Starting /dee2/code/volunteer_pipeline.sh SRR9060560
    current disk space = 841279036
    free memory = 121223288 
SRR9060560 SRAfilesize
e4dbe74e82c41655e0536a79280d487e  SRR9060560.sra
SRR9060560.sra file validated
SRR9060560 is single end
SRR9060560 is conventional basespace
SRR9060560 read1 length is 49-51 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR9060560_1.fastq
File type	Conventional base calls
Encoding	Sanger / Illumina 1.9
Total Sequences	4000
Sequences flagged as poor quality	0
Sequence length	49-51
%GC	51
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	31.218	32.0	32.0	32.0	32.0	32.0
2	31.65025	32.0	32.0	32.0	32.0	32.0
3	31.67275	32.0	32.0	32.0	32.0	32.0
4	31.76925	32.0	32.0	32.0	32.0	32.0
5	31.715	32.0	32.0	32.0	32.0	32.0
6	34.6345	36.0	36.0	36.0	36.0	36.0
7	35.21075	36.0	36.0	36.0	36.0	36.0
8	35.17	36.0	36.0	36.0	36.0	36.0
9	35.188	36.0	36.0	36.0	36.0	36.0
10	35.22875	36.0	36.0	36.0	36.0	36.0
11	35.3295	36.0	36.0	36.0	36.0	36.0
12	35.178	36.0	36.0	36.0	36.0	36.0
13	35.34875	36.0	36.0	36.0	36.0	36.0
14	35.25475	36.0	36.0	36.0	36.0	36.0
15	35.24725	36.0	36.0	36.0	36.0	36.0
16	35.38575	36.0	36.0	36.0	36.0	36.0
17	35.3835	36.0	36.0	36.0	36.0	36.0
18	35.23675	36.0	36.0	36.0	36.0	36.0
19	35.253	36.0	36.0	36.0	36.0	36.0
20	35.22675	36.0	36.0	36.0	36.0	36.0
21	35.265	36.0	36.0	36.0	36.0	36.0
22	35.31075	36.0	36.0	36.0	36.0	36.0
23	35.26825	36.0	36.0	36.0	36.0	36.0
24	35.3185	36.0	36.0	36.0	36.0	36.0
25	35.14525	36.0	36.0	36.0	36.0	36.0
26	35.38175	36.0	36.0	36.0	36.0	36.0
27	35.291	36.0	36.0	36.0	36.0	36.0
28	35.377	36.0	36.0	36.0	36.0	36.0
29	35.17375	36.0	36.0	36.0	36.0	36.0
30	35.017	36.0	36.0	36.0	36.0	36.0
31	35.284	36.0	36.0	36.0	36.0	36.0
32	35.22025	36.0	36.0	36.0	36.0	36.0
33	35.34175	36.0	36.0	36.0	36.0	36.0
34	35.15625	36.0	36.0	36.0	36.0	36.0
35	35.2135	36.0	36.0	36.0	36.0	36.0
36	35.282	36.0	36.0	36.0	36.0	36.0
37	35.1655	36.0	36.0	36.0	36.0	36.0
38	35.0645	36.0	36.0	36.0	36.0	36.0
39	34.68825	36.0	36.0	36.0	32.0	36.0
40	34.74625	36.0	36.0	36.0	36.0	36.0
41	34.7535	36.0	36.0	36.0	36.0	36.0
42	34.699	36.0	36.0	36.0	32.0	36.0
43	34.9825	36.0	36.0	36.0	36.0	36.0
44	35.11975	36.0	36.0	36.0	36.0	36.0
45	35.1325	36.0	36.0	36.0	36.0	36.0
46	34.909	36.0	36.0	36.0	36.0	36.0
47	34.61125	36.0	36.0	36.0	32.0	36.0
48	34.24575	36.0	36.0	36.0	32.0	36.0
49	34.06025	36.0	36.0	36.0	32.0	36.0
50	34.65777540677514	36.0	36.0	36.0	36.0	36.0
51	34.34454756380511	36.0	36.0	36.0	32.0	36.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
21	1.0
22	1.0
23	6.0
24	3.0
25	4.0
26	11.0
27	27.0
28	34.0
29	55.0
30	78.0
31	77.0
32	129.0
33	203.0
34	572.0
35	2799.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	11.4	47.9	15.45	25.25
2	17.1	37.75	19.425	25.724999999999998
3	43.325	15.45	22.0	19.225
4	26.75	33.575	17.125	22.55
5	43.275000000000006	18.35	16.525000000000002	21.85
6	24.04066073697586	36.46759847522236	23.354510800508262	16.13722998729352
7	27.725	32.05	19.975	20.25
8	39.25	15.1	26.825	18.825
9	43.775	18.75	25.825	11.65
10	29.475	20.775	36.05	13.700000000000001
11	46.1	22.275	18.9	12.725
12	19.0	20.925	45.275	14.799999999999999
13	20.974999999999998	24.775	23.599999999999998	30.65
14	16.25	18.425	46.9	18.425
15	26.125	13.450000000000001	41.55	18.875
16	36.9	18.275	26.625	18.2
17	25.7	15.049999999999999	19.075	40.175
18	28.475	17.75	39.125	14.649999999999999
19	46.550000000000004	20.325	19.35	13.775
20	48.75	16.55	17.825	16.875
21	27.325	16.775000000000002	24.95	30.95
22	41.375	19.35	21.825	17.45
23	35.25	20.7	20.7	23.35
24	16.175	23.025000000000002	38.525	22.275
25	21.95	42.425000000000004	17.375	18.25
