.275000000000002
41	18.65	12.0	45.5	23.849999999999998
42	22.35	11.125	27.1	39.425
43	24.6	20.8	40.525	14.075
44	45.65	31.45	10.424999999999999	12.475
45	12.625	61.1	6.275	20.0
46	6.925000000000001	57.3	9.525	26.25
47	4.25	19.85	19.225	56.675
48	3.9	15.4	38.224999999999994	42.475
49	7.95	13.200000000000001	12.525	66.325
50	17.075000000000003	20.575	11.525	50.824999999999996
51	19.225	40.925	18.375	21.475
>>END_MODULE
>>Per sequence GC content	warn
#GC Content	Count
0	0.0
1	1.0
2	2.0
3	1.0
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	0.5
14	1.0
15	0.5
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	0.5
31	1.0
32	0.5
33	0.0
34	0.5
35	1.0
36	2.0
37	3.0
38	5.0
39	7.0
40	20.5
41	34.0
42	57.0
43	80.0
44	192.5
45	305.0
46	462.5
47	620.0
48	835.0
49	1050.0
50	1078.0
51	1106.0
52	814.5
53	523.0
54	309.5
55	96.0
56	80.0
57	64.0
58	63.5
59	63.0
60	48.0
61	33.0
62	20.0
63	7.0
64	5.0
65	3.0
66	2.0
67	1.0
68	0.5
69	0.0
70	0.0
71	0.0
72	0.0
73	0.0
74	0.0
75	0.0
76	0.0
77	0.0
78	0.0
79	0.0
80	0.0
81	0.0
82	0.0
83	0.0
84	0.0
85	0.0
86	0.0
87	0.0
88	0.0
89	0.0
90	0.0
91	0.0
92	0.0
93	0.0
94	0.0
95	0.0
96	0.0
97	0.0
98	0.0
99	0.0
100	0.0
>>END_MODULE
>>Per base N content	pass
#Base	N-Count
1	0.0
2	0.675
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
51	0.0
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
51	4000.0
>>END_MODULE
>>Sequence Duplication Levels	fail
#Total Deduplicated Percentage	30.4
#Duplication Level	Percentage of deduplicated	Percentage of total
1	73.19078947368422	22.25
2	12.088815789473683	7.35
3	4.5230263157894735	4.125
4	1.644736842105263	2.0
5	1.5625	2.375
6	1.151315789473684	2.1
7	0.8223684210526315	1.7500000000000002
8	0.8223684210526315	2.0
9	0.41118421052631576	1.125
>10	2.7960526315789473	18.325
>50	0.6578947368421052	14.35
>100	0.3289473684210526	22.25
>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
TGAGATGAAGCACTGTAGCTCTAGATCGGAAGAGCACACGTCTGAACTCCA	382	9.55	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TGAGATGAAGCACTGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAG	209	5.225	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTAGATCGGAAGAGCACACGT	155	3.875	No Hit
TGAGATGAAGCACTGTAGCTAGATCGGAAGAGCACACGTCTGAACTCCAGT	144	3.5999999999999996	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
GGAGATGAAGCACTGTAGCTCTAGATCGGAAGAGCACACGTCTGAACTCCA	99	2.475	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TAGCTTATCAGACTGATGTTGAAGATCGGAAGAGCACACGTCTGAACTCCA	87	2.175	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCAGATCGGAAGAGCACACGTC	81	2.025	No Hit
TTCAAGTAATCCAGGATAGGCTAGATCGGAAGAGCACACGTCTGAACTCCA	73	1.825	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TGAGATGAAGCACTGTAGCTCCAGATCGGAAGAGCACACGTCTGAACTCCA	69	1.725	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TAGCTTATCAGACTGATGTTGACAGATCGGAAGAGCACACGTCTGAACTCC	60	1.5	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
TGAGGTAGTAGTTTGTGCTGTTAGATCGGAAGAGCACACGTCTGAACTCCA	53	1.325	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TCAGTGCACTACAGAACTTTGTAGATCGGAAGAGCACACGTCTGAACTCCA	52	1.3	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TGAGATGAAGCACTGTAGCTCAAGATCGGAAGAGCACACGTCTGAACTCCA	49	1.225	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TAGCTTATCAGACTGATGTTGAGATCGGAAGAGCACACGTCTGAACTCCAG	45	1.125	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GGAGATGAAGCACTGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAG	44	1.0999999999999999	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCCAGATCGGAAGAGCACACGT	40	1.0	No Hit
TGAGATGAAGCACTGTAGCTTAGATCGGAAGAGCACACGTCTGAACTCCAG	38	0.95	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCTAGATCGGAAGAGCACACGTC	34	0.8500000000000001	No Hit
