Starting /dee2/code/volunteer_pipeline.sh SRR12060858
    current disk space = 344674244
    free memory = 65585860 
SRR12060858 SRAfilesize
82e0b5a393aa2f9c3e018b1a3df43f30  SRR12060858.sra
SRR12060858.sra file validated
SRR12060858 is single end
SRR12060858 is conventional basespace
SRR12060858 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR12060858_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	48
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	30.7555	32.0	32.0	32.0	32.0	32.0
2	31.249	32.0	32.0	32.0	32.0	32.0
3	31.328	32.0	32.0	32.0	32.0	32.0
4	31.37575	32.0	32.0	32.0	32.0	32.0
5	31.43775	32.0	32.0	32.0	32.0	32.0
6	34.8135	36.0	36.0	36.0	32.0	36.0
7	34.76575	36.0	36.0	36.0	32.0	36.0
8	34.6315	36.0	36.0	36.0	32.0	36.0
9	34.60075	36.0	36.0	36.0	32.0	36.0
10	34.75075	36.0	36.0	36.0	32.0	36.0
11	34.896	36.0	36.0	36.0	32.0	36.0
12	34.71575	36.0	36.0	36.0	32.0	36.0
13	34.87225	36.0	36.0	36.0	32.0	36.0
14	34.808	36.0	36.0	36.0	32.0	36.0
15	34.65675	36.0	36.0	36.0	32.0	36.0
16	34.821	36.0	36.0	36.0	32.0	36.0
17	34.87875	36.0	36.0	36.0	36.0	36.0
18	34.673	36.0	36.0	36.0	32.0	36.0
19	34.81925	36.0	36.0	36.0	32.0	36.0
20	34.8355	36.0	36.0	36.0	36.0	36.0
21	34.742	36.0	36.0	36.0	32.0	36.0
22	34.76875	36.0	36.0	36.0	32.0	36.0
23	34.5365	36.0	36.0	36.0	32.0	36.0
24	34.70375	36.0	36.0	36.0	32.0	36.0
25	34.64	36.0	36.0	36.0	32.0	36.0
26	34.503	36.0	36.0	36.0	32.0	36.0
27	34.46425	36.0	36.0	36.0	32.0	36.0
28	34.55725	36.0	36.0	36.0	32.0	36.0
29	34.61325	36.0	36.0	36.0	32.0	36.0
30	34.4265	36.0	36.0	36.0	32.0	36.0
31	34.6995	36.0	36.0	36.0	32.0	36.0
32	34.4575	36.0	36.0	36.0	32.0	36.0
33	34.55175	36.0	36.0	36.0	32.0	36.0
34	34.5335	36.0	36.0	36.0	32.0	36.0
35	34.3595	36.0	36.0	36.0	32.0	36.0
36	34.297	36.0	36.0	36.0	32.0	36.0
37	34.25225	36.0	36.0	36.0	32.0	36.0
38	34.161	36.0	36.0	36.0	32.0	36.0
39	34.01175	36.0	36.0	36.0	32.0	36.0
40	34.222	36.0	36.0	36.0	32.0	36.0
41	34.2145	36.0	36.0	36.0	32.0	36.0
42	34.2125	36.0	36.0	36.0	32.0	36.0
43	34.27625	36.0	36.0	36.0	32.0	36.0
44	34.0495	36.0	36.0	36.0	32.0	36.0
45	33.7005	36.0	36.0	36.0	32.0	36.0
46	33.84525	36.0	36.0	36.0	32.0	36.0
47	33.878	36.0	36.0	36.0	27.0	36.0
48	33.98175	36.0	36.0	36.0	32.0	36.0
49	33.92775	36.0	36.0	36.0	32.0	36.0
50	33.40675	36.0	36.0	36.0	27.0	36.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
18	1.0
19	0.0
20	1.0
21	0.0
22	4.0
23	4.0
24	14.0
25	15.0
26	32.0
27	51.0
28	79.0
29	83.0
30	129.0
31	147.0
32	229.0
33	313.0
34	678.0
35	2220.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	25.124999999999996	34.050000000000004	30.099999999999998	10.725
2	26.025	18.625	28.499999999999996	26.85
3	32.375	19.2	24.05	24.375
4	35.85	24.675	23.225	16.25
5	18.4	38.45	24.375	18.775
6	22.725	22.875	35.4	19.0
7	36.199999999999996	25.324999999999996	26.275	12.2
8	18.55	29.5	39.6	12.35
9	22.775000000000002	38.0	20.45	18.775
10	40.075	16.975	29.799999999999997	13.15
11	19.6	21.425	40.375	18.6
12	22.400000000000002	21.45	28.325	27.825
13	27.775	25.324999999999996	19.475	27.425
14	19.133483596293512	43.57625845229151	24.192336589030806	13.097921362384172
15	26.525	35.699999999999996	24.275	13.5
16	18.025	38.025	26.474999999999998	17.474999999999998
17	24.5	32.975	29.549999999999997	12.975
18	40.6	20.375	19.0	20.025000000000002
19	23.575	29.45	28.675	18.3
20	27.975	27.975	31.225	12.825000000000001
21	24.625	36.125	17.325	21.925
22	26.525	37.6	21.5	14.374999999999998