26	40.275	23.549999999999997	16.825000000000003	19.35
27	30.2	21.725	35.05	13.025
28	45.175	23.3	19.8	11.725
29	43.2	22.175	19.950000000000003	14.674999999999999
30	26.3	39.925	21.0	12.775
31	22.225	36.325	25.2	16.25
32	20.849999999999998	18.025	47.25	13.875000000000002
33	22.85	17.75	40.75	18.65
34	20.3	21.125	25.4	33.175
35	28.625	18.85	40.425	12.1
36	28.349999999999998	16.75	27.800000000000004	27.1
37	40.375	22.400000000000002	22.45	14.774999999999999
38	35.575	23.974999999999998	23.1	17.349999999999998
39	29.849999999999998	22.025	28.299999999999997	19.825
40	15.475	15.075	46.150000000000006	23.3
41	35.725	5.8500000000000005	29.95	28.475
42	23.05	3.8249999999999997	33.4	39.725
43	25.95	4.925	24.7	44.425
44	36.275	24.224999999999998	21.825	17.675
45	36.975	28.125	16.0	18.9
46	53.949999999999996	15.85	14.149999999999999	16.05
47	45.725	19.975	18.65	15.65
48	28.975	36.775000000000006	15.375	18.875
49	20.65	36.7	14.725	27.925
50	23.873032808749002	15.097359295812215	11.86983195518805	49.15977594025073
51	19.334880123743233	0.0	39.24980665119877	41.415313225058
>>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	0.5
12	1.0
13	0.5
14	0.0
15	0.5
16	1.0
17	0.5
18	0.0
19	0.5
20	1.0
21	1.5
22	2.0
23	1.5
24	1.0
25	2.0
26	3.0
27	1.5
28	1.0
29	3.0
30	3.0
31	1.5
32	2.0
33	2.5
34	2.0
35	2.5
36	6.0
37	10.0
38	13.5
39	21.0
40	39.0
41	62.0
42	81.5
43	86.0
44	118.5
45	186.5
46	233.0
47	273.5
48	329.0
49	394.0
50	466.0
51	463.5
52	790.5
53	1269.5
54	1094.5
55	686.5
56	473.5
57	361.0
58	223.0
59	93.0
60	70.0
61	49.0
62	30.5
63	18.5
64	7.5
65	1.0
66	1.5
67	1.5
68	1.0
69	1.0
70	0.5
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	0.5
92	1.0
93	0.5
94	0.0
95	0.5
96	1.0
97	0.5
98	0.0
99	1.0
100	2.0
>>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	1.625
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	warn
#Length	Count
49	251.0
50	1163.0
51	2586.0
>>END_MODULE
>>Sequence Duplication Levels	warn
#Total Deduplicated Percentage	59.025000000000006
#Duplication Level	Percentage of deduplicated	Percentage of total
1	90.38542990258365	53.349999999999994
2	4.870817450232952	5.75
3	1.4400677678949596	2.55
4	0.8894536213468869	2.1
5	0.5506141465480728	1.625
6	0.5082592121982211	1.7999999999999998
7	0.08470986869970351	0.35000000000000003
8	0.21177467174925876	1.0
9	0.16941973739940702	0.8999999999999999
>10	0.7623888182973316	9.0
>50	0.042354934349851756	1.7000000000000002
>100	0.042354934349851756	3.8249999999999997
>500	0.042354934349851756	16.05
>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
AAGAGAAGGTGTCTTGCTGGCGGTAGTGGAATTCTCGGGTGCCAAGGAACT	642	16.05	RNA PCR Primer, Index 1 (100% over 25bp)
CCTCCAGTTGGTACGTCTGGTTCAGGGTTGTTTTGGAATTCTCGGGTGCC	153	3.8249999999999997	No Hit
CGGGGTGCAATTATTAGAACAGACCAAACTGGAATTCTCGGGTGCCAAGG	68	1.7000000000000002	Illumina Small RNA Adapter 2 (100% over 21bp)
GATTGTGCTTGCTTGCGGACGCTTTCTGGTGTTGGAATTCTCGGGTGCCA	50	1.25	No Hit
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTTGTAATCTCGTATGCC	44	1.0999999999999999	RNA PCR Primer, Index 12 (100% over 51bp)
ATACTGCGATCTGTTGAGACTATCCTTTGATTGAGTGGAATTCTCGGGTGC	41	1.0250000000000001	No Hit
AACTGTGGTCGTGACTTCTAATTTGCTGGTTTGTGGAATTCTCGGGTGCC	26	0.65	No Hit
GATTGTGCTTGCTTGCGGACGCTTTCTGGTGTGGAATTCTCGGGTGCCA	22	0.5499999999999999	No Hit
ATTGTGCTTGCTTGCGGACGCTTTCTGGTGTGGAATTCTCGGGTGCCAAGG	22	0.5499999999999999	Illumina Small RNA Adapter 2 (100% over 21bp)
CTTGGTCAAGGTGTTGTATTCAGTAGAGCAGTCCTTGGAATTCTCGGGTGC	18	0.44999999999999996	No Hit
ACGGACCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTTGTAATCTC	15	0.375	RNA PCR Primer, Index 12 (100% over 44bp)
