Starting /dee2/code/volunteer_pipeline.sh SRR14127853
    current disk space = 672386988
    free memory = 196859496 
SRR14127853 SRAfilesize
43a6821b8c07ab94af848b0f8fcf5fdf  SRR14127853.sra
SRR14127853.sra file validated
SRR14127853 is single end
SRR14127853 is conventional basespace
SRR14127853 read1 length is 51 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR14127853_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	34.1865	37.0	37.0	37.0	25.0	37.0
2	35.74025	37.0	37.0	37.0	37.0	37.0
3	35.782	37.0	37.0	37.0	37.0	37.0
4	36.354	37.0	37.0	37.0	37.0	37.0
5	36.1995	37.0	37.0	37.0	37.0	37.0
6	36.359	37.0	37.0	37.0	37.0	37.0
7	36.3135	37.0	37.0	37.0	37.0	37.0
8	36.449	37.0	37.0	37.0	37.0	37.0
9	36.3935	37.0	37.0	37.0	37.0	37.0
10	36.4285	37.0	37.0	37.0	37.0	37.0
11	36.4375	37.0	37.0	37.0	37.0	37.0
12	36.5705	37.0	37.0	37.0	37.0	37.0
13	36.496	37.0	37.0	37.0	37.0	37.0
14	36.393	37.0	37.0	37.0	37.0	37.0
15	36.431	37.0	37.0	37.0	37.0	37.0
16	36.352	37.0	37.0	37.0	37.0	37.0
17	36.215	37.0	37.0	37.0	37.0	37.0
18	36.3635	37.0	37.0	37.0	37.0	37.0
19	36.4695	37.0	37.0	37.0	37.0	37.0
20	36.501	37.0	37.0	37.0	37.0	37.0
21	36.463	37.0	37.0	37.0	37.0	37.0
22	36.615	37.0	37.0	37.0	37.0	37.0
23	36.4665	37.0	37.0	37.0	37.0	37.0
24	36.3775	37.0	37.0	37.0	37.0	37.0
25	36.59	37.0	37.0	37.0	37.0	37.0
26	36.588	37.0	37.0	37.0	37.0	37.0
27	36.5155	37.0	37.0	37.0	37.0	37.0
28	36.4535	37.0	37.0	37.0	37.0	37.0
29	36.418	37.0	37.0	37.0	37.0	37.0
30	36.6305	37.0	37.0	37.0	37.0	37.0
31	36.5545	37.0	37.0	37.0	37.0	37.0
32	36.5725	37.0	37.0	37.0	37.0	37.0
33	36.6245	37.0	37.0	37.0	37.0	37.0
34	36.4745	37.0	37.0	37.0	37.0	37.0
35	36.5295	37.0	37.0	37.0	37.0	37.0
36	36.6485	37.0	37.0	37.0	37.0	37.0
37	36.584	37.0	37.0	37.0	37.0	37.0
38	36.6495	37.0	37.0	37.0	37.0	37.0
39	36.5035	37.0	37.0	37.0	37.0	37.0
40	36.4125	37.0	37.0	37.0	37.0	37.0
41	36.466	37.0	37.0	37.0	37.0	37.0
42	36.479	37.0	37.0	37.0	37.0	37.0
43	36.3465	37.0	37.0	37.0	37.0	37.0
44	36.381	37.0	37.0	37.0	37.0	37.0
45	36.6115	37.0	37.0	37.0	37.0	37.0
46	36.724	37.0	37.0	37.0	37.0	37.0
47	36.628	37.0	37.0	37.0	37.0	37.0
48	36.531	37.0	37.0	37.0	37.0	37.0
49	36.5735	37.0	37.0	37.0	37.0	37.0
50	36.4785	37.0	37.0	37.0	37.0	37.0
51	36.6335	37.0	37.0	37.0	37.0	37.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
26	1.0
27	4.0
28	7.0
29	32.0
30	27.0
31	40.0
32	59.0
33	49.0
34	89.0
35	197.0
36	1503.0
37	1992.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	25.650000000000002	7.625	61.25000000000001	5.475
2	36.68594417902942	23.48503897410108	10.711591651998994	29.117425194870506
3	23.425	55.525000000000006	7.3	13.750000000000002
4	38.324999999999996	13.100000000000001	25.074999999999996	23.5
5	16.7	35.4	40.225	7.675
6	34.949999999999996	9.2	47.975	7.875
7	47.875	25.324999999999996	13.450000000000001	13.350000000000001
8	17.45	36.425000000000004	41.449999999999996	4.675
9	28.299999999999997	30.325000000000003	20.05	21.325
10	48.25	26.775	15.35	9.625
11	27.925	13.100000000000001	28.025	30.95
12	10.274999999999999	40.425	32.05	17.25
13	8.325000000000001	19.25	15.725	56.699999999999996
14	17.25	29.025000000000002	46.75	6.9750000000000005
15	69.45	17.625	7.7	5.225
16	8.525	33.300000000000004	51.475	6.7
17	27.875	32.75	27.3	12.075
18	60.975	11.425	17.275	10.325
19	16.7	13.05	46.949999999999996	23.3
20	24.2	26.224999999999998	44.25	5.325
21	44.525	14.899999999999999	16.075	24.5
22	14.875	49.4	28.499999999999996	7.225
23	17.7	62.949999999999996	8.125	11.225
24	41.9	26.400000000000002	26.8	4.9