23	34.0	35.525	18.375	12.1
24	23.95	38.375	25.324999999999996	12.35
25	24.099999999999998	41.625	20.025000000000002	14.249999999999998
26	35.65	27.35	18.325	18.675
27	24.474999999999998	40.8	15.35	19.375
28	29.099999999999998	23.65	27.224999999999998	20.025000000000002
29	26.1	27.275	11.975	34.65
30	42.238357536304456	30.696044066099148	7.461191787681522	19.604406609914875
31	42.875	28.95	9.85	18.325
32	25.874999999999996	46.650000000000006	11.05	16.425
33	29.45	41.8	8.5	20.25
34	36.809202300575144	29.43235808952238	11.652913228307076	22.1055263815954
35	24.512256128064035	39.21960980490245	12.031015507753876	24.23711855927964
36	30.638297872340424	33.09136420525657	8.610763454317897	27.659574468085108
37	18.222778473091363	33.41677096370463	11.13892365456821	37.221526908635795
38	22.900000000000002	38.074999999999996	9.35	29.675
39	21.825	27.325	13.075000000000001	37.775
40	18.90808915602304	39.04332582018532	14.800901577761083	27.247683446030553
41	22.275	21.5	15.6	40.625
42	29.825000000000003	23.849999999999998	21.2	25.124999999999996
43	24.63078848560701	19.59949937421777	32.59073842302879	23.178973717146434
44	20.655163790947736	22.83070767691923	18.97974493623406	37.53438359589897
45	20.075000000000003	29.2	27.0	23.724999999999998
46	31.038798498122656	28.16020025031289	14.44305381727159	26.357947434292868
47	14.2	41.75	16.725	27.325
48	13.725000000000001	37.475	13.425	35.375
49	17.958979489744873	24.787393696848426	13.006503251625812	44.24712356178089
50	14.032016008004003	22.536268134067033	26.23811905952976	37.1935967983992
>>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	0.5
20	1.0
21	1.0
22	1.0
23	0.5
24	0.0
25	1.0
26	2.0
27	4.0
28	6.0
29	5.0
30	4.0
31	6.5
32	9.0
33	10.5
34	12.0
35	22.5
36	33.0
37	59.5
38	86.0
39	122.5
40	159.0
41	249.5
42	340.0
43	479.5
44	619.0
45	534.0
46	449.0
47	439.0
48	429.0
49	445.0
50	461.0
51	447.5
52	434.0
53	442.5
54	451.0
55	356.5
56	262.0
57	194.0
58	126.0
59	95.0
60	64.0
61	46.5
62	29.0
63	22.0
64	15.0
65	10.0
66	5.0
67	2.5
68	0.0
69	0.5
70	1.0
71	1.0
72	1.0
73	0.5
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	0.5
100	1.0
>>END_MODULE
>>Per base N content	pass
#Base	N-Count
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	0.17500000000000002
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	0.15
31	0.0
32	0.0
33	0.0
34	0.025
35	0.05
36	0.125
37	0.125
38	0.0
39	0.0
40	0.17500000000000002
41	0.0
42	0.0
43	0.125
44	0.025
45	0.0
46	0.125
47	0.0
48	0.0
49	0.05
50	0.05
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
50	4000.0
>>END_MODULE
>>Sequence Duplication Levels	warn
#Total Deduplicated Percentage	69.72500000000001
#Duplication Level	Percentage of deduplicated	Percentage of total
1	92.14772319827895	64.25
2	3.6213696665471495	5.050000000000001
3	1.219074937253496	2.55
4	0.46611688777339555	1.3
5	0.5378271782000718	1.875
6	0.32269630692004303	1.35
7	0.10756543564001435	0.525
8	0.17927572606669057	1.0
9	0.10756543564001435	0.675
>10	1.1832197920401577	13.900000000000002
>50	0.035855145213338116	2.325
>100	0.07171029042667623	5.2
>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
TTCATGGACGTTGATAAGATCTTTCAGATCGGAAGAGCACACGTCTGAAC	106	2.65	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
GCGGATATAGTCGAATGGTAAAATTTCTCCTTGCCAAGGAGATCGGAAGA	102	2.55	No Hit
AGTTACTAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCC	93	2.325	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGGC	35	0.8750000000000001	TruSeq Adapter, Index 6 (97% over 36bp)
TTGACAGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGGCTACAT	32	0.8	TruSeq Adapter, Index 11 (100% over 41bp)
TCCGCTGTAGCACATCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	28	0.7000000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TCCCAAATGTAGACAAAGCAAGATCGGAAGAGCACACGTCTGAACTCCAG	28	0.7000000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
AGTTACTAATTCATGATCTGGCATAGATCGGAAGAGCACACGTCTGAACT	27	0.675	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
GGGGATATGGCGGAATTGGTAGACGCTACGGACTTAGATCGGAAGAGCAC	24	0.6	No Hit
GCGTCTGTAGTCCAACGGTTAGGATAAGATCGGAAGAGCACACGTCTGAA	24	0.6	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
TCCGCTGTAGCACACAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	23	0.575	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TTCATGGACGTTGATAAGATCTTTCCAGATCGGAAGAGCACACGTCTGAA	22	0.5499999999999999	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGGC	19	0.475	TruSeq Adapter, Index 6 (97% over 36bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCAGATCGGAAGAGCACAC	18	0.44999999999999996	No Hit
CGGCTCTGATACCAATTGATGAGATCGGAAGAGCACACGTCTGAACTCCA	18	0.44999999999999996	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TTAGGGAAGTACTTTAAGAAACATATGTATAAGATCGGAAGAGCACACGT	15	0.375	No Hit
TCCCAAATGTAGACAAAGCAGATCGGAAGAGCACACGTCTGAACTCCAGT	15	0.375	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
GCGTCTGTAGTCCAACGGTTAGGATAATTGCAGATCGGAAGAGCACACGT	15	0.375	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGCAGATCGGA	15	0.375	No Hit
GCGTCTGTAGTCCAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	14	0.35000000000000003	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TCCGATGTCGTCCAGCGGTTAGGATATCTGGCTAGATCGGAAGAGCACAC	14	0.35000000000000003	No Hit
AGTTACTAATTCATGATCTGGTAGATCGGAAGAGCACACGTCTGAACTCC	14	0.35000000000000003	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
GGTGAGGGACGACGATTAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
TTCATGGACGTTGATAAGATCTTTAGATCGGAAGAGCACACGTCTGAACT	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGGCTACATCTCGTATG	13	0.325	TruSeq Adapter, Index 11 (100% over 49bp)
AGTTACTAATTCATGATCTGGCAAGATCGGAAGAGCACACGTCTGAACTC	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
TCCGATGTCGTCCAGCGGTTAGGATATCTGGCTTAGATCGGAAGAGCACA	12	0.3	No Hit
AGTTACTAATTCATGATCTGGCAAAGATCGGAAGAGCACACGTCTGAACT	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
TTTGGATTGAAGGGAGCTCTTAGATCGGAAGAGCACACGTCTGAACTCCA	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GCGGACTGCTCGAGCTGCAGATCGGAAGAGCACACGTCTGAACTCCAGTC	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
GCGTCTGTAGTCCAACGGTTAGGATAATTGCCAGATCGGAAGAGCACACG	10	0.25	No Hit
GCGGATATAGTCGAATGGTAAAATTTCTCCTTGCCAAGGAAGATCGGAAG	10	0.25	No Hit
CTTCGTGATTGATTTGCCATATTTTCTGATCAGATCGGAAGAGCACACGT	10	0.25	No Hit
GAGGGACGACGATTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGG	10	0.25	TruSeq Adapter, Index 2 (97% over 35bp)
GGGTTGATATGAGAACACACGAGATCGGAAGAGCACACGTCTGAACTCCA	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTAGATCGGAAGAGCACAC	10	0.25	No Hit
TAACATTGATGATACTTCTGCAATTCTGAGGCAGATCGGAAGAGCACACG	9	0.22499999999999998	No Hit
TCCGCTTTTATGTTAGTTCGTACTATAAGATCGGAAGAGCACACGTCTGA	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