CCGGCGCAGTTCTGTCTGCTTGATACTTTCTGGAATTCTCGGGTGCCAAGG	14	0.35000000000000003	Illumina Small RNA Adapter 2 (100% over 21bp)
GTGCTTGGACCTCGGTTCTAGTATCCTGATCGCTCTGGAATTCTCGGGTGC	14	0.35000000000000003	No Hit
AACTGTGGTCGTGACTTCTAATTTGCTGGTTTTGGAATTCTCGGGTGCCA	14	0.35000000000000003	No Hit
CTTGGTCAAGGTGTTGTATTCAGTAGAGCAGTCCTGGAATTCTCGGGTGCC	14	0.35000000000000003	No Hit
TCAACTGTGGTCGTGACTTCTAATTTGCTGGTTTGTGGAATTCTCGGGTGC	12	0.3	No Hit
CCCGGCCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTTGTAATCTC	12	0.3	RNA PCR Primer, Index 12 (100% over 44bp)
AAGAGNAGGTGTCTTGCTGGCGGTAGTGGAATTCTCGGGTGCCAAGGAACT	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 25bp)
CCGGCCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTTGTAATCTCG	11	0.27499999999999997	RNA PCR Primer, Index 12 (100% over 45bp)
GGCCAGTTGGTTGATGCTTGTCCGGCGCAGTGGAATTCTCGGGTGCCAAGG	10	0.25	Illumina Small RNA Adapter 2 (100% over 21bp)
CGGGCCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTTGTAATCTCG	10	0.25	RNA PCR Primer, Index 12 (100% over 45bp)
ATTGTGCTTGCTTGCGGACGCTTTCTGGTGTTGGAATTCTCGGGTGCCA	9	0.22499999999999998	No Hit
AAGGCGGGGTGCAATTATTAGAACAGACCAAACTGGAATTCTCGGGTGCC	9	0.22499999999999998	No Hit
TTGCGGACGCTTTCTGGTGTGTGCTTGGACCTCTGGAATTCTCGGGTGCC	9	0.22499999999999998	No Hit
TTGTGATCGTTGCCGGGTGTCGTTTCCTTGGAATTCTCGGGTGCCAAGGA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 22bp)
AGTGATTGTGCTTGCTTGCGGACGCTTTCTGGTGTTGGAATTCTCGGGTGC	8	0.2	No Hit
GGTTGATGGCGGACTAGTGATTGTGCTTGCTGGAATTCTCGGGTGCCAAGG	8	0.2	Illumina Small RNA Adapter 2 (100% over 21bp)
CCCCGGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTTGTAATCTC	8	0.2	RNA PCR Primer, Index 12 (100% over 44bp)
TCAACTGTGGTCGTGACTTCTAATTTGCTGGTTTTGGAATTCTCGGGTGCC	8	0.2	No Hit
CCGGGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTTGTAATCTCG	8	0.2	RNA PCR Primer, Index 12 (100% over 45bp)
CAAGAGAAGGTGTCTTGCTGGCGGTAGTGGAATTCTCGGGTGCCAAGGAAC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 24bp)
AACTGTGGTCGTGACTTCTAATTTGCTGGTGGAATTCTCGGGTGCCAAGG	7	0.17500000000000002	Illumina Small RNA Adapter 2 (100% over 21bp)
GGGGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTTGTAATCTCGT	6	0.15	RNA PCR Primer, Index 12 (100% over 46bp)
TCTCAACCTGAACTCAGTCGTGATTACCCGTGGAATTCTCGGGTGCCAAGG	6	0.15	Illumina Small RNA Adapter 2 (100% over 21bp)
CCAGTTGGTTGATGCTTGTCCGGCGCAGTGGAATTCTCGGGTGCCAAGGA	6	0.15	RNA PCR Primer, Index 1 (100% over 22bp)
GCGGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTTGTAATCTCGT	6	0.15	RNA PCR Primer, Index 12 (100% over 46bp)
GCGGCCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTTGTAATCTCG	6	0.15	RNA PCR Primer, Index 12 (100% over 45bp)
CCTCCNGTTGGTACGTCTGGTTCAGGGTTGTTTTGGAATTCTCGGGTGCC	6	0.15	No Hit
ATACTGCGATCTGTTGAGACTATCCTTTGATTGTGGAATTCTCGGGTGCC	6	0.15	No Hit
CGGGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTTGTAATCTCGT	6	0.15	RNA PCR Primer, Index 12 (100% over 46bp)
CGCGACTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTTGTAATCTCG	6	0.15	RNA PCR Primer, Index 12 (100% over 45bp)
GCATCGGTGGTTCAGTGGTAGAATGCTCGCCTGTGGAATTCTCGGGTGCC	6	0.15	No Hit
CGCGACCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTTGTAATCTC	6	0.15	RNA PCR Primer, Index 12 (100% over 44bp)
ACGGCCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTTGTAATCTCG	6	0.15	RNA PCR Primer, Index 12 (100% over 45bp)
GGCCAGTTGGTTGATGCTTGTCCGGCGCAGTTCTGGAATTCTCGGGTGCC	5	0.125	No Hit
AACTGTGGTCGTGACTTCTAATTTGCTGGTTTGGAATTCTCGGGTGCCA	5	0.125	No Hit
TACCTGATTGATTCTGTCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	5	0.125	RNA PCR Primer, Index 1 (100% over 33bp)
CCCGGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTTGTAATCTCG	5	0.125	RNA PCR Primer, Index 12 (100% over 45bp)
TTGTCTAGCGCCAGGTCGTAACGAGTAGGAATGGAATTCTCGGGTGCCA	5	0.125	No Hit
AAGCAGAACTGGCGCTGTGGGATGAACCTGGAATTCTCGGGTGCCAAGGA	5	0.125	RNA PCR Primer, Index 1 (100% over 22bp)
CTCCATTGAGCCTTGGAATTGAAACAGCTGTGGAATTCTCGGGTGCCAAGG	5	0.125	Illumina Small RNA Adapter 2 (100% over 21bp)
ACGGCCTGGGAATCCTGGATGTTGTAAGCTTGGAATTCTCGGGTGCCAAGG	5	0.125	Illumina Small RNA Adapter 2 (100% over 21bp)
CCTCCAGTTGGTACGTCTGGTTCAGGGTTGTGGAATTCTCGGGTGCCAAGG	5	0.125	Illumina Small RNA Adapter 2 (100% over 21bp)
GCGGACCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTTGTAATCTC	5	0.125	RNA PCR Primer, Index 12 (100% over 44bp)
GCCGGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTTGTAATCTCG	5	0.125	RNA PCR Primer, Index 12 (100% over 45bp)
TCTCAACCTGAACTCAGTCGTGATTACCCGCTGATGGAATTCTCGGGTGCC	5	0.125	No Hit
AGTTGGTACGTCTGGTTCAGGGTTGTTTTGGAATTCTCGGGTGCCAAGGA	5	0.125	RNA PCR Primer, Index 1 (100% over 22bp)
>>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	1.225	0.0	0.0	0.0
2	0.0	1.225	0.0	0.0	0.0
3	0.0	1.225	0.0	0.0	0.0
4	0.0	1.275	0.0	0.0	0.0
5	0.0	1.575	0.0	0.0	0.0
6	0.0	2.8	0.0	0.0	0.0
7	0.0	5.95	0.0	0.0	0.0
8	0.0	10.55	0.0	0.0	0.0
9	0.0	12.825	0.0	0.0	0.0
10	0.0	14.125	0.0	0.0	0.0
11	0.0	14.7	0.0	0.0	0.0
12	0.0	15.05	0.0	0.0	0.0
13	0.0	15.225	0.0	0.0	0.0
14	0.0	15.325	0.0	0.0	0.0
15	0.0	15.525	0.0	0.0	0.0
16	0.0	15.9	0.0	0.0	0.0
17	0.0	16.275	0.0	0.0	0.0
18	0.0	16.55	0.0	0.0	0.0
19	0.0	16.825	0.0	0.0	0.0
20	0.0	17.1	0.0	0.0	0.0
21	0.0	17.45	0.0	0.0	0.0
22	0.0	18.0	0.0	0.0	0.0
23	0.0	18.525	0.0	0.0	0.0
24	0.0	18.875	0.0	0.0	0.0
25	0.0	19.425	0.0	0.0	0.0
26	0.0	20.825	0.0	0.0	0.0
27	0.0	39.725	0.0	0.0	0.0
28	0.0	42.6	0.0	0.0	0.0
29	0.0	45.625	0.0	0.0	0.0
30	0.0	51.175	0.0	0.0	0.0
31	0.0	57.05	0.0	0.0	0.0
32	0.0	62.8	0.0	0.0	0.0
33	0.0	69.25	0.0	0.0	0.0
34	0.0	81.075	0.0	0.0	0.0
35	0.0	87.425	0.0	0.0	0.0
36	0.0	94.75	0.0	0.0	0.0
37	0.0	96.7	0.0	0.0	0.0
38	0.0	97.4	0.0	0.0	0.0
39	0.0	97.725	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TAATCTC	35	1.3948249E-5	50.871426	45
GAGAAGG	55	0.0	45.07595	3
AAGAGAA	55	0.0	45.07595	1
GATTGTG	20	6.161671E-4	45.07595	1
CCTCCAG	20	6.161671E-4	45.07595	1
ATTGTGC	20	6.161671E-4	45.07595	2
AGAGAAG	55	0.0	45.07595	2
TTGTGCT	20	6.161671E-4	45.07595	3
TAGTGGA	55	0.0	44.512497	24
GCGGTAG	55	0.0	44.512497	20
GGTAGTG	55	0.0	44.512497	22
CGGTAGT	55	0.0	44.512497	21
GTAGTGG	55	0.0	44.512497	23
AGAAGGT	60	1.8189894E-12	41.319622	4
AAGGTGT	60	1.8189894E-12	41.319622	6
GAAGGTG	60	1.8189894E-12	41.319622	5
GTGTCTT	60	1.8189894E-12	40.803127	9
TGTCTTG	60	1.8189894E-12	40.803127	10
GCTGGCG	60	1.8189894E-12	40.803127	16
TGCTGGC	60	1.8189894E-12	40.803127	15
>>END_MODULE
Rejected 334151 READS because READLEN < 1
Read 334151 spots for SRR9060560.sra
Written 334151 spots for SRR9060560.sra
Rejected 334151 READS because READLEN < 1
Read 334151 spots for SRR9060560.sra
Written 334151 spots for SRR9060560.sra
Rejected 334151 READS because READLEN < 1
Read 334151 spots for SRR9060560.sra
Written 334151 spots for SRR9060560.sra
Rejected 334151 READS because READLEN < 1
Read 334151 spots for SRR9060560.sra
Written 334151 spots for SRR9060560.sra
Rejected 334151 READS because READLEN < 1
Read 334151 spots for SRR9060560.sra
Written 334151 spots for SRR9060560.sra
Rejected 334151 READS because READLEN < 1
Read 334151 spots for SRR9060560.sra
Written 334151 spots for SRR9060560.sra
Rejected 334151 READS because READLEN < 1
Read 334151 spots for SRR9060560.sra
Written 334151 spots for SRR9060560.sra
Rejected 334151 READS because READLEN < 1
Read 334151 spots for SRR9060560.sra