25	16.275000000000002	45.574999999999996	29.25	8.9
26	13.850000000000001	15.5	39.050000000000004	31.6
27	17.825	11.65	28.65	41.875
28	51.525	9.45	7.1	31.924999999999997
29	67.35	19.15	2.825	10.674999999999999
30	22.475	50.824999999999996	3.4000000000000004	23.3
31	20.3	54.525	5.050000000000001	20.125
32	45.300000000000004	32.875	14.374999999999998	7.449999999999999
33	31.974999999999998	54.50000000000001	4.7	8.825
34	51.849999999999994	22.75	5.800000000000001	19.6
35	15.024999999999999	30.349999999999998	8.825	45.800000000000004
36	11.55	49.025	11.275	28.15
37	13.55	26.875	4.625	54.949999999999996
38	19.475	49.525000000000006	5.325	25.674999999999997
39	22.3	19.825	10.424999999999999	47.449999999999996
40	42.55	21.3	14.075	22.075
41	22.650000000000002	15.475	41.449999999999996	20.424999999999997
42	24.15	12.65	22.425	40.775
43	18.65	22.45	42.1	16.8
44	48.65	24.2	12.7	14.45
45	16.75	55.675	8.1	19.475
46	9.049999999999999	62.9	5.575	22.475
47	6.275	24.675	12.4	56.65
48	5.0	20.349999999999998	37.325	37.325
49	7.725	13.65	13.700000000000001	64.925
50	15.075	16.775000000000002	12.3	55.85
51	13.975000000000001	44.875	15.5	25.650000000000002
>>END_MODULE
>>Per sequence GC content	pass
#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	0.0
24	0.0
25	0.0
26	1.0
27	2.0
28	1.0
29	0.0
30	0.0
31	0.0
32	1.5
33	3.0
34	3.5
35	4.0
36	5.5
37	7.0
38	8.5
39	10.0
40	16.0
41	22.0
42	56.5
43	91.0
44	283.0
45	475.0
46	653.5
47	832.0
48	840.5
49	849.0
50	862.5
51	876.0
52	693.0
53	510.0
54	331.5
55	153.0
56	114.0
57	75.0
58	67.5
59	60.0
60	41.5
61	23.0
62	14.0
63	5.0
64	4.0
65	3.0
66	1.5
67	0.0
68	0.0
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	0.575
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	35.75
#Duplication Level	Percentage of deduplicated	Percentage of total
1	75.1048951048951	26.85
2	12.447552447552447	8.9
3	3.8461538461538463	4.125
4	1.6083916083916083	2.3
5	1.1888111888111887	2.125
6	0.7692307692307693	1.6500000000000001
7	0.5594405594405595	1.4000000000000001
8	0.4195804195804196	1.2
9	0.4195804195804196	1.35
>10	2.937062937062937	22.7
>50	0.34965034965034963	7.000000000000001
>100	0.34965034965034963	20.4
>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	275	6.875000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTAGATCGGAAGAGCACACGT	157	3.925	No Hit
TAGCTTATCAGACTGATGTTGAAGATCGGAAGAGCACACGTCTGAACTCCA	134	3.35	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TCAGTGCACTACAGAACTTTGTAGATCGGAAGAGCACACGTCTGAACTCCA	126	3.15	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TAGCTTATCAGACTGATGTTGACAGATCGGAAGAGCACACGTCTGAACTCC	124	3.1	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCAGATCGGAAGAGCACA	62	1.55	No Hit
TGAGATGAAGCACTGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAG	58	1.4500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TGAGGTAGTAGTTTGTGCTGTTAGATCGGAAGAGCACACGTCTGAACTCCA	57	1.425	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTAGATCGGAAGAGCACACGTCTGAACTCCA	52	1.3	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TGAGATGAAGCACTGTAGCTCCAGATCGGAAGAGCACACGTCTGAACTCCA	51	1.275	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCAGATCGGAAGAGCACACGTC	48	1.2	No Hit
TGAGATGAAGCACTGTAGCTAGATCGGAAGAGCACACGTCTGAACTCCAGT	48	1.2	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
TAGCTTATCAGACTGATGTTGACTAGATCGGAAGAGCACACGTCTGAACTC	46	1.15	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
