Open AUldry opened 3 months ago
Hello! Indeed It seems like I forgot to update the documentation on the new version of the config file! Let me get back to you on this one later in the day!
Although I believe these are all the fields you might need right now... (I am working on re-parametrizing them and finding good defaults so they don't have to be specified by hand ...)
[denoise_config]
mz_scaling = 0.015
max_mz_expansion_ratio = 1.5
ims_scaling = 0.015
max_ims_expansion_ratio = 5.0
ms2_min_n = 5
ms1_min_n = 10
ms1_min_cluster_intensity = 100
ms2_min_cluster_intensity = 50
[tracing_config]
mz_scaling = 0.015
max_mz_expansion_ratio = 1.5 # This is the one throwing the error .. (I will also make a better error message ...)
rt_scaling = 2.4
max_rt_expansion_ratio = 3.0 # But this one was added at the same time
ims_scaling = 0.02
max_ims_expansion_ratio = 4.0 # And this one ...
min_n = 3
min_neighbor_intensity = 450
[pseudoscan_generation_config]
rt_scaling = 2.4
max_rt_expansion_ratio = 5.0 # ... and this one
quad_scaling = 5.0
max_quad_expansion_ratio = 1.0 # ...
ims_scaling = 0.015
max_ims_expansion_ratio = 2.0 # ...
min_n = 6
min_neighbor_intensity = 6000
[sage_search_config]
static_mods = [[
"C",
57.0215,
]]
variable_mods = [
["M", [15.9949]],
]
fasta_path = "UP000005640_9606.fasta"
Many thanks for your reply!
I think the config file does need the output_config, as otherwise we get a "missing field output_config
" error.
The software now runs, but now I have the problem that I need to find a suitable example to test, or a suitable machine to run on, as I seem to eventually go on my local machine into a memory problem (at least I believe that's what causes the "Killed" output). What RAM would you say I need for, say, a 7.3 GB .d sample?
Well ... it depends ...
If we break down the process in 'processing' and 'search'.
I test everything on a 16 GB mac air ... which so far has worked for 44 min diaPASEF data on human with those mods. If you send me an email I could send you one of the raw files I use for testing (jspaezp1 in twitter if you dont want to post it here)
best!
Dear Sebastian,
I would gladly take up your offer of trying your own example. My email is anne-christine.uldry followed by at, foloowed by unibe.ch (hope it's clear!). Thanks!
Dear all,
I wanted to try this interesting piece of software but when I ran it with the exact same config file (bar for the path to the fasta file, which is adjusted to my set up)
ionmesh -c ionmesh_config.toml test.d
I get the following message:
thread 'main' panicked at src/main.rs:97:49: called
Result::unwrap()
on anErr
value: Error { inner: Error { inner: TomlError { message: "missing fieldmax_mz_expansion_ratio
", raw: Some("[denoise_config]\r\nmz_scaling = 0.015\r\nims_scaling = 0.03\r\nms2_min_n = 2\r\nms1_min_n = 3\r\nms1_min_cluster_intensity = 100\r\nms2_min_cluster_intensity = 50\r\n\r\n[tracing_config]\r\nmz_scaling = 0.019999999552965164\r\nrt_scaling = 2.200000047683716\r\nims_scaling = 0.02\r\nmin_n = 2\r\nmin_neighbor_intensity = 200\r\n\r\n[pseudoscan_generation_config]\r\nrt_scaling = 0.7\r\nquad_scaling = 5.0\r\nims_scaling = 0.02\r\nmin_n = 4\r\nmin_neighbor_intensity = 500\r\n\r\n[sage_search_config]\r\nstatic_mods = [[\r\n \"C\",\r\n 57.0215,\r\n]]\r\nvariable_mods = [[\r\n \"M\",\r\n [15.9949],\r\n]]\r\nfasta_path = \"myfasta.fasta\"\r\n\r\n[output_config] # These options can be missing, if missing will not output the files.\r\nout_features_csv = \"features.csv\"\r\ndebug_traces_csv = \"debug_traces.csv\"\r\ndebug_scans_json = \"debug_scans.json\"\r\n"), keys: ["denoise_config"], span: Some(0..151) } } } note: run withRUST_BACKTRACE=1
environment variable to display a backtraceAny idea what I do wrong? Many thanks in advance!
Anne-Christine