Channel or BArcode not found in toml

[Rokoenig]

Preemptively, please excuse any formal mistakes. This is my first time commenting on GitHub. If I misuse any conventions or etiquette, I will try to do better.

The error message I get is:
('Channel 54 not found in Channel Map or', 'Barcode barcode08 not found in toml …')

I ran a depletion experiment on a GridION last year and still have all files from the run.

My command was:

readfish stats
--toml toml_file.toml
--fastq-directory ~/readfish_depletion_run/.../fastq_pass
--html html_name

The TOML file was based on the example human_chr_depletion.toml.

How can I run the stats analysis correctly in this case?

I tried modifying the TOML file to work around the error, but then ran into other issues.
If you need more information, I am happy to provide it.

Best regards,
Robin

[mattloose]

Hi,

I suspect that readfish stats is expecting to see the folder above fastq_pass - i.e it needs both pass and fail data to process.

Can you share the full error output that you get from readfish stats here?

[Rokoenig]

i changed the comments to _# because it made it a headline
error:
toml'
2025-12-21 20:36:10,617 readfish Version=2024.3.0
2025-12-21 20:36:10,617 readfish.stats 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
2025-12-21 20:36:10,622 readfish.stats Loaded TOML config without error
Aligning FASTQ, please wait | ▶▶▶▶▶▶▶▶▶▶▶▶▶▶ | ⠠⢀⡀Y ( ) Y⡀⢀⠄⡀ 0 in 1s (0.0/s) Internal error returning data, the receiver iterator has finished. sending on a disconnected channel 19995
Aligning FASTQ, please wait |████████████████████████████████████████| 1 in 1.5s (0.68/s)
('Channel 58 not found in Channel Map or', ' Barcode barcode08 not found in toml /mnt/localdata/homes/MY_mail/robin_analyze/toml_file_robin_20250420.toml')

my toml file:

_#Summary: This is a TOML config file for real-time base-calling and rejection of
_# two chromosomes from the human genome in a single region.
_# In other words, a depletion experiment.
_# In essence depletion is performed by reversing the actions taken for an enrichment experiment,
_# for on and off target mappings.

_# In this example a single region will apply to all channels across the entire flowcell.
_# This example is configured for running with an R9.4.1 bulk file for testing.

_# Genomic targets are specified directly in the toml file in the form
_# "contig"
_# or as:
_# "contig,start,end,strand"
_# for example, "chr2,0,100,+"" or "chr2".
_# If chr2 is specified, the entire contig will be considered a target, on both strands.
_# These patterns can be mixed, both in the toml or in a .csv file.

_# This config file will unblock any reads mapping to chr20 or chr21, depleting them.
_# All of the below fields are explained in more detail in the documentation -
_# https://looselab.github.io/readfish/toml.html

_# Basecaller configuration

[caller_settings.dorado] #ROBIN: changed by me
_# ^^^^^^ - ".guppy" specifies our chosen basecaller
_# If using dorado >7.3.9, this should be ".dorado".
_# All other parameters are shared between the two basecallers.
_# Guppy/Dorado base-calling configuration file name
_#config = "dna_r9.4.1_450bps_fast"#original
config = "dna_r10.4.1_e8.2_400bps_5khz_fast.cfg" #crk hanged by me, see notion what config possibl
address = "ipc:///tmp/.guppy/5555" #robin: gupy is the standard so dont chage
_# Fastq output for individual reads. This is OPTIONAL - as these files can become quite large.
_# Remove line to disable.
debug_log = "live_reads.fq" #RK: choose to stay because we hav nice pcs

_# Aligner Configuration
[mapper_settings.mappy_rs] #rk: because we can
_# ^^^^^^ - ".mappy" specifies mappy as the aligner. Use mappy_rs for the multithreaded rust version (required on PromethION)
_# Alignment reference to use. Should be either FASTA or an MMI
fn_idx_in = "/mnt/localdata/homes/MY_mail/robin_analyze/rk_target2.mmi" #my fasta to deplete
_# Optional PAF output for live alignments.
_# Remove line to disable.
debug_log = "live_alignments.paf"
_# Number of threads for indexing (mappy and mappy-rs) and mapping (mappy-rs only)
n_threads = 12 #rk: because we have 16GPUs (2 threads per core and 8 core per socket)

_# Region Configuration - see https://looselab.github.io/readfish/toml.html#analysis-regions for more information.
_# Definitions of "unblock", "proceed" and "stop_receivings" are as follows

_# proceed: Allow one more chunk to be captured, before trying to make another decision, i.e proceed for now

_ # unblock: Unblock the read

_ # stop_receiving: Allow the read to be sequenced, and stop receiving signal chunks for it.
# This region will enrich for reads mapping to chr20 and chr21.
[[regions]]
name = "Rodents"
min_chunks = 1 # minimum number of chunks before a decision can be made
max_chunks = 4 # maximum number of chunks to use in decision making - after this perform the above_max_chunks action
targets = ["pbp2X-_45652196","NC_012374","AJ301644"]# Genomic targets for this region
single_on = "unblock" # Action to take if there is one mapping on target.
multi_on = "unblock" # Action to take if there is more than one mapping, with at least one target.
single_off = "stop_receiving" # Action to take if there is one mapping and it is off target
multi_off = "stop_receiving" # Action to take if there are multiple mappings, where all are off target.
no_seq = "proceed" # Action to take if no sequence data.
no_map = "proceed" # Action to take if no alignments returned.
above_max_chunks = "unblock" # Action to take if above max_chunks.
below_min_chunks = "proceed" # Action to take if below min_chunks.