GGAGATGAAGCACTGTAGCTCTAGATCGGAAGAGCACACGTCTGAACTCCA	45	1.125	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TAGCTTATCAGACTGATGTTGAGATCGGAAGAGCACACGTCTGAACTCCAG	43	1.075	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TGAGATGAAGCACTGTAGCTCAAGATCGGAAGAGCACACGTCTGAACTCCA	43	1.075	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCTAGATCGGAAGAGCACA	38	0.95	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCCAGATCGGAAGAGCACACGT	37	0.9249999999999999	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCAAGATCGGAAGAGCACACGT	33	0.8250000000000001	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCTAGATCGGAAGAGCACACGTC	31	0.775	No Hit
TAGCTTATCAGACTGATGTTGATAGATCGGAAGAGCACACGTCTGAACTCC	27	0.675	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTAGATCGGAAGAGCACACGTCTGAACTCCA	26	0.65	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TACCCTGTAGATCCGAATTTGTAGATCGGAAGAGCACACGTCTGAACTCCA	26	0.65	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GCATGGGTGGTTCAGTGGTAGAATTCTCGCCTAGATCGGAAGAGCACACGT	25	0.625	No Hit
TGAGGTAGTAGTTTGTACAGTTAGATCGGAAGAGCACACGTCTGAACTCCA	24	0.6	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCAGATCGGAAGAGCACAC	22	0.5499999999999999	No Hit
TAGCTTATCAGACTGATGTTGACAAGATCGGAAGAGCACACGTCTGAACTC	20	0.5	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
GTGCTGTAGGCTTTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAG	18	0.44999999999999996	TruSeq Adapter, Index 7 (100% over 36bp)
TAACACTGTCTGGTAACGATGTAGATCGGAAGAGCACACGTCTGAACTCCA	17	0.42500000000000004	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TGAGATGAAGCACTGTAGCTCTTAGATCGGAAGAGCACACGTCTGAACTCC	17	0.42500000000000004	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
TGAGGTAGTAGGTTGTATGGTTAGATCGGAAGAGCACACGTCTGAACTCCA	17	0.42500000000000004	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TGAGAACTGAATTCCATGGGTTAGATCGGAAGAGCACACGTCTGAACTCCA	16	0.4	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GCATGGGTGGTTCAGTGGTAGAATTCTCGCCAGATCGGAAGAGCACACGTC	16	0.4	No Hit
AAGAAAGTATGCAAGAACTAGATCGGAAGAGCACACGTCTGAACTCCAGTC	15	0.375	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
TGAGATGAAGCACTGTAGCTTAGATCGGAAGAGCACACGTCTGAACTCCAG	14	0.35000000000000003	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GGAGATGAAGCACTGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAG	14	0.35000000000000003	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TCAGTGCACTACAGAACTTTGCAGATCGGAAGAGCACACGTCTGAACTCCA	14	0.35000000000000003	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCGAGATCGGAAGAGCACACGT	13	0.325	No Hit
TCGTACCGTGAGTAATAATGCAGATCGGAAGAGCACACGTCTGAACTCCAG	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCAGATCGGAAGAGCACACGTCT	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
TGCTGTAGGCTTTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGA	12	0.3	TruSeq Adapter, Index 7 (100% over 37bp)
GCATTGTGGTTCAGTGGTAGAATTCTCGCCTAGATCGGAAGAGCACACGTC	12	0.3	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCAAGATCGGAAGAGCACA	11	0.27499999999999997	No Hit
TGAGATGAAGCACTGTAGCTCGAGATCGGAAGAGCACACGTCTGAACTCCA	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTAGATCGGAAGAGCACACGTCTGAACTCCAG	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TAGCTTATCAGACTGATGTTGACCAGATCGGAAGAGCACACGTCTGAACTC	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