TCCGCTGTAGCACACAGGAGATCGGAAGAGCACACGTCTGAACTCCAGTC	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
GGGGATATAGCTCAGTTGGTAGAGCTCCGCTCTTGCAAAGATCGGAAGAG	8	0.2	No Hit
TCCGTTGTAGTCTAGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TTTGGATTGAAGGGAGCTCTAAGATCGGAAGAGCACACGTCTGAACTCCA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GTGGACGTGCCGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGG	8	0.2	TruSeq Adapter, Index 2 (97% over 35bp)
ATTCTTTGACGAGAAAAACGCTGGCTTACTGAGGTAAGATCGGAAGAGCA	8	0.2	No Hit
GGGGATGTAGCTCAGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TCGGACCAGGCTTCATTCCCCAGATCGGAAGAGCACACGTCTGAACTCCA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GCGGATATAGTCGAATGGTAAAATTTCTCCTTGAGATCGGAAGAGCACAC	7	0.17500000000000002	No Hit
TTAAGTGTCACGGAAATCCCTAGATCGGAAGAGCACACGTCTGAACTCCA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TTCATGGACGTTGATAAGATCTTTAAGATCGGAAGAGCACACGTCTGAAC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
TCCGATGTCGTCCAGCGGTTAGGATATCTGGCAGATCGGAAGAGCACACG	6	0.15	No Hit
ATTGTATCATTAACTATTTCTTTATAGATCGGAAGAGCACACGTCTGAAC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
ATGATATTTGTAGTAATGGCGAGATCGGAAGAGCACACGTCTGAACTCCA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
AGTTACTAATTCATGATCTGGCACAGATCGGAAGAGCACACGTCTGAACT	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
ACTCATAAGATCGTGACACGTAGATCGGAAGAGCACACGTCTGAACTCCA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
AAGGAAGCTATAAGTAATGAAGATCGGAAGAGCACACGTCTGAACTCCAG	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TTTGGATTGAAGGGAGCTCTAGATCGGAAGAGCACACGTCTGAACTCCAG	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TGAAAGTGACTACATCGGGGTAGATCGGAAGAGCACACGTCTGAACTCCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TTAGGGAAGTACTTTAAGAAACATATGTAAGATCGGAAGAGCACACGTCT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
GCGTCTGTAGTCCAACGGTAGGATAATTGCAGATCGGAAGAGCACACGTC	5	0.125	No Hit
CCGCTGTAGCACATCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GCGGATATAGTCGAATGGTAAAATTTCTCCTTGCCAAGAAGATCGGAAGA	5	0.125	No Hit
GCGGCGACGTGGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGGC	5	0.125	TruSeq Adapter, Index 6 (97% over 36bp)
TCCGCTTTTATGTTAGTTCGTACTATAGATCGGAAGAGCACACGTCTGAA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
AAACAAGAATTCTTGAACAGCGAGATCGGAAGAGCACACGTCTGAACTCC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
GCGGATATAGTCGAATGGTAAAATTTCTCCTTGCCAGATCGGAAGAGCAC	5	0.125	No Hit
TCCCAAATGTAGACAAAGCTAGATCGGAAGAGCACACGTCTGAACTCCAG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TGACAGAAGAGAGTGAGCACAGATCGGAAGAGCACACGTCTGAACTCCAG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
AACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTCCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
CTAACAGACCGGTAGACTTGAACAGATCGGAAGAGCACACGTCTGAACTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
GGGGATATAGCTCAGTTGGTAGAGCTCCGCTCAGATCGGAAGAGCACACG	5	0.125	No Hit
TGACAGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGGCTACATC	5	0.125	TruSeq Adapter, Index 11 (100% over 42bp)
>>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	0.375	0.0	0.0	0.0	0.0
2	0.425	0.0	0.0	0.0	0.0
3	0.425	0.0	0.0	0.0	0.0
4	0.45	0.0	0.0	0.0	0.0
5	0.5	0.0	0.0	0.0	0.0
6	0.55	0.0	0.0	0.0	0.0
7	0.675	0.0	0.0	0.0	0.0
8	0.975	0.0	0.0	0.0	0.0
9	1.925	0.0	0.0	0.0	0.0
10	2.05	0.0	0.0	0.0	0.0
11	2.325	0.0	0.0	0.0	0.0
12	2.95	0.0	0.0	0.0	0.0