GTCCAGTTTTCCCAGGAATCCCTAGATCGGAAGAGCACACGTCTGAACTCC	32	0.8	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTAGATCGGAAGAGCACACGTCTGAACTCCA	30	0.75	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TGAGATGAAGCACTGTAGCTCTTAGATCGGAAGAGCACACGTCTGAACTCC	30	0.75	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCAGATCGGAAGAGCACA	25	0.625	No Hit
AAGAAAGTATGCAAGAACTAGATCGGAAGAGCACACGTCTGAACTCCAGTC	25	0.625	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
TGAGGTAGTAGTTTGTACAGTTAGATCGGAAGAGCACACGTCTGAACTCCA	23	0.575	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCAAGATCGGAAGAGCACACGT	23	0.575	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCTAGATCGGAAGAGCACA	22	0.5499999999999999	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCAGATCGGAAGAGCACACGTCT	19	0.475	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
TGAGGTAGTAGGTTGTATGGTTAGATCGGAAGAGCACACGTCTGAACTCCA	19	0.475	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TGAGATGAAGCACTGTAGCCAGATCGGAAGAGCACACGTCTGAACTCCAGT	18	0.44999999999999996	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
GGAGATGAAGCACTGTAGCTAGATCGGAAGAGCACACGTCTGAACTCCAGT	18	0.44999999999999996	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
TGGAATGTAAAGAAGTATGTATAGATCGGAAGAGCACACGTCTGAACTCCA	15	0.375	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GGAGATGAAGCACTGTAGCTCAAGATCGGAAGAGCACACGTCTGAACTCCA	15	0.375	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TAGCTTATCAGACTGATGTTGACTAGATCGGAAGAGCACACGTCTGAACTC	15	0.375	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
TCGTACCGTGAGTAATAATGCAGATCGGAAGAGCACACGTCTGAACTCCAG	15	0.375	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
AACCCGTAGATCCGATCTTGTAGATCGGAAGAGCACACGTCTGAACTCCAG	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TGAGGTAGTAGGTTGTATAGTTAGATCGGAAGAGCACACGTCTGAACTCCA	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCCAGATCGGAAGAGCACACGTCTGAACTCCA	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TTCACAGTGGCTAAGTTCTGCAGATCGGAAGAGCACACGTCTGAACTCCAG	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TACCCTGTAGATCCGAATTTGTAGATCGGAAGAGCACACGTCTGAACTCCA	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TAGCTTATCAGACTGATGTTGACAAGATCGGAAGAGCACACGTCTGAACTC	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
GGAGATGAAGCACTGTAGCTCCAGATCGGAAGAGCACACGTCTGAACTCCA	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TGAGATGAAGCACTGTAGCTAAGATCGGAAGAGCACACGTCTGAACTCCAG	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TGTAAACATCCTCGACTGGAAGAGATCGGAAGAGCACACGTCTGAACTCCA	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TTCAAGTAATTCAGGATAGGTTAGATCGGAAGAGCACACGTCTGAACTCCA	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TCCTTCATTCCACCGGAGTCTGTAGATCGGAAGAGCACACGTCTGAACTCC	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTAGATCGGAAGAGCACACGTCTGAACTCCAG	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TCGTACCGTGAGTAATAATGCGAGATCGGAAGAGCACACGTCTGAACTCCA	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TGAGATGAAGCACTGTAGCTTTAGATCGGAAGAGCACACGTCTGAACTCCA	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TAGCACCATCTGAAATCGGTTAGATCGGAAGAGCACACGTCTGAACTCCAG	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TGAGATGAAGCACTGTAGCAAGATCGGAAGAGCACACGTCTGAACTCCAGT	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
TAGCTTATCAGACTGATGTTGATAGATCGGAAGAGCACACGTCTGAACTCC	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
TCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTAGATCGG	8	0.2	No Hit
ACAGTAGTCTGCACATTGGTTAGATCGGAAGAGCACACGTCTGAACTCCAG	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TGAGGTAGTAGTTTGTGCTGTTTAGATCGGAAGAGCACACGTCTGAACTCC	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