Written 334151 spots for SRR9060560.sra
Rejected 334151 READS because READLEN < 1
Read 334151 spots for SRR9060560.sra
Written 334151 spots for SRR9060560.sra
Rejected 334151 READS because READLEN < 1
Read 334151 spots for SRR9060560.sra
Written 334151 spots for SRR9060560.sra
Rejected 334151 READS because READLEN < 1
Read 334151 spots for SRR9060560.sra
Written 334151 spots for SRR9060560.sra
Rejected 334151 READS because READLEN < 1
Read 334151 spots for SRR9060560.sra
Written 334151 spots for SRR9060560.sra
Rejected 334151 READS because READLEN < 1
Read 334151 spots for SRR9060560.sra
Written 334151 spots for SRR9060560.sra
Rejected 334186 READS because READLEN < 1
Read 334186 spots for SRR9060560.sra
Written 334186 spots for SRR9060560.sra
Rejected 334151 READS because READLEN < 1
Read 334151 spots for SRR9060560.sra
Written 334151 spots for SRR9060560.sra
Rejected 334151 READS because READLEN < 1
Read 334151 spots for SRR9060560.sra
Written 334151 spots for SRR9060560.sra
Rejected 334151 READS because READLEN < 1
Read 334151 spots for SRR9060560.sra
Written 334151 spots for SRR9060560.sra
Rejected 334151 READS because READLEN < 1
Read 334151 spots for SRR9060560.sra
Written 334151 spots for SRR9060560.sra
Rejected 334151 READS because READLEN < 1
Read 334151 spots for SRR9060560.sra
Written 334151 spots for SRR9060560.sra
Rejected 334151 READS because READLEN < 1
Read 334151 spots for SRR9060560.sra
Written 334151 spots for SRR9060560.sra
Rejected 334151 READS because READLEN < 1
Read 334151 spots for SRR9060560.sra
Written 334151 spots for SRR9060560.sra
Rejected 334151 READS because READLEN < 1
Read 334151 spots for SRR9060560.sra
Written 334151 spots for SRR9060560.sra
Rejected 334151 READS because READLEN < 1
Read 334151 spots for SRR9060560.sra
Written 334151 spots for SRR9060560.sra
Rejected 334151 READS because READLEN < 1
Read 334151 spots for SRR9060560.sra
Written 334151 spots for SRR9060560.sra
Rejected 334151 READS because READLEN < 1
Read 334151 spots for SRR9060560.sra
Written 334151 spots for SRR9060560.sra
Rejected 334151 READS because READLEN < 1
Read 334151 spots for SRR9060560.sra
Written 334151 spots for SRR9060560.sra
Rejected 334151 READS because READLEN < 1
Read 334151 spots for SRR9060560.sra
Written 334151 spots for SRR9060560.sra
Rejected 334151 READS because READLEN < 1
Read 334151 spots for SRR9060560.sra
Written 334151 spots for SRR9060560.sra
Rejected 334151 READS because READLEN < 1
Read 334151 spots for SRR9060560.sra
Written 334151 spots for SRR9060560.sra
Rejected 334151 READS because READLEN < 1
Read 334151 spots for SRR9060560.sra
Written 334151 spots for SRR9060560.sra
Rejected 334151 READS because READLEN < 1
Read 334151 spots for SRR9060560.sra
Written 334151 spots for SRR9060560.sra
Rejected 334151 READS because READLEN < 1
Read 334151 spots for SRR9060560.sra
Written 334151 spots for SRR9060560.sra
Rejected 334151 READS because READLEN < 1
Read 334151 spots for SRR9060560.sra
Written 334151 spots for SRR9060560.sra
Rejected 334151 READS because READLEN < 1
Read 334151 spots for SRR9060560.sra
Written 334151 spots for SRR9060560.sra
Rejected 334151 READS because READLEN < 1
Read 334151 spots for SRR9060560.sra
Written 334151 spots for SRR9060560.sra
Rejected 334151 READS because READLEN < 1
Read 334151 spots for SRR9060560.sra
Written 334151 spots for SRR9060560.sra
Rejected 334151 READS because READLEN < 1
Read 334151 spots for SRR9060560.sra
Written 334151 spots for SRR9060560.sra
Rejected 334151 READS because READLEN < 1
Read 334151 spots for SRR9060560.sra
Written 334151 spots for SRR9060560.sra