13	3.825	0.0	0.0	0.0	0.0
14	6.825	0.0	0.0	0.0	0.0
15	9.275	0.0	0.0	0.0	0.0
16	11.1	0.0	0.0	0.0	0.0
17	15.4	0.0	0.0	0.0	0.0
18	17.675	0.0	0.0	0.0	0.0
19	20.125	0.0	0.0	0.0	0.0
20	23.075	0.0	0.0	0.0	0.0
21	26.725	0.0	0.0	0.0	0.0
22	34.05	0.0	0.0	0.0	0.0
23	41.675	0.0	0.0	0.0	0.0
24	48.4	0.0	0.0	0.0	0.0
25	65.675	0.0	0.0	0.0	0.0
26	70.775	0.0	0.0	0.0	0.0
27	73.525	0.0	0.0	0.0	0.0
28	74.875	0.0	0.0	0.0	0.0
29	75.775	0.0	0.0	0.0	0.0
30	76.625	0.0	0.0	0.0	0.0
31	77.625	0.0	0.0	0.0	0.0
32	80.15	0.0	0.0	0.0	0.0
33	82.05	0.0	0.0	0.0	0.0
34	84.625	0.0	0.0	0.0	0.0
35	86.125	0.0	0.0	0.0	0.0
36	88.05	0.0	0.0	0.0	0.0
37	89.0	0.0	0.0	0.0	0.0
38	89.875	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TCCTTGC	20	6.952051E-4	44.000004	28
AAATTTC	20	6.952051E-4	44.000004	21
CTCCTTG	20	6.952051E-4	44.000004	27
TGGTAAA	20	6.952051E-4	44.000004	16
AATTTCT	20	6.952051E-4	44.000004	22
TTTCTCC	20	6.952051E-4	44.000004	24
TAAAATT	20	6.952051E-4	44.000004	19
TCGAATG	20	6.952051E-4	44.000004	11
ATGGTAA	20	6.952051E-4	44.000004	15
GTCGAAT	20	6.952051E-4	44.000004	10
CCTTGCC	20	6.952051E-4	44.000004	29
CGGATAT	20	6.952051E-4	44.000004	2
GCGGATA	20	6.952051E-4	44.000004	1
TAGTCGA	20	6.952051E-4	44.000004	8
GAATGGT	20	6.952051E-4	44.000004	13
ATAGTCG	20	6.952051E-4	44.000004	7
TTCTCCT	20	6.952051E-4	44.000004	25
CGAATGG	20	6.952051E-4	44.000004	12
AATGGTA	20	6.952051E-4	44.000004	14
AGTCGAA	20	6.952051E-4	44.000004	9
>>END_MODULE
Rejected 2874834 READS because READLEN < 1
Read 2874834 spots for SRR12060858.sra
Written 2874834 spots for SRR12060858.sra
Rejected 2874834 READS because READLEN < 1
Read 2874834 spots for SRR12060858.sra
Written 2874834 spots for SRR12060858.sra
Rejected 2874834 READS because READLEN < 1
Read 2874834 spots for SRR12060858.sra
Written 2874834 spots for SRR12060858.sra
Rejected 2874834 READS because READLEN < 1
Read 2874834 spots for SRR12060858.sra
Written 2874834 spots for SRR12060858.sra
Rejected 2874834 READS because READLEN < 1
Read 2874834 spots for SRR12060858.sra
Written 2874834 spots for SRR12060858.sra
Rejected 2874834 READS because READLEN < 1
Read 2874834 spots for SRR12060858.sra
Written 2874834 spots for SRR12060858.sra
Rejected 2874843 READS because READLEN < 1
Read 2874843 spots for SRR12060858.sra
Written 2874843 spots for SRR12060858.sra
Rejected 2874834 READS because READLEN < 1
Read 2874834 spots for SRR12060858.sra
Written 2874834 spots for SRR12060858.sra
Rejected 2874834 READS because READLEN < 1
Read 2874834 spots for SRR12060858.sra
Written 2874834 spots for SRR12060858.sra
Rejected 2874834 READS because READLEN < 1
Read 2874834 spots for SRR12060858.sra
Written 2874834 spots for SRR12060858.sra
Rejected 2874834 READS because READLEN < 1
Read 2874834 spots for SRR12060858.sra
Written 2874834 spots for SRR12060858.sra
Rejected 2874834 READS because READLEN < 1
Read 2874834 spots for SRR12060858.sra
Written 2874834 spots for SRR12060858.sra
Rejected 2874834 READS because READLEN < 1
Read 2874834 spots for SRR12060858.sra
Written 2874834 spots for SRR12060858.sra
Rejected 2874834 READS because READLEN < 1
Read 2874834 spots for SRR12060858.sra
Written 2874834 spots for SRR12060858.sra
Rejected 2874834 READS because READLEN < 1
Read 2874834 spots for SRR12060858.sra
Written 2874834 spots for SRR12060858.sra
Rejected 2874834 READS because READLEN < 1
Read 2874834 spots for SRR12060858.sra