TTCAAGTAATTCAGGATAGGTTAGATCGGAAGAGCACACGTCTGAACTCCA	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TCAGTGCACTACAGAACTTTGGAGATCGGAAGAGCACACGTCTGAACTCCA	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TGAGATGAAGCACTGTAGCTTTAGATCGGAAGAGCACACGTCTGAACTCCA	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TAGCTTATCAGACTGATGTTAAGATCGGAAGAGCACACGTCTGAACTCCAG	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TAACACTGTCTGGTAACGATGTTAGATCGGAAGAGCACACGTCTGAACTCC	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCAAGATCGGAAGAGCACACGTC	10	0.25	No Hit
TGAGATGAAGCACTGTAGCTAAGATCGGAAGAGCACACGTCTGAACTCCAG	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TGAGGTAGTAGATTGTATAGTCAGATCGGAAGAGCACACGTCTGAACTCCA	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
ACAGTAGTCTGCACATTGGTTAGATCGGAAGAGCACACGTCTGAACTCCAG	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GCATGGGTGGTTCAGTGGTAGAATTCTCGCCCAGATCGGAAGAGCACACGT	9	0.22499999999999998	No Hit
TTCACAGTGGCTAAGTTCTGCAGATCGGAAGAGCACACGTCTGAACTCCAG	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TGTAAACATCCTTGACTGGAAGAGATCGGAAGAGCACACGTCTGAACTCCA	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TACCCTGTAGATCCGAATTTGTGAGATCGGAAGAGCACACGTCTGAACTCC	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
TTCAAGTAATCCAGGATAGGAGATCGGAAGAGCACACGTCTGAACTCCAGT	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
AACCCGTAGATCCGATCTTGTAGATCGGAAGAGCACACGTCTGAACTCCAG	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TGAGATGAAGCACTGTAGCGCTAGATCGGAAGAGCACACGTCTGAACTCCA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCAAGATCGGAAGAGCACACGTCTGAACTCCA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGTAGATCGGAAGAGCACAC	8	0.2	No Hit
TGAGGTAGTAGGTTGTGTGGTTAGATCGGAAGAGCACACGTCTGAACTCCA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
CTGTAGGCTTTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATC	7	0.17500000000000002	TruSeq Adapter, Index 7 (100% over 39bp)
GGAGATGAAGCACTGTAGCTCCAGATCGGAAGAGCACACGTCTGAACTCCA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TAGCTTATCAGACTGATGTTGGAGATCGGAAGAGCACACGTCTGAACTCCA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TAGCTTATCAGACTGATGTTGTAGATCGGAAGAGCACACGTCTGAACTCCA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TCCTTCATTCCACCGGAGTCTGTAGATCGGAAGAGCACACGTCTGAACTCC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
TGAGGTAGTAGTTTGTACAGTCAGATCGGAAGAGCACACGTCTGAACTCCA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TGAGGTAGTAGTTTGTGCTGTTAAGATCGGAAGAGCACACGTCTGAACTCC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
TAGCTTATCAGACTGATGTTAGATCGGAAGAGCACACGTCTGAACTCCAGT	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
TAGCTTATCAGACTGATGTTGAAAGATCGGAAGAGCACACGTCTGAACTCC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
GCATGGGTGGTTCAGTGGTAGAATTCTCGCAGATCGGAAGAGCACACGTCT	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
TTCACAGTGGCTAAGTTCTGAGATCGGAAGAGCACACGTCTGAACTCCAGT	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
TGCTGTAGGCTTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGAT	6	0.15	TruSeq Adapter, Index 7 (100% over 38bp)
TCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTAGATCGG	6	0.15	No Hit
TGTAAACATCCTCGACTGGAAGAGATCGGAAGAGCACACGTCTGAACTCCA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GCATGGGTGGTTCAGTGGTAGAATTCTCGCCAAGATCGGAAGAGCACACGT	6	0.15	No Hit
TGAGGTAGTAGTTTGTGCTGTCAGATCGGAAGAGCACACGTCTGAACTCCA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TGAGATGAAGCACTGTAGCAAGATCGGAAGAGCACACGTCTGAACTCCAGT	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
GGTGCTGTAGGCTTTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCA	6	0.15	TruSeq Adapter, Index 7 (100% over 35bp)