Rejected 334151 READS because READLEN < 1
Read 334151 spots for SRR9060560.sra
Written 334151 spots for SRR9060560.sra
Rejected 334151 READS because READLEN < 1
Read 334151 spots for SRR9060560.sra
Written 334151 spots for SRR9060560.sra
Rejected 334151 READS because READLEN < 1
Read 334151 spots for SRR9060560.sra
Written 334151 spots for SRR9060560.sra
Rejected 334151 READS because READLEN < 1
Read 334151 spots for SRR9060560.sra
Written 334151 spots for SRR9060560.sra
Rejected 334151 READS because READLEN < 1
Read 334151 spots for SRR9060560.sra
Written 334151 spots for SRR9060560.sra
Rejected 334151 READS because READLEN < 1
Read 334151 spots for SRR9060560.sra
Written 334151 spots for SRR9060560.sra
Rejected 334151 READS because READLEN < 1
Read 334151 spots for SRR9060560.sra
Written 334151 spots for SRR9060560.sra
Rejected 334151 READS because READLEN < 1
Read 334151 spots for SRR9060560.sra
Written 334151 spots for SRR9060560.sra
Rejected 334151 READS because READLEN < 1
Read 334151 spots for SRR9060560.sra
Written 334151 spots for SRR9060560.sra
Rejected 334151 READS because READLEN < 1
Read 334151 spots for SRR9060560.sra
Written 334151 spots for SRR9060560.sra
Rejected 334151 READS because READLEN < 1
Read 334151 spots for SRR9060560.sra
Written 334151 spots for SRR9060560.sra
Rejected 334151 READS because READLEN < 1
Read 334151 spots for SRR9060560.sra
Written 334151 spots for SRR9060560.sra
Rejected 334151 READS because READLEN < 1
Read 334151 spots for SRR9060560.sra
Written 334151 spots for SRR9060560.sra
Rejected 334151 READS because READLEN < 1
Read 334151 spots for SRR9060560.sra
Written 334151 spots for SRR9060560.sra
Rejected 334151 READS because READLEN < 1
Read 334151 spots for SRR9060560.sra
Written 334151 spots for SRR9060560.sra
Rejected 334151 READS because READLEN < 1
Read 334151 spots for SRR9060560.sra
Written 334151 spots for SRR9060560.sra
Rejected 334151 READS because READLEN < 1
Read 334151 spots for SRR9060560.sra
Written 334151 spots for SRR9060560.sra
Rejected 334151 READS because READLEN < 1
Read 334151 spots for SRR9060560.sra
Written 334151 spots for SRR9060560.sra
Rejected 334151 READS because READLEN < 1
Read 334151 spots for SRR9060560.sra
Written 334151 spots for SRR9060560.sra
Rejected 334151 READS because READLEN < 1
Read 334151 spots for SRR9060560.sra
Written 334151 spots for SRR9060560.sra
Rejected 334151 READS because READLEN < 1
Read 334151 spots for SRR9060560.sra
Written 334151 spots for SRR9060560.sra
Rejected 334151 READS because READLEN < 1
Read 334151 spots for SRR9060560.sra
Written 334151 spots for SRR9060560.sra
Rejected 334151 READS because READLEN < 1
Read 334151 spots for SRR9060560.sra
Written 334151 spots for SRR9060560.sra
Rejected 334151 READS because READLEN < 1
Read 334151 spots for SRR9060560.sra
Written 334151 spots for SRR9060560.sra
Rejected 334151 READS because READLEN < 1
Read 334151 spots for SRR9060560.sra
Written 334151 spots for SRR9060560.sra
Rejected 334151 READS because READLEN < 1
Read 334151 spots for SRR9060560.sra
Written 334151 spots for SRR9060560.sra
SRR ids: ['SRR9060560.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_exafrzi8
SRR9060560.sra spots: 21385699
