## Instalando MetaMobilePicker ### Instalando Mamba Instalando [miniforge](https://github.com/conda-forge/miniforge#mambaforge) ``` curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh" bash Miniforge3-$(uname)-$(uname -m).sh ``` Luego puse ``` conda init eval "$(/home/lauramarcos/miniforge3/bin/conda shell.bash hook) ``` :::danger Como ahora tengo Mamba y Conda hay envs en uno y otro lado... :scream: ::: ### MetaMobilePicker ``` conda create --name metamobilepicker python=3.10 conda activate metamobilepicker conda install -c conda-forge mamba mamba install -c bioconda metamobilepicker conda install -c bioconda biopython ``` Probando la instalación ``` metamobilepicker run --test --dryrun ``` Me sale un error. Creo que falta Snakemake. ### Instalando snakemake ``` mamba create -c conda-forge -c bioconda -n snakemake snakemake ``` El error creo qu esque falta Singularity... Ya que hay un pequeño e imperceptible comentari oque dice: *"Note: For running the pipeline, you will need Singularity (v3.8 or later) installed on your system."* ### Instalando Singularuty Conseguí este [tutorial](https://singularity-tutorial.github.io/01-installation/). ``` sudo apt-get install -y build-essential libssl-dev uuid-dev libgpgme11-dev \ squashfs-tools libseccomp-dev wget pkg-config git cryptsetup debootstrap ``` Se tiene que instalar Go ``` wget https://dl.google.com/go/go1.16.12.linux-amd64.tar.gz sudo tar --directory=/usr/local -xzvf go1.16.12.linux-amd64.tar.gz export PATH=/usr/local/go/bin:$PATH ``` Ahora si, he puesto la version v3.8.7 ``` wget https://github.com/singularityware/singularity/releases/download/v3.8.7/singularity-3.8.7.tar.gz tar -xzvf singularity-3.8.7.tar.gz ``` :memo: Tuve un error y es poque había instalado una versión de Go antigua (go1.13) necesitaba la go1.16.12 así que la actualicé. Ya está arreglado el codigo con la version necesaria. ```bash cd singularity-3.8.7 ./mconfig cd builddir make sudo make install ``` Lo conseguí :smile: ``` ____________________________________ / You tread upon my patience. \ | | \ -- William Shakespeare, "Henry IV" / ------------------------------------ \ ^__^ \ (oo)\_______ (__)\ )\/\ ||----w | || || ``` **Seguimos con MetaMobilePicker** ```bash metamobilepicker run --test --dryrun ``` Sin erroreeees :hamster: ```bash metamobilepicker run --test ``` Me salió este comentario mientras: > Your conda installation is not configured to use strict channel priorities. This is however crucial for having robust and correct environments (for details, see https://conda-forge.org/docs/user/tipsandtricks.html). Please consider to configure strict priorities by executing 'conda config --set channel_priority strict'. Lo arreglaré cuando termine de correr (No modificarlo xD) :warning: ERROR ``` Activating conda environment: .snakemake/conda/06b220d26a41a458692266b4e3a75986 ERROR: This cross-compiler package contains no program /home/lauramarcos/anaconda3/envs/metamobilepicker/lib/python3.10/site-packages/MetaMobilePicker/.snakemake/conda/06b220d26a41a458692266b4e3a75986/bin/x86_64-conda_cos6-linux-gnu-gfortran INFO: activate-gfortran_linux-64.sh made the following environmental changes: +HOST=x86_64-conda_cos6-linux-gnu -HOST=x86_64-conda-linux-gnu [Tue Apr 2 12:50:50 2024] Error in rule simplify_names: jobid: 18 output: test/mmp_test/test/test_anvio/test_MGEs_simplified.fasta, test/mmp_test/test/test_anvio/test_MGEs_simplified.names log: test/mmp_test/test/log/anvio/test_simplify_fasta_error.txt, test/mmp_test/test/log/anvio/test_simplify_fasta_out.txt (check log file(s) for error message) conda-env: /home/lauramarcos/anaconda3/envs/metamobilepicker/lib/python3.10/site-packages/MetaMobilePicker/.snakemake/conda/06b220d26a41a458692266b4e3a75986 shell: anvi-script-reformat-fasta test/mmp_test/test/test_MGEs/test_MetaMobilePicker.fasta -o test/mmp_test/test/test_anvio/test_MGEs_simplified.fasta -l 0 --simplify-names --report-file test/mmp_test/test/test_anvio/test_MGEs_simplified.names 1> test/mmp_test/test/log/anvio/test_simplify_fasta_out.txt 2> test/mmp_test/test/log/anvio/test_simplify_fasta_error.txt (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!) Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Workflow finished with errors. [2024-04-02 12:50 CRITICAL] Command 'snakemake --use-conda --snakefile /home/lauramarcos/anaconda3/envs/metamobilepicker/lib/python3.10/site-packages/MetaMobilePicker/Snakefile --cores 16 --configfile /home/lauramarcos/anaconda3/envs/metamobilepicker/lib/python3.10/site-packages/MetaMobilePicker/config/test.yaml --rerun-incomplete --nolock --latency-wait 60 --directory /home/lauramarcos/anaconda3/envs/metamobilepicker/lib/python3.10/site-packages/MetaMobilePicker --use-singularity --singularity-prefix /home/lauramarcos/anaconda3/envs/metamobilepicker/lib/python3.10/site-packages/MetaMobilePicker/.snakemake --singularity-args '--home $PWD/.. --bind $TMPDIR,$PWD/..'' returned non-zero exit status 13. ``` :clown_face: Tuve que abrir un comentario en el foro de metamobile. Aquí está la [solución](https://gitlab.com/jkerkvliet/metamobilepicker/-/issues/28#note_1909293068). Funcionó para ejecutar test sin errores. ### Prueba con muestras pasar los archivos test a una carpeta `/home/lauramarcos/metamobile/mmp_data ` Crear un archivo de texto, separado pro comas indicando la ubicacion de los archivos: `testsample,mmp_data/test_reads_10k_R1.fastq,mmp_data/test_reads_10k_R2.fastq` Configurar archivo yaml `metamobilepicker config --samples samples.txt --output config.yaml --outdir mmp_test_output` Me pone estos Warnings: > WARNING: a host sequence file wasn't specified. I'll use a mock sequence file, but consider adding a real host file! > WARNING: No output file was specified, it will be written to config.yaml. Please make sure that's okay! Se crea archivo config.yaml **Ejecutar prueba:** `metamobilepicker run -c config.yaml --dryrun` No da errores. Probar sin dryrun :warning: Me está dando un error de Atlas_QC ``` Error in rule atlasQC: jobid: 6 output: test/mmp_test/test/test_ATLAS/test_atlas.txt, test/mmp_test/test/test_processed_reads/test_QC_R1.fastq.gz, test/mmp_test/test/test_processed_reads/test_QC_R2.fastq.gz log: test/mmp_test/test/log/QC/test_QC_error.txt, test/mmp_test/test/log/QC/test_QC_out.txt (check log file(s) for error message) conda-env: /home/lauramarcos/miniforge3/envs/metamobilepicker/lib/python3.10/site-packages/MetaMobilePicker/.snakemake/conda/08ade8b6a970379f2cd205ca0ae8ad7f shell: # Gets sample name with - in stead of _ (Atlas preference) sample=$(echo test | sed 's/_/-/g') # Runs the QC module of Metagenome-Atlas atlas run qc --config-file test/mmp_test/test/test_ATLAS/config_modified.yaml --working-dir test/mmp_test/test/test_ATLAS --jobs 6 --resources mem=8 java_mem=8 --conda-prefix /home/lauramarcos/miniforge3/envs/metamobilepicker/lib/python3.10/site-packages/snakemake 1>test/mmp_test/test/log/QC/test_QC_out.txt 2>test/mmp_test/test/log/QC/test_QC_error.txt touch test/mmp_test/test/test_ATLAS/test_atlas.txt echo "Finished QC, copying reads" >> test/mmp_test/test/log/QC/test_QC_out.txt # Copies the QC'ed reads to the output directory mv test/mmp_test/test/test_ATLAS/${sample}/sequence_quality_control/${sample}_QC_R1.fastq.gz test/mmp_test/test/test_processed_reads/test_QC_R1.fastq.gz mv test/mmp_test/test/test_ATLAS/${sample}/sequence_quality_control/${sample}_QC_R2.fastq.gz test/mmp_test/test/test_processed_reads/test_QC_R2.fastq.gz echo "Finished QC step" >> test/mmp_test/test/log/QC/test_QC_out.txt (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!) ``` El log del error en snakemake: ``` este es el log del error: [Mon May 20 11:24:09 2024] localrule write_read_counts: input: test/sequence_quality_control/read_stats/raw_read_counts.tsv, test/sequence_quality_control/read_stats/deduplicated_read_counts.tsv, test/sequence_quality_control/read_stats/filtered_read_counts.tsv, test/sequence_quality_control/read_stats/clean_read_counts.tsv, test/sequence_quality_control/read_stats/QC_read_counts.tsv