[main_samview] fail to read the header from "test_example.slow5".

[Koeng101]

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]

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]

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]

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!