Written 2874834 spots for SRR12060858.sra
SRR ids: ['SRR12060858.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_sge2m3m0
SRR12060858.sra spots: 45997353
blocks: [[1, 2874834], [2874835, 5749668], [5749669, 8624502], [8624503, 11499336], [11499337, 14374170], [14374171, 17249004], [17249005, 20123838], [20123839, 22998672], [22998673, 25873506], [25873507, 28748340], [28748341, 31623174], [31623175, 34498008], [34498009, 37372842], [37372843, 40247676], [40247677, 43122510], [43122511, 45997353]]
SRR12060858 file size 6491600
SRR12060858 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -f sanger -l 18 -q 10 -k inf -t 16 -o SRR12060858 SRR12060858_1.fastq
Input file:	SRR12060858_1.fastq
trimmed:	SRR12060858-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):	16
Fri Apr 26 13:28:16 2024 >> started

Fri Apr 26 13:28:46 2024 >> done (29.962s)
45997353 reads processed; of these:
 8571122 (18.63%) short reads filtered out after trimming by size control
  256735 ( 0.56%) empty reads filtered out after trimming by size control
37169496 (80.81%) reads available; of these:
 1059852 ( 2.85%) trimmed reads available after processing
36109644 (97.15%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	 1055030	  2.84%
 19	       0	  0.00%
 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	      20	  0.00%
 36	      18	  0.00%
 37	      11	  0.00%
 38	      35	  0.00%
 39	       9	  0.00%
 40	      47	  0.00%
 41	       5	  0.00%
 42	       6	  0.00%
 43	       8	  0.00%
 44	       2	  0.00%
 45	       0	  0.00%
 46	     356	  0.00%
 47	     316	  0.00%
 48	    1807	  0.00%
 49	    2182	  0.01%
 50	36109644	 97.15%
37169496 reads passed initial QC


criterion=sequence-density
sequence-density=86.78
sequence-density-rank=1
fanout-score=47.83
fanout-score-rank=1
prefix-density=92.68
prefix-fanout=44.8
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGGCTACAT


criterion=fanout-score
sequence-density=86.78
sequence-density-rank=1
fanout-score=47.83
fanout-score-rank=1
prefix-density=92.68
prefix-fanout=44.8
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGGCTACAT
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 -f sanger -l 18 -t 16 -x AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGGCTACAT -o SRR12060858 -
Input file:	STDIN
trimmed:	SRR12060858-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGGCTACAT
-- 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):	16
Fri Apr 26 13:29:46 2024 >> started

Fri Apr 26 13:30:24 2024 >> done (38.569s)
36315025 reads processed; of these:
   27162 ( 0.07%) short reads filtered out after trimming by size control
     239 ( 0.00%) empty reads filtered out after trimming by size control
36287624 (99.92%) reads available; of these:
34908932 (96.20%) trimmed reads available after processing
 1378692 ( 3.80%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	 1050377	  2.89%
 19	 1303339	  3.59%
 20	 1844485	  5.08%
 21	 3589845	  9.89%
 22	 3548478	  9.78%
 23	 2922264	  8.05%
 24	 7608024	 20.97%
 25	 2409622	  6.64%
 26	 1329670	  3.66%
 27	  562905	  1.55%
 28	  444601	  1.23%
 29	  520699	  1.43%
 30	  607564	  1.67%
 31	 1175722	  3.24%
 32	  928851	  2.56%
 33	 1085625	  2.99%
 34	  782497	  2.16%
 35	  843067	  2.32%
 36	  421852	  1.16%
 37	  278174	  0.77%
 38	  277549	  0.76%
 39	 1286366	  3.54%
 40	  341822	  0.94%
 41	  224178	  0.62%