blocks: [[1, 334151], [334152, 668302], [668303, 1002453], [1002454, 1336604], [1336605, 1670755], [1670756, 2004906], [2004907, 2339057], [2339058, 2673208], [2673209, 3007359], [3007360, 3341510], [3341511, 3675661], [3675662, 4009812], [4009813, 4343963], [4343964, 4678114], [4678115, 5012265], [5012266, 5346416], [5346417, 5680567], [5680568, 6014718], [6014719, 6348869], [6348870, 6683020], [6683021, 7017171], [7017172, 7351322], [7351323, 7685473], [7685474, 8019624], [8019625, 8353775], [8353776, 8687926], [8687927, 9022077], [9022078, 9356228], [9356229, 9690379], [9690380, 10024530], [10024531, 10358681], [10358682, 10692832], [10692833, 11026983], [11026984, 11361134], [11361135, 11695285], [11695286, 12029436], [12029437, 12363587], [12363588, 12697738], [12697739, 13031889], [13031890, 13366040], [13366041, 13700191], [13700192, 14034342], [14034343, 14368493], [14368494, 14702644], [14702645, 15036795], [15036796, 15370946], [15370947, 15705097], [15705098, 16039248], [16039249, 16373399], [16373400, 16707550], [16707551, 17041701], [17041702, 17375852], [17375853, 17710003], [17710004, 18044154], [18044155, 18378305], [18378306, 18712456], [18712457, 19046607], [19046608, 19380758], [19380759, 19714909], [19714910, 20049060], [20049061, 20383211], [20383212, 20717362], [20717363, 21051513], [21051514, 21385699]]
SRR9060560 file size 3009560
SRR9060560 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 64 -o SRR9060560 SRR9060560_1.fastq
Input file:	SRR9060560_1.fastq
trimmed:	SRR9060560-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):	32
Thu Feb 13 06:34:28 2020 >> started

Thu Feb 13 06:34:47 2020 >> done (19.286s)
21385699 reads processed; of these:
       0 ( 0.00%) short reads filtered out after trimming by size control
       0 ( 0.00%) empty reads filtered out after trimming by size control
21385699 (100.00%) reads available; of these:
     147 ( 0.00%) trimmed reads available after processing
21385552 (100.00%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 40	       2	  0.00%
 41	       3	  0.00%
 42	       2	  0.00%
 43	       2	  0.00%
 44	       4	  0.00%
 45	     296	  0.00%
 46	     284	  0.00%
 47	     323	  0.00%
 48	    2663	  0.01%
 49	 1350892	  6.32%
 50	 6436850	 30.10%
 51	13594378	 63.57%
21385699 reads passed initial QC


criterion=sequence-density
sequence-density=97.73
sequence-density-rank=1
fanout-score=17.95
fanout-score-rank=1
prefix-density=96.77
prefix-fanout=18.0
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTTGTAATCTCGTATGCCG


criterion=fanout-score
sequence-density=97.73
sequence-density-rank=1
fanout-score=17.95
fanout-score-rank=1
prefix-density=96.77
prefix-fanout=18.0
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTTGTAATCTCGTATGCCG
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 64 -x TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTTGTAATCTCGTATGCCG -o SRR9060560 -
Input file:	STDIN
trimmed:	SRR9060560-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTTGTAATCTCGTATGCCG
-- 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):	32
Thu Feb 13 06:35:36 2020 >> started

Thu Feb 13 06:36:08 2020 >> done (32.401s)
20949256 reads processed; of these:
 3575562 (17.07%) short reads filtered out after trimming by size control
  322363 ( 1.54%) empty reads filtered out after trimming by size control
17051331 (81.39%) reads available; of these:
16869756 (98.94%) trimmed reads available after processing
  181575 ( 1.06%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	   78692	  0.46%
 19	   67899	  0.40%
 20	   75236	  0.44%
 21	  106260	  0.62%
 22	  115246	  0.68%
 23	   92000	  0.54%
 24	  154306	  0.90%
 25	  287977	  1.69%
 26	 3605409	 21.14%
 27	  592768	  3.48%
 28	  662177	  3.88%
 29	 1216792	  7.14%
 30	 1280120	  7.51%
 31	 1198732	  7.03%
 32	 1512784	  8.87%
 33	 2449396	 14.36%
 34	 1307684	  7.67%
 35	 1328215	  7.79%
 36	  458768	  2.69%
 37	  128568	  0.75%
 38	   66497	  0.39%
 39	   25689	  0.15%
