[main_samview] fail to read the header from "test_example.slow5".
Koeng101 opened this issue · 3 comments
Koeng101 commented
Here is the file:
The error ("fail to read header") is a bit unhelpful in diagnosing the problem. I also have a larger example that was failing as well, I'll put it at the bottom.
The simple example failing:
#slow5_version 0.2.0
#num_read_groups 1
@asic_id 4175987214
#char* uint32_t double double double double uint64_t int16_t* uint64_t int32_t uint8_t double enum{unknown,partial,mux_change,unblock_mux_change,data_service_unblock_mux_change,signal_positive,signal_negative} char*
#read_id read_group digitisation offset range sampling_rate len_raw_signal raw_signal start_time read_number start_mux median_before end_reason channel_number
0026631e-33a3-49ab-aa22-3ab157d71f8b 0 8192 16 1489.52832 4000 5347 430,472,463 8318394 5383 1 219.133423 5 10
The full example failing:
#slow5_version 0.2.0
#num_read_groups 1
@asic_id 4175987214
@asic_id_eeprom 5910407
@asic_temp 31.649540
@asic_version IA02D
@auto_update 0
@auto_update_source https://mirror.oxfordnanoportal.com/software/MinKNOW/
@barcoding_enabled 0
@basecall_config_filename dna_r9.4.1_450bps_sup.cfg
@bream_is_standard 0
@configuration_version 4.3.11
@device_id MN33517
@device_type minion
@distribution_status stable
@distribution_version 21.06.10
@exp_script_name sequencing/sequencing_MIN106_DNA:FLO-FLG001:SQK-LSK109
@exp_script_purpose sequencing_run
@exp_start_time 2021-10-25T16:34:06.237443-07:00
@experiment_duration_set 1440
@experiment_type genomic_dna
@file_type multi-read
@file_version 2.3
@flongle_adapter_id FA-02253
@flow_cell_id AEI279
@flow_cell_product_code FLO-FLG001
@guppy_version 5.0.13+bbad52987
@heatsink_temp 35.003906
@host_product_code unknown
@host_product_serial_number .
@hostname trilo
@installation_type nc
@local_basecalling 1
@local_firmware_file 1
@operating_system ubuntu 18.04
@package bream4
@package_version 6.2.6
@pore_type not_set
@protocol_group_id op_1
@protocol_run_id ebe410af-7ff2-4117-9bff-f1bbae5be87d
@protocol_start_time 2021-10-25T16:33:39.151434-07:00
@protocols_version 6.2.6
@run_id 521e7966d4fd3d8fd57e3c264b9babd253db4c96
@sample_frequency 4000
@sample_id no_sample
@sequencing_kit sqk-lsk109
@usb_config MinION_fx3_1.1.1_ONT#MinION_fpga_1.1.0#bulk#Auto
@version 4.3.12
#char* uint32_t double double double double uint64_t int16_t* uint64_t int32_t uint8_t double enum{unknown,partial,mux_change,unblock_mux_change,data_service_unblock_mux_change,signal_positive,signal_negative} char*
#read_id read_group digitisation offset range sampling_rate len_raw_signal raw_signal start_time read_number start_mux median_before end_reason channel_number
0026631e-33a3-49ab-aa22-3ab157d71f8b 0 8192 16 1489.52832 4000 5347 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8318394 5383 1 219.133423 5 10
I'm specifically trying to create blow5 files to implement and test a blow5 parser in Golang, on top of / complementing the existing slow5 parser. I'd appreciate knowing what is going wrong in those headers, so I can make the two code-bases a bit more compatible!
hasindu2008 commented
Hello @Koeng101
Could you please attach the first example as a file here so I can investigate? When I copy-paste, the content, it seems the header is fine.
The error I get is not relevant to the header:
#slow5_version 0.2.0
#num_read_groups 1
@asic_id 4175987214
#char* uint32_t double double double double uint64_t int16_t* uint64_t int32_t uint8_tdouble enum{unknown,partial,mux_change,unblock_mux_change,data_service_unblock_mux_change,signal_positive,signal_negative} char*
#read_id read_group digitisation offset range sampling_rate len_raw_signal raw_signal start_time read_number start_mux median_before end_reason channel_number
[slow5_rec_parse::ERROR] Raw signal length '5347' does not match the number of signals parsed '3'. Raw signal is potentially truncated. At src/slow5.c:2770
[slow5_rec_parse::ERROR] Missing auxiliary fields in record, but present in header. At src/slow5.c:2793
[slow5_rec_depress_parse::ERROR] Record parsing failed. At src/slow5.c:2600
Koeng101 commented
Uh, I actually can't attach them, because github doesn't like the file extension. Here are where the files are.
I haven't implemented any checks yet, like with auxiliary fields or len_raw_signal.
Koeng101 commented
I'm closing this because I got the command working. I have no idea what I was doing wrong, but sorry about the low quality issue! My apologies!