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reads connection error #339

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Bessem06 opened this issue Apr 5, 2023 · 0 comments
Open

reads connection error #339

Bessem06 opened this issue Apr 5, 2023 · 0 comments

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@Bessem06
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Bessem06 commented Apr 5, 2023

Hi,

I am trying to run megalodon on my machine (ubuntu 22.04, nvidia quadro P1000) using this comand:
megalodon --guppy-server-path /usr/bin/guppy_basecall_server --guppy-config dna_r9.4.1_450bps_modbases_5hmc_5mc_cg_hac.cfg barcode01/ --overwrite --processes 6 --outputs basecalls mappings mod_mappings mods --reference Mal.contigs.PolcaCorr95.fa --output-directory megalodon_barcode_01 --devices 0 --guppy-timeout 1200

After some time I get this error message:
"[guppy/error] basecall_service::BasecallClient::worker_loop: Connection error. [timed_out] Timeout waiting for reply to request: LOAD_CONFIG"

When looking at the log file I see this:
[10:31:32] Running Megalodon version 2.5.0
DBG 10:31:32 : Command: """/home/skynet/.local/bin/megalodon --guppy-server-path /usr/bin/guppy_basecall_server --guppy-config dna_r9.4.1_450bps_modbases_5hmc_5mc_cg_hac.cfg barcode01/ --overwrite --processes 6 --outputs basecalls mappings mod_mappings mods --reference Mal.contigs.PolcaCorr95.fa --output-directory megalodon_barcode_01 --devices 0 --guppy-timeout 1200""" --- MainProcess-MainThread megalodon.py:1787
******************** WARNING: "mods" output requested, so "per_read_mods" will be added to outputs. ********************
[10:31:32] Loading guppy basecalling backend
DBG 10:31:32 : Guppy version: "6.4.6" --- MainProcess-MainThread backends.py:938
DBG 10:31:32 : Pyguppy version: "6.4.6" --- MainProcess-MainThread backends.py:939
DBG 10:31:32 : guppy server init command: "/usr/bin/guppy_basecall_server -p auto -l megalodon_barcode_01/guppy_log -c dna_r9.4.1_450bps_modbases_5hmc_5mc_cg_hac.cfg --quiet --post_out -x cuda:0" --- MainProcess-MainThread backends.py:1016
DBG 10:31:32 : Found guppy log file: megalodon_barcode_01/guppy_log/guppy_basecall_server_log-2023-04-05_10-31-32.log --- MainProcess-MainThread backends.py:1032
DBG 10:31:33 : Guppy server started on port ipc:///tmp/b240-57ce-3204-792b --- MainProcess-MainThread backends.py:973
DBG 10:31:33 : Connecting to server --- MainProcess-MainThread backends.py:872
DBG 10:31:33 : pyguppy server status: result.success --- MainProcess-MainThread backends.py:909
DBG 10:31:33 : Could not load guppy server configuration state: 'Configurations' --- MainProcess-MainThread backends.py:913
DBG 10:31:53 : Get reads connection error "Not connected to server. status code: <status.preparing_connection: 1>. <super: <class 'PyGuppyClient'>, >" --- MainProcess-MainThread backends.py:1228
DBG 10:31:54 : Get reads connection error "Not connected to server. status code: <status.loading_config: 2>. <super: <class 'PyGuppyClient'>, >" --- MainProcess-MainThread backends.py:1228
DBG 10:31:55 : Get reads connection error "Not connected to server. status code: <status.loading_config: 2>. <super: <class 'PyGuppyClient'>, >" --- MainProcess-MainThread backends.py:1228
DBG 10:31:56 : Get reads connection error "Not connected to server. status code: <status.loading_config: 2>. <super: <class 'PyGuppyClient'>, >" --- MainProcess-MainThread backends.py:1228
...
DBG 10:47:03 : Get reads connection error "Not connected to server. status code: <status.error_state: 7>. <super: <class 'PyGuppyClient'>, >" --- MainProcess-MainThread backends.py:1228
DBG 10:47:04 : Get reads connection error "Not connected to server. status code: <status.error_state: 7>. <super: <class 'PyGuppyClient'>, >" --- MainProcess-MainThread backends.py:1228
DBG 10:47:05 : Get reads connection error "Not connected to server. status code: <status.error_state: 7>. <super: <class 'PyGuppyClient'>, >" --- MainProcess-MainThread backends.py:1228
DBG 10:47:06 : Get reads connection error "Not connected to server. status code: <status.error_state: 7>. <super: <class 'PyGuppyClient'>, >" --- MainProcess-MainThread backends.py:1228"

Can you help me with this problem
Thanks
Bessem

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