GGAGATGAAGCACTGTAGCTTAGATCGGAAGAGCACACGTCTGAACTCCAG	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TGAGATGAGGCACTGTAGCTCTAGATCGGAAGAGCACACGTCTGAACTCCA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TGAGATGAAGCACTGTAGCTCGAGATCGGAAGAGCACACGTCTGAACTCCA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TGAGATGAAGCACTGTAGCTCTCAGATCGGAAGAGCACACGTCTGAACTCC	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
TGAGGTAGTAGTTTGTGCTGTCAGATCGGAAGAGCACACGTCTGAACTCCA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GCATTGTGGTTCAGTGGTAGAATTCTCGCCTAGATCGGAAGAGCACACGTC	8	0.2	No Hit
GGAATACCGGGTGCTGTAGGCTTTAGATCGGAAGAGCACACGTCTGAACTC	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
ACCGCCTGGGAATACCGGGTGCTGTAGGCTAGATCGGAAGAGCACACGTCT	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
GCATTGTGGTTCAGTGGTAGAATTCTCGCCAGATCGGAAGAGCACACGTCT	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGTAGATCGGAAGAGCACACGTCT	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
TACCCTGTAGAACCGAATTTGTAGATCGGAAGAGCACACGTCTGAACTCCA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCAGATCGGAAGAGCACAC	7	0.17500000000000002	No Hit
GCATGGGTGGTTCAGTGGTAGAATTCTCGCTAGATCGGAAGAGCACACGTC	7	0.17500000000000002	No Hit
TAACACTGTCTGGTAACGATGTTAGATCGGAAGAGCACACGTCTGAACTCC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
TAGCTTATCAGACTGATGTTGACCAGATCGGAAGAGCACACGTCTGAACTC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCAAGATCGGAAGAGCACACGTC	7	0.17500000000000002	No Hit
TGGCTCAGTTCAGCAGGAACAGTAGATCGGAAGAGCACACGTCTGAACTCC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCAAGATCGGAAGAGCACA	6	0.15	No Hit
TTCACAGTGGCTAAGTTCTGAGATCGGAAGAGCACACGTCTGAACTCCAGT	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
TGTAAACATCCCCGACTGGAAGAGATCGGAAGAGCACACGTCTGAACTCCA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TGAGGTAGTAGGTTGTATGGTTTAGATCGGAAGAGCACACGTCTGAACTCC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCAAGATCGGAAGAGCACACGTCTGAACTCCA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCGAGATCGGAAGAGCACACGT	6	0.15	No Hit
TGAGGTAGTAGGTTGTATGGTAGATCGGAAGAGCACACGTCTGAACTCCAG	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TGAGATGAAGCACTGTAGCCCAGATCGGAAGAGCACACGTCTGAACTCCAG	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
AAGCTGCCAGTTGAAGAACTGTAGATCGGAAGAGCACACGTCTGAACTCCA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GGTGCTGTAGGCTTTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTA	6	0.15	TruSeq Adapter, Index 7 (97% over 35bp)
GCATGGGTGGTTCAGTGGTAGAATTCTCGCCAGATCGGAAGAGCACACGTC	6	0.15	No Hit
GTCCAGTTTTCCCAGGAATCCAGATCGGAAGAGCACACGTCTGAACTCCAG	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TGAGGTAGTAGTTTGTGCTGTTAAGATCGGAAGAGCACACGTCTGAACTCC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
GGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTTTAGATCGGAAGAGCAC	6	0.15	No Hit
TCGTACCGTGAGTAATAATGTAGATCGGAAGAGCACACGTCTGAACTCCAG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
ATCACATTGCCAGGGATTACCACTAGATCGGAAGAGCACACGTCTGAACTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
TCCTTCATTCCACCGGAGTCTGAAGATCGGAAGAGCACACGTCTGAACTCC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
GGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTTTAGATCGGAAGAGCA	5	0.125	No Hit
TGAGGTAGTAGGTTGTGTGGTTAGATCGGAAGAGCACACGTCTGAACTCCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTAGATCG	5	0.125	No Hit
TGGCTCAGTTCAGCAGGAACAAGATCGGAAGAGCACACGTCTGAACTCCAG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
CTTCTCACTACTGCACTTGACTAGTCTTAGATCGGAAGAGCACACGTCTGA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
