Open cvermeulen88 opened 1 year ago
Megalodon version: 2.5.0
(megalodon_env) MAB@Axceleron-WKS:~/2748_NP_methylation/fast5_pass$ megalodon barcode12/ --guppy-config /data/MAB/bin/ont-guppy-cpu/data/dna_r10.3_450bps_fast.cfg --remora-modified-bases dna_r10.4.1_e8 fast 4.0.0 5hmc_5mc CG 2 --outputs basecalls mappings mod_mappings mods --reference /data/MAB/2748_NP_methylation/fastq_pass/barcode12/assembly/assembly.fasta --processes 24 --guppy-server-path /data/MAB/bin/ont-guppy-cpu/bin/guppy_basecaller --overwrite
[16:37:13] Running Megalodon version 2.5.0
******************** WARNING: "mods" output requested, so "per_read_mods" will be added to outputs. ********************
[16:37:13] Loading guppy basecalling backend
****************************************************************************************************
ERROR: Guppy server initialization failed. See guppy logs in [--output-directory] for more details.
Try running the guppy server initialization command found in log.txt in order to pinpoint the source of this issue.
****************************************************************************************************
from the log:
(megalodon_env) MAB@Axceleron-WKS:~/2748_NP_methylation/fast5_pass/megalodon_results$ /data/MAB/bin/ont-guppy-cpu/bin/guppy_basecaller -p auto -l megalodon_results/guppy_log -c /data/MAB/bin/ont-guppy-cpu/data/dna_r10.3_450bps_fast.cfg --quiet
Unexpected token '-p' on command-line.
Unexpected token 'auto' on command-line.
Try 'guppy_basecaller --help' for more information.
(megalodon_env) MAB@Axceleron-WKS:~/2748_NP_methylation/fast5_pass/megalodon_results$
Yesterday megalodon stopped working, and now consistently gives the error:
ERROR: Guppy server initialization failed. See guppy logs in [--output-directory] for more details.
However when I run the guppy server initialization command in the log file, it starts up just fine.
These are the commands:
Output:
This is the command in the log.txt:
/home/cog/cvermeulen/compdir/guppy/v6.3/ont-guppy/bin/guppy_basecall_server -p auto -l megalodon_output_rerio_baseenv/guppy_log -c res_dna_r941_min_modbases_5mC_CpG_v001.cfg --quiet -x cuda:0 -d ~/asmetha/rerio/basecall_models/
This works, with only output: CRASHPAD MESSAGE:
And when I remove the --quiet tag:
I tried a lot (new conda environments, reinstalling megalodon, different guppy versions), but I really can't figure out why it isn't working, so any help is really appreciated.