TCAGTGCACTACAGAACTTTGAAGATCGGAAGAGCACACGTCTGAACTCCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TGAGATGAAGCACTGTAGCCAGATCGGAAGAGCACACGTCTGAACTCCAGT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
TTCAAGTAATCCAGGATAGGCTCAGATCGGAAGAGCACACGTCTGAACTCC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
TCAGTGCATGACAGAACTTGGAGATCGGAAGAGCACACGTCTGAACTCCAG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TGGAATGTAAAGAAGTATGTATAGATCGGAAGAGCACACGTCTGAACTCCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
CTGAAATGAAGAGAAAACTCTCTGCTGATCAGATCGGAAGAGCACACGTCT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
TGAGGTAGTAGATTGTATAGTAAGATCGGAAGAGCACACGTCTGAACTCCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TGTAAACATCCTTGACTGGAAGCTAGATCGGAAGAGCACACGTCTGAACTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
GCATTGTGGTTCAGTGGTAGAATTCTCGCCTGCAGATCGGAAGAGCACACG	5	0.125	No Hit
TAGCTTATCAGACTGATGTTGACGAGATCGGAAGAGCACACGTCTGAACTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
TAGCACCATCTGAAATCGGTTAGATCGGAAGAGCACACGTCTGAACTCCAG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GCATTTGTGGTTCAGTGGTAGAATTCTCGCCTAGATCGGAAGAGCACACGT	5	0.125	No Hit
GGAGATGAAGCACTGTAGCTCAAGATCGGAAGAGCACACGTCTGAACTCCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TTCAAGTAATTCAGGATAGGTAGATCGGAAGAGCACACGTCTGAACTCCAG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GTCCAGTTTTCCCAGGAATCCCTAGATCGGAAGAGCACACGTCTGAACTCC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
GGAATACCGGGTGCTGTAGGCTTTAGATCGGAAGAGCACACGTCTGAACTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
TGAGGTAGTAGTTTGTGCTGTAAGATCGGAAGAGCACACGTCTGAACTCCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
>>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	0.05	0.0	0.0	0.0	0.0
2	0.05	0.0	0.0	0.0	0.0
3	0.05	0.0	0.0	0.0	0.0
4	0.05	0.0	0.0	0.0	0.0
5	0.05	0.0	0.0	0.0	0.0
6	0.05	0.0	0.0	0.0	0.0
7	0.15	0.0	0.0	0.0	0.0
8	0.3	0.0	0.0	0.0	0.0
9	0.475	0.0	0.0	0.0	0.0
10	0.7	0.0	0.0	0.0	0.0
11	1.225	0.0	0.0	0.0	0.0
12	2.25	0.0	0.0	0.0	0.0
13	3.325	0.0	0.0	0.0	0.0
14	4.925	0.0	0.0	0.0	0.0
15	6.275	0.0	0.0	0.0	0.0
16	7.25	0.0	0.0	0.0	0.0
17	7.975	0.0	0.0	0.0	0.0
18	8.5	0.0	0.0	0.0	0.0
19	9.3	0.0	0.0	0.0	0.0
20	10.625	0.0	0.0	0.0	0.0
21	14.15	0.0	0.0	0.0	0.0
22	24.125	0.0	0.0	0.0	0.0
23	59.15	0.0	0.0	0.0	0.0
24	68.8	0.0	0.0	0.0	0.0
25	73.4	0.0	0.0	0.0	0.0
26	73.7	0.0	0.0	0.0	0.0
27	74.075	0.0	0.0	0.0	0.0
28	74.45	0.0	0.0	0.0	0.0
29	75.025	0.0	0.0	0.0	0.0
30	75.425	0.0	0.0	0.0	0.0
31	77.05	0.0	0.0	0.0	0.0
32	81.25	0.0	0.0	0.0	0.0
33	89.675	0.0	0.0	0.0	0.0
34	90.9	0.0	0.0	0.0	0.0
35	92.6	0.0	0.0	0.0	0.0
36	96.375	0.0	0.0	0.0	0.0
37	96.825	0.0	0.0	0.0	0.0
38	97.15	0.0	0.0	0.0	0.0
39	97.425	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
GTAGAAT	90	0.0	45.000004	18
TGGTTCA	95	0.0	45.000004	8
AATTCTC	95	0.0	45.000004	22
TGGTAGA	90	0.0	45.000004	16
ATTGGTG	90	0.0	45.000004	3
AGTGGTA	90	0.0	45.000004	14
GGTTCAG	95	0.0	45.000004	9
GTTCAGT	95	0.0	45.000004	10
AGAATTC	95	0.0	45.000004	20
TCAGTGG	95	0.0	45.000004	12
TTCTCGC	90	0.0	45.000004	24
GAATTCT	95	0.0	45.000004	21
GGTAGAA	90	0.0	45.000004	17
GGTGGTT	90	0.0	45.000004	6
TTGGTGG	90	0.0	45.000004	4
GTGGTTC	95	0.0	45.000004	7
GTGGTAG	90	0.0	45.000004	15
ATTCTCG	95	0.0	45.000004	23
TTCAGTG	95	0.0	45.000004	11
TGGTGGT	90	0.0	45.000004	5
>>END_MODULE
Rejected 2102169 READS because READLEN < 1
Read 2102169 spots for SRR14127853.sra
Written 2102169 spots for SRR14127853.sra
Rejected 2102169 READS because READLEN < 1
Read 2102169 spots for SRR14127853.sra