TGAGGTAGTAGATTGTATAGTCAGATCGGAAGAGCACACGTCTGAACTCCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
AGAGGTAGTAGGTTGCATAGTTAGATCGGAAGAGCACACGTCTGAACTCCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
ACTGGACTTGGAGTCAGAAGGCAGATCGGAAGAGCACACGTCTGAACTCCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GTGCTGTAGGCTTTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTAG	5	0.125	TruSeq Adapter, Index 7 (97% over 36bp)
TCAGTGCATGACAGAACTTGGAGATCGGAAGAGCACACGTCTGAACTCCAG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TGTAAACATCCTTGACTGGAAGCTAGATCGGAAGAGCACACGTCTGAACTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
TTCACAGTGGCTAAGTTCTGTAGATCGGAAGAGCACACGTCTGAACTCCAG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TTCAAGTAATCCAGGATAGGCAGATCGGAAGAGCACACGTCTGAACTCCAG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GCCCGGCTAGCTCAGTCGGTAGAGCATGAGACTAGATCGGAAGAGCACACG	5	0.125	No Hit
AGCAGCATTGTACAGGGCTATGAAGATCGGAAGAGCACACGTCTGAACTCC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
TGTAAACATCCCCGACTGGAAGCTAGATCGGAAGAGCACACGTCTGAACTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (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	0.1	0.0	0.0	0.0	0.0
2	0.1	0.0	0.0	0.0	0.0
3	0.1	0.0	0.0	0.0	0.0
4	0.1	0.0	0.0	0.0	0.0
5	0.1	0.0	0.0	0.0	0.0
6	0.1	0.0	0.0	0.0	0.0
7	0.1	0.0	0.0	0.0	0.0
8	0.175	0.0	0.0	0.0	0.0
9	0.25	0.0	0.0	0.0	0.0
10	0.425	0.0	0.0	0.0	0.0
11	0.65	0.0	0.0	0.0	0.0
12	1.0	0.0	0.0	0.0	0.0
13	1.225	0.0	0.0	0.0	0.0
14	1.85	0.0	0.0	0.0	0.0
15	2.4	0.0	0.0	0.0	0.0
16	3.175	0.0	0.0	0.0	0.0
17	3.95	0.0	0.0	0.0	0.0
18	4.55	0.0	0.0	0.0	0.0
19	5.1	0.0	0.0	0.0	0.0
20	6.8	0.0	0.0	0.0	0.0
21	14.3	0.0	0.0	0.0	0.0
22	30.875	0.0	0.0	0.0	0.0
23	66.55	0.0	0.0	0.0	0.0
24	74.7	0.0	0.0	0.0	0.0
25	77.825	0.0	0.0	0.0	0.0
26	78.2	0.0	0.0	0.0	0.0
27	78.575	0.0	0.0	0.0	0.0
28	78.775	0.0	0.0	0.0	0.0
29	79.45	0.0	0.0	0.0	0.0
30	79.775	0.0	0.0	0.0	0.0
31	81.3	0.0	0.0	0.0	0.0
32	86.175	0.0	0.0	0.0	0.0
33	93.225	0.0	0.0	0.0	0.0
34	93.85	0.0	0.0	0.0	0.0
35	94.575	0.0	0.0	0.0	0.0
36	96.4	0.0	0.0	0.0	0.0
37	96.975	0.0	0.0	0.0	0.0
38	97.375	0.0	0.0	0.0	0.0
39	97.6	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TGTAGCT	95	0.0	45.000004	14
CTCGCCT	45	2.2009772E-10	45.000004	26
GGAGATG	20	6.222983E-4	45.0	1
GAGGTAG	25	3.236105E-5	45.0	2
GTAGAAT	75	0.0	45.0	18
TGGTTCA	75	0.0	45.0	8
CATTGGT	70	0.0	45.0	2
TCAAGAT	20	6.222983E-4	45.0	20
TAAACAT	20	6.222983E-4	45.0	3
AGCTCAA	20	6.222983E-4	45.0	17
AATTCTC	75	0.0	45.0	22
AAACATC	20	6.222983E-4	45.0	4
TGGTAGA	75	0.0	45.0	16
CGCCTAG	40	4.3564796E-9	45.0	28
GCCTAGA	40	4.3564796E-9	45.0	29
ATTGGTG	70	0.0	45.0	3
AGTGGTA	75	0.0	45.0	14
GGTTCAG	75	0.0	45.0	9
GTTCAGT	75	0.0	45.0	10
AGAATTC	75	0.0	45.0	20
>>END_MODULE
Rejected 2833819 READS because READLEN < 1
Read 2833819 spots for SRR14127852.sra
Written 2833819 spots for SRR14127852.sra
Rejected 2833819 READS because READLEN < 1
Read 2833819 spots for SRR14127852.sra
Written 2833819 spots for SRR14127852.sra
Rejected 2833819 READS because READLEN < 1
Read 2833819 spots for SRR14127852.sra
Written 2833819 spots for SRR14127852.sra
Rejected 2833819 READS because READLEN < 1
Read 2833819 spots for SRR14127852.sra
Written 2833819 spots for SRR14127852.sra
Rejected 2833819 READS because READLEN < 1
Read 2833819 spots for SRR14127852.sra
Written 2833819 spots for SRR14127852.sra
Rejected 2833819 READS because READLEN < 1
Read 2833819 spots for SRR14127852.sra
Written 2833819 spots for SRR14127852.sra
Rejected 2833822 READS because READLEN < 1
Read 2833822 spots for SRR14127852.sra
Written 2833822 spots for SRR14127852.sra
Rejected 2833819 READS because READLEN < 1
Read 2833819 spots for SRR14127852.sra
Written 2833819 spots for SRR14127852.sra
