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The output.fa is null #18

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myshu2017-03-14 opened this issue Oct 16, 2017 · 0 comments
Open

The output.fa is null #18

myshu2017-03-14 opened this issue Oct 16, 2017 · 0 comments

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@myshu2017-03-14
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Hi,
I installed the nanocall on Ubuntu 16.04. The command I used just as below:

nanocall /nanopore-datas/20170907_1414_FAH10633-RS-20170907/fast5/pass/0/DESKTOP_QKGLFDD_20170907_FAH10633_MN20782_sequencing_run_FAH10633_RS_20170907_53523_read_1023_ch_3_strand.fast5 >output.fa 2>log

And the results of nanocall basecalling(output.fa) using our sequencing fast5 file (I choosed the local basecalling in the MinKNOW, the test fast5 file directory is /nanopore-datas/20170907_1414_FAH10633-RS-20170907/fast5/pass/0/) is null.
The log file just as below:

= main.2 nanocall.cpp:913 main program: nanocall
= main.2 nanocall.cpp:914 main version: 2f92983
= main.2 nanocall.cpp:915 main args: /analysis/software_han/1-data/nanopore-datas/20170907_1414_FAH10633-RS-20170907/fast5/pass/0/DESKTOP_QKGLFDD_20170907_FAH10633_MN20782_sequencing_run_FAH10633_RS_20170907_53523_read_1023_ch_3_strand.fast5
= main.2 nanocall.cpp:916 main num_threads=1
= main.2 nanocall.cpp:930 main eventdetection_group=smallest
= main.2 nanocall.cpp:971 main ed_event_trimming: sq_start=50 sq_end=50 hp_start=50 hp_end=50
= main.2 nanocall.cpp:979 main hairpin_detection: abasic_level_top_percent=1 abasic_level_top_offset=0 hairpin_island_window_size=10 hairpin_island_window_load=5
= main.2 nanocall.cpp:1063 main train=1
= main.2 nanocall.cpp:1066 main train_scaling=1
= main.2 nanocall.cpp:1067 main train_transitions=1
= main.2 nanocall.cpp:1070 main double_strands_scaling=1
= main.2 nanocall.cpp:1071 main scaling_num_events=200
= main.2 nanocall.cpp:1072 main scaling_max_rounds=10
= main.2 nanocall.cpp:1073 main scaling_min_progress=1
= main.2 nanocall.cpp:1074 main scaling_select_threshold=20
= main.2 nanocall.cpp:1075 main train_drift=0
= main.2 nanocall.cpp:1078 main basecall=1
= main.2 nanocall.cpp:165 init_models loaded builtin module [r9.t.007.ont.model] for strand [0] statistics [mean=87.2151, stdv=12.9112]
= main.2 nanocall.cpp:165 init_models loaded builtin module [r9.c.p1.007.ont.model] for strand [1] statistics [mean=87.2151, stdv=12.9112]
= main.2 nanocall.cpp:165 init_models loaded builtin module [r9.c.p2.007.ont.model] for strand [1] statistics [mean=92.5249, stdv=13.1801]
= main.2 nanocall.cpp:190 init_transitions init_state_transitions pr_skip=[0.3], pr_stay=[0.1]
= main.2 nanocall.cpp:228 init_files adding input file [/analysis/software_han/1-data/nanopore-datas/20170907_1414_FAH10633-RS-20170907/fast5/pass/0/DESKTOP_QKGLFDD_20170907_FAH10633_MN20782_sequencing_run_FAH10633_RS_20170907_53523_read_1023_ch_3_strand.fast5]
= Fast5_Summary.2 Fast5_Summary.hpp:176 summarize /analysis/software_han/1-data/nanopore-datas/20170907_1414_FAH10633-RS-20170907/fast5/pass/0/DESKTOP_QKGLFDD_20170907_FAH10633_MN20782_sequencing_run_FAH10633_RS_20170907_53523_read_1023_ch_3_strand.fast5: missing eventdetection events
= main.2 nanocall.cpp:270 init_reads summary: [base_file_name=DESKTOP_QKGLFDD_20170907_FAH10633_MN20782_sequencing_run_FAH10633_RS_20170907_53523_read_1023_ch_3_strand valid=1 num_ed_events=0]
= main.2 Parameter_Trainer.hpp:56 init using [2160] states for state trainsition training
= main.2 nanocall.cpp:581 train_reads training user_cpu_secs=0
= main.2 nanocall.cpp:868 basecall_reads basecalling user_cpu_secs=0

There are no error when running...
So what the wrong here? Can you help me?

Looking for your reply. Thank you very much!
Best wishes,
myshu

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