Written 2102169 spots for SRR14127853.sra
Rejected 2102169 READS because READLEN < 1
Read 2102169 spots for SRR14127853.sra
Written 2102169 spots for SRR14127853.sra
Rejected 2102169 READS because READLEN < 1
Read 2102169 spots for SRR14127853.sra
Written 2102169 spots for SRR14127853.sra
Rejected 2102173 READS because READLEN < 1
Read 2102173 spots for SRR14127853.sra
Written 2102173 spots for SRR14127853.sra
Rejected 2102169 READS because READLEN < 1
Read 2102169 spots for SRR14127853.sra
Written 2102169 spots for SRR14127853.sra
Rejected 2102169 READS because READLEN < 1
Read 2102169 spots for SRR14127853.sra
Written 2102169 spots for SRR14127853.sra
Rejected 2102169 READS because READLEN < 1
Read 2102169 spots for SRR14127853.sra
Written 2102169 spots for SRR14127853.sra
SRR ids: ['SRR14127853.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_w2wwn3z8
SRR14127853.sra spots: 16817356
blocks: [[1, 2102169], [2102170, 4204338], [4204339, 6306507], [6306508, 8408676], [8408677, 10510845], [10510846, 12613014], [12613015, 14715183], [14715184, 16817356]]
SRR14127853 file size 2392512
SRR14127853 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 SRR14127853 SRR14127853_1.fastq
Input file:	SRR14127853_1.fastq
trimmed:	SRR14127853-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 21:25:28 2025 >> started

Tue Dec  2 21:25:35 2025 >> done (6.489s)
16817356 reads processed; of these:
 1454551 ( 8.65%) short reads filtered out after trimming by size control
   13118 ( 0.08%) empty reads filtered out after trimming by size control
15349687 (91.27%) reads available; of these:
  352137 ( 2.29%) trimmed reads available after processing
14997550 (97.71%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  114112	  0.74%
 19	  238025	  1.55%
 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	14997550	 97.71%
15349687 reads passed initial QC


criterion=sequence-density
sequence-density=94.95
sequence-density-rank=1
fanout-score=21.99
fanout-score-rank=1
prefix-density=95.80
prefix-fanout=21.8
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGCCGTCT


criterion=fanout-score
sequence-density=94.95
sequence-density-rank=1
fanout-score=21.99
fanout-score-rank=1
prefix-density=95.80
prefix-fanout=21.8
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGCCGTCT
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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGCCGTCT -o SRR14127853 -
Input file:	STDIN
trimmed:	SRR14127853-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGCCGTCT
-- 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 21:25:48 2025 >> started

Tue Dec  2 21:26:00 2025 >> done (12.016s)
15026536 reads processed; of these:
    6056 ( 0.04%) short reads filtered out after trimming by size control
      28 ( 0.00%) empty reads filtered out after trimming by size control
15020452 (99.96%) reads available; of these:
14606691 (97.25%) trimmed reads available after processing
  413761 ( 2.75%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  109952	  0.73%
 19	  235888	  1.57%
 20	  583407	  3.88%
 21	 1684002	 11.21%
 22	 5766177	 38.39%
 23	 1686981	 11.23%
 24	  838549	  5.58%
 25	   85736	  0.57%
 26	   60775	  0.40%
 27	   60730	  0.40%
 28	   65011	  0.43%
 29	   59326	  0.39%
 30	  224233	  1.49%
 31	  683458	  4.55%
 32	 1439824	  9.59%
 33	  157635	  1.05%
 34	  358952	  2.39%
 35	  571638	  3.81%
 36	   50069	  0.33%
 37	   49080	  0.33%
 38	   37344	  0.25%
 39	   25461	  0.17%