SRR ids: ['SRR14127852.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_dy02883k
SRR14127852.sra spots: 22670555
blocks: [[1, 2833819], [2833820, 5667638], [5667639, 8501457], [8501458, 11335276], [11335277, 14169095], [14169096, 17002914], [17002915, 19836733], [19836734, 22670555]]
SRR14127852 file size 3232764
SRR14127852 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	/usr/local/bin/skewer -f sanger -l 18 -q 10 -k inf -t 8 -o SRR14127852 SRR14127852_1.fastq
Input file:	SRR14127852_1.fastq
trimmed:	SRR14127852-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 
-- minimum overlap length for adapter detection (-k):	inf
-- number of concurrent threads (-t):	8
Tue Dec  2 21:22:32 2025 >> started

Tue Dec  2 21:22:41 2025 >> done (8.726s)
22670555 reads processed; of these:
 1008802 ( 4.45%) short reads filtered out after trimming by size control
   18469 ( 0.08%) empty reads filtered out after trimming by size control
21643284 (95.47%) reads available; of these:
  592460 ( 2.74%) trimmed reads available after processing
21050824 (97.26%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  157445	  0.73%
 19	  435015	  2.01%
 20	       0	  0.00%
 21	       0	  0.00%
 22	       0	  0.00%
 23	       0	  0.00%
 24	       0	  0.00%
 25	       0	  0.00%
 26	       0	  0.00%
 27	       0	  0.00%
 28	       0	  0.00%
 29	       0	  0.00%
 30	       0	  0.00%
 31	       0	  0.00%
 32	       0	  0.00%
 33	       0	  0.00%
 34	       0	  0.00%
 35	       0	  0.00%
 36	       0	  0.00%
 37	       0	  0.00%
 38	       0	  0.00%
 39	       0	  0.00%
 40	       0	  0.00%
 41	       0	  0.00%
 42	       0	  0.00%
 43	       0	  0.00%
 44	       0	  0.00%
 45	       0	  0.00%
 46	       0	  0.00%
 47	       0	  0.00%
 48	       0	  0.00%
 49	       0	  0.00%
 50	       0	  0.00%
 51	21050824	 97.26%
21643284 reads passed initial QC


criterion=sequence-density
sequence-density=94.35
sequence-density-rank=1
fanout-score=17.33
fanout-score-rank=1
prefix-density=95.29
prefix-fanout=17.2
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACTAGCTTATC


criterion=fanout-score
sequence-density=94.35
sequence-density-rank=1
fanout-score=17.33
fanout-score-rank=1
prefix-density=95.29
prefix-fanout=17.2
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACTAGCTTATC
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:	/usr/local/bin/skewer -f sanger -l 18 -t 8 -x AGATCGGAAGAGCACACGTCTGAACTCCAGTCACTAGCTTATC -o SRR14127852 -
Input file:	STDIN
trimmed:	SRR14127852-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	AGATCGGAAGAGCACACGTCTGAACTCCAGTCACTAGCTTATC
-- 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):		Sanger/Illumina 1.8+ FASTQ 
-- minimum overlap length for adapter detection (-k):	3
-- number of concurrent threads (-t):	8
Tue Dec  2 21:22:59 2025 >> started

Tue Dec  2 21:23:14 2025 >> done (14.877s)
21187636 reads processed; of these:
    8372 ( 0.04%) short reads filtered out after trimming by size control
      29 ( 0.00%) empty reads filtered out after trimming by size control
21179235 (99.96%) reads available; of these:
20524792 (96.91%) trimmed reads available after processing
  654443 ( 3.09%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  151837	  0.72%
 19	  430005	  2.03%
 20	 1631267	  7.70%
 21	 3845389	 18.16%
 22	 7971552	 37.64%
 23	 1977805	  9.34%
 24	  633012	  2.99%
 25	   98151	  0.46%
 26	   68714	  0.32%
 27	   76121	  0.36%
 28	   97236	  0.46%
 29	   75717	  0.36%
 30	  278470	  1.31%
 31	  950248	  4.49%
 32	 1538871	  7.27%
 33	  174048	  0.82%
 34	  176778	  0.83%
 35	  399073	  1.88%
 36	  102089	  0.48%
 37	   75812	  0.36%
 38	   66270	  0.31%