 40	   12361	  0.07%
 41	    9996	  0.06%
 42	    4061	  0.02%
 43	    7446	  0.04%
 44	    4196	  0.02%
 45	    3564	  0.02%
 46	    3508	  0.02%
 47	    8681	  0.05%
 48	    5819	  0.03%
 49	   10515	  0.06%
 50	   64960	  0.38%
 51	  105009	  0.62%


criterion=sequence-density
sequence-density=0.26
sequence-density-rank=1
fanout-score=2.10
fanout-score-rank=6
prefix-density=0.27
prefix-fanout=2.0
sequence=GATAAAGGAATT


criterion=fanout-score
sequence-density=0.13
sequence-density-rank=5
fanout-score=22.42
fanout-score-rank=1
prefix-density=2.83
prefix-fanout=1.0
sequence=TTGCTGGTTTGAGGTTGGGTTCG
                                 Started job on |	Feb 13 06:36:54
                             Started mapping on |	Feb 13 06:36:54
                                    Finished on |	Feb 13 06:38:04
       Mapping speed, Million of reads per hour |	899.37

                          Number of input reads |	17487774
                      Average input read length |	30
                                    UNIQUE READS:
                   Uniquely mapped reads number |	12539642
                        Uniquely mapped reads % |	71.71%
                          Average mapped length |	29.88
                       Number of splices: Total |	509649
            Number of splices: Annotated (sjdb) |	495864
                       Number of splices: GT/AG |	502992
                       Number of splices: GC/AG |	3022
                       Number of splices: AT/AC |	73
               Number of splices: Non-canonical |	3562
                      Mismatch rate per base, % |	0.08%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.40
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.03
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	3985494
             % of reads mapped to multiple loci |	22.79%
        Number of reads mapped to too many loci |	415022
             % of reads mapped to too many loci |	2.37%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	3.13%
                     % of reads unmapped: other |	0.00%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	962638	962638	962638
N_multimapping	3985494	3985494	3985494
N_noFeature	37853	47730	12489908
N_ambiguous	52498	13908	169
UnstrandedReadsAssigned:12449291 PositiveStrandReadsAssigned:12478004 NegativeStrandReadsAssigned:49565
Dataset is classified positive stranded
MeadianReadLen=31 20thPercentileLength=26 echo kmer=21
SRR9060560 Starting Kallisto single end mapping to ensembl reference transcriptome. kmer=21

[quant] fragment length distribution is truncated gaussian with mean = 100, sd = 20
[index] k-mer length: 21
[index] number of targets: 33,746
[index] number of k-mers: 28,900,170
[index] number of equivalence classes: 64,378
[quant] running in single-end mode
[quant] will process file 1: SRR9060560-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 17,487,774 reads, 6,535,411 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,272 rounds

  33747 SRR9060560.ke.tsv
  46739 SRR9060560.se.tsv
  80486 total
==> SRR9060560.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
Y110A7A.10	1787	1688	230	20.2109
F27C8.1	1940	1841	13	1.04742
F07C3.7	1728	1629	19	1.73007
F52H2.2a	1739	1640	11	0.994898
F52H2.2b	1840	1741	0	0
T13A10.10a	1734	1635	0	0
T13A10.10b	1598	1499	14	1.38534
C55C2.5a	1840	1741	0	0
C55C2.5b	1606	1507	0	0

==> SRR9060560.se.tsv <==
WBGene00197333	0
WBGene00198386	0
WBGene00015153	3
WBGene00002061	5282
WBGene00255704	2
WBGene00235314	0
WBGene00001177	71
WBGene00169236	0
WBGene00219784	0
WBGene00015152	1
SRR9060560 completed mapping pipeline successfully