 42	  271670	  0.75%
 43	   90428	  0.25%
 44	   49943	  0.14%
 45	   48251	  0.13%
 46	   31790	  0.09%
 47	   40898	  0.11%
 48	     967	  0.00%
 49	     333	  0.00%
 50	  365768	  1.01%


criterion=sequence-density
sequence-density=5.44
sequence-density-rank=1
fanout-score=2.00
fanout-score-rank=4
prefix-density=0.02
prefix-fanout=2.0
sequence=AGTTACTAATTCATGATCTGGCATAG


criterion=fanout-score
sequence-density=0.23
sequence-density-rank=18
fanout-score=12.42
fanout-score-rank=1
prefix-density=2.77
prefix-fanout=1.0
sequence=GTAGACAAAGCTTTTT
                                 Started job on |	Apr 26 13:31:02
                             Started mapping on |	Apr 26 13:31:02
                                    Finished on |	Apr 26 13:34:10
       Mapping speed, Million of reads per hour |	711.23

                          Number of input reads |	37142095
                      Average input read length |	26
                                    UNIQUE READS:
                   Uniquely mapped reads number |	16533085
                        Uniquely mapped reads % |	44.51%
                          Average mapped length |	26.22
                       Number of splices: Total |	126425
            Number of splices: Annotated (sjdb) |	33788
                       Number of splices: GT/AG |	113114
                       Number of splices: GC/AG |	1235
                       Number of splices: AT/AC |	255
               Number of splices: Non-canonical |	11821
                      Mismatch rate per base, % |	0.29%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.16
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.03
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	16950184
             % of reads mapped to multiple loci |	45.64%
        Number of reads mapped to too many loci |	2136199
             % of reads mapped to too many loci |	5.75%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	3.69%
                     % of reads unmapped: other |	0.41%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	3658826	3658826	3658826
N_multimapping	16950184	16950184	16950184
N_noFeature	8162404	8892445	15330593
N_ambiguous	778154	300051	10419
UnstrandedReadsAssigned:7592527 PositiveStrandReadsAssigned:7340589 NegativeStrandReadsAssigned:1192073
Dataset is classified positive stranded
MeadianReadLen=24 20thPercentileLength=21 echo kmer=19
SRR12060858 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: 48,359
[index] number of k-mers: 44,957,248
[index] number of equivalence classes: 195,259
[quant] running in single-end mode
[quant] will process file 1: SRR12060858-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 37,142,095 reads, 1,760,392 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 974 rounds

  48360 SRR12060858.ke.tsv
  32833 SRR12060858.se.tsv
  81193 total
==> SRR12060858.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
AT1G19090.1	2509	2410	504	71.031
AT1G18320.1	699	600	0	0
AT5G11100.1	1709	1610	0	0
AT4G35335.1	1280	1181	16	4.60155
AT1G60930.1	3876	3777	6	0.539559
AT1G17000.1	2351	2252	0	0
AT3G55270.1	3130	3031	20	2.24119
AT4G16150.1	3181	3082	37.6473	4.14892
AT3G18150.1	1370	1271	13	3.47402

==> SRR12060858.se.tsv <==
AT1G01010	8
AT1G01020	13
AT1G03987	0
AT1G01030	3
AT1G01040	187
AT1G03993	2
AT1G01046	78
AT1G01050	10
AT1G03997	1
AT1G01060	23
SRR12060858 completed mapping pipeline successfully