 39	   54989	  0.26%
 40	   31616	  0.15%
 41	   21436	  0.10%
 42	   19103	  0.09%
 43	   33697	  0.16%
 44	   66297	  0.31%
 45	   36773	  0.17%
 46	    7225	  0.03%
 47	    3683	  0.02%
 48	    3830	  0.02%
 49	       0	  0.00%
 50	       0	  0.00%
 51	   82121	  0.39%


criterion=sequence-density
sequence-density=11.75
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=12
prefix-density=0.00
prefix-fanout=1.0
sequence=GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGC


criterion=fanout-score
sequence-density=0.25
sequence-density-rank=36
fanout-score=146.39
fanout-score-rank=1
prefix-density=36.11
prefix-fanout=1.0
sequence=AGCACTGTAGCCCT
                                 Started job on |	Dec 02 21:23:28
                             Started mapping on |	Dec 02 21:23:28
                                    Finished on |	Dec 02 21:25:09
       Mapping speed, Million of reads per hour |	771.14

                          Number of input reads |	21634883
                      Average input read length |	24
                                    UNIQUE READS:
                   Uniquely mapped reads number |	13384841
                        Uniquely mapped reads % |	61.87%
                          Average mapped length |	21.48
                       Number of splices: Total |	12370
            Number of splices: Annotated (sjdb) |	5523
                       Number of splices: GT/AG |	12032
                       Number of splices: GC/AG |	108
                       Number of splices: AT/AC |	6
               Number of splices: Non-canonical |	224
                      Mismatch rate per base, % |	0.10%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.31
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.22
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	5035068
             % of reads mapped to multiple loci |	23.27%
        Number of reads mapped to too many loci |	2701771
             % of reads mapped to too many loci |	12.49%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	2.33%
                     % of reads unmapped: other |	0.05%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	3214974	3214974	3214974
N_multimapping	5035068	5035068	5035068
N_noFeature	335035	1112710	12591714
N_ambiguous	166350	150876	36
UnstrandedReadsAssigned:12883456 PositiveStrandReadsAssigned:12121255 NegativeStrandReadsAssigned:793091
Dataset is classified positive stranded
MeadianReadLen=22 20thPercentileLength=21 echo kmer=19
SRR14127852 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: 31,715
[index] number of k-mers: 49,362,984
[index] number of equivalence classes: 166,181
[quant] running in single-end mode
[quant] will process file 1: SRR14127852-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 21,634,883 reads, 435,053 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 883 rounds

  31716 SRR14127852.ke.tsv
  32883 SRR14127852.se.tsv
  64599 total
==> SRR14127852.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
ENSRNOT00000047550.4	955	856	4807	7648.9
ENSRNOT00000040993.4	1039	940	5169	7489.92
ENSRNOT00000050156.3	1545	1446	19626	18486.8
ENSRNOT00000043693.3	684	585	5189	12081.7
ENSRNOT00000046201.3	204	105	1211	15709.2
ENSRNOT00000046108.3	681	582	4705	11011.2
ENSRNOT00000049683.3	784	685	6745	13411.9
ENSRNOT00000041241.3	348	249	518	2833.54
ENSRNOT00000044582.3	297	198	1088	7484.49

==> SRR14127852.se.tsv <==
ENSRNOG00000046319	0
ENSRNOG00000047964	0
ENSRNOG00000050370	0
ENSRNOG00000032365	0
ENSRNOG00000040300	0
ENSRNOG00000058808	0
ENSRNOG00000061316	3
ENSRNOG00000050129	0
ENSRNOG00000040316	0
ENSRNOG00000023659	0
SRR14127852 completed mapping pipeline successfully