 40	   16899	  0.11%
 41	   11649	  0.08%
 42	   11246	  0.07%
 43	   15252	  0.10%
 44	   26733	  0.18%
 45	   23210	  0.15%
 46	    3728	  0.02%
 47	    1481	  0.01%
 48	    2103	  0.01%
 49	       0	  0.00%
 50	       0	  0.00%
 51	   73923	  0.49%


criterion=sequence-density
sequence-density=15.58
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=11
prefix-density=0.00
prefix-fanout=1.0
sequence=GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGC


criterion=fanout-score
sequence-density=0.21
sequence-density-rank=36
fanout-score=96.28
fanout-score-rank=1
prefix-density=20.00
prefix-fanout=1.0
sequence=AGCACTGTAGCCCT
                                 Started job on |	Dec 02 21:26:11
                             Started mapping on |	Dec 02 21:26:11
                                    Finished on |	Dec 02 21:27:21
       Mapping speed, Million of reads per hour |	789.10

                          Number of input reads |	15343603
                      Average input read length |	25
                                    UNIQUE READS:
                   Uniquely mapped reads number |	9193194
                        Uniquely mapped reads % |	59.92%
                          Average mapped length |	22.03
                       Number of splices: Total |	10398
            Number of splices: Annotated (sjdb) |	4494
                       Number of splices: GT/AG |	10096
                       Number of splices: GC/AG |	96
                       Number of splices: AT/AC |	7
               Number of splices: Non-canonical |	199
                      Mismatch rate per base, % |	0.13%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.28
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.21
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	3563513
             % of reads mapped to multiple loci |	23.22%
        Number of reads mapped to too many loci |	2205566
             % of reads mapped to too many loci |	14.37%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	2.44%
                     % of reads unmapped: other |	0.05%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	2586896	2586896	2586896
N_multimapping	3563513	3563513	3563513
N_noFeature	291987	930465	8537527
N_ambiguous	155074	137868	34
UnstrandedReadsAssigned:8746133 PositiveStrandReadsAssigned:8124861 NegativeStrandReadsAssigned:655633
Dataset is classified positive stranded
MeadianReadLen=22 20thPercentileLength=22 echo kmer=19
SRR14127853 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: SRR14127853-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 15,343,603 reads, 324,844 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 804 rounds

  31716 SRR14127853.ke.tsv
  32883 SRR14127853.se.tsv
  64599 total
==> SRR14127853.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
ENSRNOT00000047550.4	955	856	3319	8428.51
ENSRNOT00000040993.4	1039	940	2674	6183.73
ENSRNOT00000050156.3	1545	1446	21487	32301.7
ENSRNOT00000043693.3	684	585	6532	24272.1
ENSRNOT00000046201.3	204	105	646	13374
ENSRNOT00000046108.3	681	582	3007	11231.2
ENSRNOT00000049683.3	784	685	4289	13610.8
ENSRNOT00000041241.3	348	249	556	4853.92
ENSRNOT00000044582.3	297	198	697	7652.17

==> SRR14127853.se.tsv <==
ENSRNOG00000046319	0
ENSRNOG00000047964	0
ENSRNOG00000050370	0
ENSRNOG00000032365	0
ENSRNOG00000040300	0
ENSRNOG00000058808	3
ENSRNOG00000061316	3
ENSRNOG00000050129	0
ENSRNOG00000040316	0
ENSRNOG00000023659	0
SRR14127853 completed mapping pipeline successfully
