location of readfish output

[bjaysheel]

Hi, I have setup a playback run using MinKNOW v5.8.13, minION MK1B, selected all default options and using readfish for basecalling. I can't figure out from the documentation where is the output.

a.) Is the data stored in minKnow/data folder (from minKNOW GUI) the same as the output for readfish? or b.) Is the file listed in debug_log for guppy and mappy_rs in the readfish toml file the final output of readfish.

if option a, I don't see a consolidated .fastq file just folder called fastq_pass and fastq_fail, does that mean something went wrong or am I missing a step/option in minKNOW.

Thanks Jaysheel

here is the toml file, and command used to run readfish

`[caller_settings.guppy] config = "dna_r10.4.1_e8.2_400bps_5khz_hac" address = "ipc:///nanopore/5000" debug_log = "pathogen_selection_basecalled_chunks.fq"

[mapper_settings.mappy_rs] fn_idx_in = "/nanopore/ref/Pathogen_contigs_samba_M1000.fa" n_threads = 4 debug_log = "pathogen_selection_mapped_chunks.paf" best_n = 1

[[regions]] name = "select_pathogen" control = false min_chunks = 0 max_chunks = 4 targets = "/nanopore/ref/Pathogen_contigs.name" single_on = "stop_receiving" multi_on = "stop_receiving" single_off = "unblock" multi_off = "unblock" no_seq = "proceed" no_map = "proceed" above_max_chunks = "unblock" below_min_chunks = "proceed" `

readfish targets --device MN44041 --experiment-name "SimulateRun_ReadFish_Pathogen_Selection" --toml /nanopore/readfish_pathogen_selection.toml --log-file pathogen_selection_run1.log --debug-log pathogen_selection_run1_chunks.tsv

[github-actions[bot]]

We found the following entries in the FAQ which you may find helpful:

• Which branch of readfish should I use?
• How do I create a readfish python environment?

Feel free to close this issue if you found an answer in the FAQ. Otherwise, please give us a little time to review.

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[mattloose]

Hi,

Thanks for your interest in using readfish. The final output is the reads that are contained within the fastq_pass and fastq_fail folders - i.e the reads that have been written as a consequence of running readfish during sequence.

The various log files written by readfish contain information about what readfish was doing.

I hope this helps?

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