Muffin run ends without any error message but not with the proper outputs

[chayanroy]

Hi,

I guess my issue is similar with a previous one #33 but not sure entirely so creating a new one.

Here is the complete screen out put with the commands used to run.

(base) croy@thoth: nextflow run MUFFIN/ --output muffin_out --assembler metaflye --illumina path_to/SR/muffin_input/ --ont path_to/ONT/cleaned_reads/ --cpus 64 --memory 250 --modular full -profile local,conda -work-dir muffin_out/work

N E X T F L O W ~ version 22.04.5 Launching /home/croy/nextflow/MUFFIN/main.nf [sharp_dubinsky] DSL2 - revision: ab9fe45525 [- ] process > sourmash_download_db - [- ] process > checkm_download_db - executor > local (2) [88/550294] process > sourmash_download_db [ 0%] 0 of 1 [85/cc5de1] process > checkm_download_db [ 0%] 0 of 1 executor > local (2) [88/550294] process > sourmash_download_db [ 0%] 0 of 1 [85/cc5de1] process > checkm_download_db [ 0%] 0 of 1 executor > local (3) [88/550294] process > sourmash_download_db [100%] 1 of 1 ✔ [85/cc5de1] process > checkm_download_db [ 0%] 0 of 1 executor > local (3) [88/550294] process > sourmash_download_db [100%] 1 of 1 ✔ [85/cc5de1] process > checkm_download_db [ 0%] 0 of 1 executor > local (4) [88/550294] process > sourmash_download_db [100%] 1 of 1 ✔ [85/cc5de1] process > checkm_download_db [ 0%] 0 of 1 executor > local (4) [88/550294] process > sourmash_download_db [100%] 1 of 1 ✔ [85/cc5de1] process > checkm_download_db [ 0%] 0 of 1 executor > local (4) [88/550294] process > sourmash_download_db [100%] 1 of 1 ✔ [85/cc5de1] process > checkm_download_db [ 0%] 0 of 1 executor > local (4) [88/550294] process > sourmash_download_db [100%] 1 of 1 ✔ [85/cc5de1] process > checkm_download_db [ 0%] 0 of 1 executor > local (4) [88/550294] process > sourmash_download_db [100%] 1 of 1 ✔ [85/cc5de1] process > checkm_download_db [ 0%] 0 of 1 executor > local (4) [88/550294] process > sourmash_download_db [100%] 1 of 1 ✔ [85/cc5de1] process > checkm_download_db [ 0%] 0 of 1 executor > local (5) executor > local (5) executor > local (6) executor > local (6) executor > local (6) executor > local (7) executor > local (7) executor > local (8) executor > local (8) executor > local (9) executor > local (9) executor > local (9) executor > local (34) executor > local (34) executor > local (34) executor > local (36) executor > local (37) executor > local (38) executor > local (42) [88/550294] process > sourmash_download_db [100%] 1 of 1 ✔ [85/cc5de1] process > checkm_download_db [100%] 1 of 1 ✔ [4d/33969c] process > checkm_setup_db [100%] 1 of 1 ✔ [24/fb2a09] process > discard_short (25) [100%] 25 of 25 ✔ [2c/003539] process > merge (2) [100%] 2 of 2 ✔ [dc/88b8da] process > fastp (1) [100%] 2 of 2 ✔ [ed/d1fc8b] process > flye (1) [100%] 2 of 2 ✔ [f8/5b4965] process > minimap_polish (2) [100%] 2 of 2 ✔ [03/8dde72] process > racon (2) [100%] 2 of 2 ✔ [26/1b6e84] process > medaka (2) [100%] 2 of 2 ✔ [- ] process > pilon - [- ] process > minimap2 - [- ] process > bwa - [- ] process > metabat2 - [- ] process > maxbin2 - [- ] process > concoct - [- ] process > refine3 - [- ] process > checkm - [- ] process > sourmash_bins - [- ] process > sourmash_checkm_parser - [84/c4f062] process > eggnog_download_db [100%] 1 of 1 ✔ [- ] process > eggnog_bin - [- ] process > parser_bin - [cd/8b55ce] process > readme_output [100%] 1 of 1 ✔

Done! Results are stored here --> /DATA_1/croy/MATRIX/Cultured_meta/muffin_rerun/ The Readme file in /DATA_1/croy/MATRIX/Cultured_meta/muffin_rerun/ describe the structure of the results directories.

However when I checked the directory it only contain the

assemble/quality_control/illumina

I have also attached the execution reports and execution timeline here but could not find what went wrong. execution_report.zip execution_timeline.zip

Any help is much appreciated.

Thanks and regards, Chayan

[chayanroy]

Incase you wonder, here is how my files look like

ONT = R1PE.fastq.gz Illumina = R1PE_R1.fastq.gz and R1PE_R2.fastq.gz

I tried the same with singularity as well but no result yet, without any proper error message.

Thank you