output: test/sequence_quality_control/read_stats/read_counts.tsv jobid: 17 wildcards: sample=test resources: tmpdir=/tmp, mem=8, mem_mb=60000, time=5 [Mon May 20 11:24:10 2024] Error in rule write_read_counts:  jobid: 0  output: test/sequence_quality_control/read_stats/read_counts.tsv  RuleException: AttributeError in line 730 of /home/lauramarcos/miniforge3/envs/metamobilepicker/lib/python3.10/site-packages/MetaMobilePicker/.snakemake/conda/08ade8b6a970379f2cd205ca0ae8ad7f/lib/python3.8/site-packages/atlas/rules/qc.smk: 'DataFrame' object has no attribute 'append' File "/home/lauramarcos/miniforge3/envs/metamobilepicker/lib/python3.10/site-packages/MetaMobilePicker/.snakemake/conda/08ade8b6a970379f2cd205ca0ae8ad7f/lib/python3.8/site-packages/atlas/rules/qc.smk", line 730, in __rule_write_read_counts File "/home/lauramarcos/.local/lib/python3.8/site-packages/pandas/core/generic.py", line 5989, in __getattr__ File "/home/lauramarcos/miniforge3/envs/metamobilepicker/lib/python3.10/site-packages/MetaMobilePicker/.snakemake/conda/08ade8b6a970379f2cd205ca0ae8ad7f/lib/python3.8/concurrent/futures/thread.py", line 57, in run Exiting because a job execution failed. Look above for error message Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: /home/lauramarcos/miniforge3/envs/metamobilepicker/lib/python3.10/site-packages/MetaMobilePicker/test/mmp_test/test/test_ATLAS/.snakemake/log/2024-05-20T112200.873202.snakemake.log [2024-05-20 11:24 CRITICAL] Command 'snakemake --snakefile /home/lauramarcos/miniforge3/envs/metamobilepicker/lib/python3.10/site-packages/MetaMobilePicker/.snakemake/conda/08ade8b6a970379f2cd205ca0ae8ad7f/lib/python3.8/site-packages/atlas/Snakefile --directory /home/lauramarcos/miniforge3/envs/metamobilepicker/lib/python3.10/site-packages/MetaMobilePicker/test/mmp_test/test/test_ATLAS --jobs 6 --rerun-incomplete --configfile '/home/lauramarcos/miniforge3/envs/metamobilepicker/lib/python3.10/site-packages/MetaMobilePicker/test/mmp_test/test/test_ATLAS/config_modified.yaml' --nolock --use-conda --conda-prefix /home/lauramarcos/miniforge3/envs/metamobilepicker/lib/python3.10/site-packages/MetaMobilePicker/test/mmp_test/test/test_ATLAS/test_databases/conda_envs --scheduler greedy qc --resources mem=8 java_mem=8 --conda-prefix /home/lauramarcos/miniforge3/envs/metamobilepicker/lib/python3.10/site-packages/snakemake ' returned non-zero exit status 1. ``` ### Muestras reales :warning: Actualización Julio 25: conda activate metamobilepicker :nerd_face: Lo repito con muestras reales. Uso la muestras V1_783_R1 y V1_783_R2. Crear un archivo de texto (`samples.txt`), separado por comas indicando la ubicacion de los archivos: `V1_783,data/V1_783_R1.fastq,data/V1_783_R2.fastq` Configurar archivo yaml ``` metamobilepicker config --samples samples.txt --output V1_783config.yaml --outdir output ``` Ejecuto: ``` metamobilepicker run -c V1_783config.yaml ``` Mismo error :::spoiler ``` [Mon May 20 16:41:04 2024] Error in rule atlasQC: jobid: 6 output: /home/lauramarcos/metamobile/results/V1783/V1783_ATLAS/V1783_atlas.txt, /home/lauramarcos/metamobile/results/V1783/V1783_processed_reads/V1783_QC_R1.fastq.gz, /home/lauramarcos/metamobile/results/V1783/V1783_processed_reads/V1783_QC_R2.fastq.gz log: /home/lauramarcos/metamobile/results/V1783/log/QC/V1783_QC_error.txt, /home/lauramarcos/metamobile/results/V1783/log/QC/V1783_QC_out.txt (check log file(s) for error message) conda-env: /home/lauramarcos/anaconda3/envs/metamobilepicker/lib/python3.10/site-packages/MetaMobilePicker/.snakemake/conda/cd9fc1fe765bf2e3f5a276243a16e9e8 shell: # Gets sample name with - in stead of _ (Atlas preference) sample=$(echo V1783 | sed 's/_/-/g') # Runs the QC module of Metagenome-Atlas atlas run qc --config-file /home/lauramarcos/metamobile/results/V1783/V1783_ATLAS/config_modified.yaml --working-dir /home/lauramarcos/metamobile/results/V1783/V1783_ATLAS --jobs 6 --resources mem=8 java_mem=8 --conda-prefix /home/lauramarcos/anaconda3/envs/metamobilepicker/lib/python3.10/site-packages/snakemake 1>/home/lauramarcos/metamobile/results/V1783/log/QC/V1783_QC_out.txt 2>/home/lauramarcos/metamobile/results/V1783/log/QC/V1783_QC_error.txt touch /home/lauramarcos/metamobile/results/V1783/V1783_ATLAS/V1783_atlas.txt echo "Finished QC, copying reads" >> /home/lauramarcos/metamobile/results/V1783/log/QC/V1783_QC_out.txt # Copies the QC'ed reads to the output directory mv /home/lauramarcos/metamobile/results/V1783/V1783_ATLAS/${sample}/sequence_quality_control/${sample}_QC_R1.fastq.gz /home/lauramarcos/metamobile/results/V1783/V1783_processed_reads/V1783_QC_R1.fastq.gz mv /home/lauramarcos/metamobile/results/V1783/V1783_ATLAS/${sample}/sequence_quality_control/${sample}_QC_R2.fastq.gz /home/lauramarcos/metamobile/results/V1783/V1783_processed_reads/V1783_QC_R2.fastq.gz echo "Finished QC step" >> /home/lauramarcos/metamobile/results/V1783/log/QC/V1783_QC_out.txt (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!) Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Workflow finished with errors. [2024-05-20 16:41 CRITICAL] Command 'snakemake --use-conda --snakefile /home/lauramarcos/anaconda3/envs/metamobilepicker/lib/python3.10/site-packages/MetaMobilePicker/Snakefile --cores 16 --configfile V1783_config.yaml --rerun-incomplete --nolock --latency-wait 60 --directory /home/lauramarcos/anaconda3/envs/metamobilepicker/lib/python3.10/site-packages/MetaMobilePicker --use-singularity --singularity-prefix /home/lauramarcos/anaconda3/envs/metamobilepicker/lib/python3.10/site-packages/MetaMobilePicker/.snakemake --singularity-args '--home $PWD/.. --bind $TMPDIR,$PWD/..'' returned non-zero exit status 13. ``` ::: :upside_down_face: Creo que es por el nombre de las muestras. Pruebo quitando los guiones bajos del nombre y renombro a `V1783R1.fastq` y `V1783R2.fastq` y repito `metamobilepicker run -c V1783config.yaml ` :warning: Sigue el mismo error, parece que es algo del script *qm.sqk*, me he envalentonado y lo he cambiado. He modificado el script qm.smk tal que asi: ```python=716 rule write_read_counts: input: read_count_files=expand( "{{sample}}/sequence_quality_control/read_stats/{step}_read_counts.tsv", step=PROCESSED_STEPS, ), output: read_stats="{sample}/sequence_quality_control/read_stats/read_counts.tsv", run: import pandas as pd all_read_counts = [] for read_stats_file in input.read_count_files: d = pd.read_csv(read_stats_file, index_col=[0, 1], sep="\t") all_read_counts.append(d) all_read_counts_df = pd.concat(all_read_counts) all_read_counts_df.to_csv(output.read_stats, sep="\t") rule combine_read_counts: input: expand( "{sample}/sequence_quality_control/read_stats/read_counts.tsv", sample=SAMPLES, ), output: "stats/read_counts.tsv", run: import pandas as pd all_read_counts = [] for f in input: d = pd.read_csv(f, index_col=[0, 1], sep="\t") all_read_counts.append(d) all_read_counts_df = pd.concat(all_read_counts) all_read_counts_df.to_csv(output[0], sep="\t") ``` :::spoiler Aquí el script original: ```pyhtonh=711 localrules: combine_read_counts, write_read_counts, rule write_read_counts: input: read_count_files=expand( "{{sample}}/sequence_quality_control/read_stats/{step}_read_counts.tsv", step=PROCESSED_STEPS, ), output: read_stats="{sample}/sequence_quality_control/read_stats/read_counts.tsv", run: import pandas as pd all_read_counts = pd.DataFrame() for read_stats_file in input.read_count_files: d = pd.read_csv(read_stats_file, index_col=[0, 1], sep="\t") all_read_counts = all_read_counts.append(d) all_read_counts.to_csv(output.read_stats, sep="\t") rule combine_read_counts: input: expand( "{sample}/sequence_quality_control/read_stats/read_counts.tsv", sample=SAMPLES, ), output: "stats/read_counts.tsv", run: import pandas as pd stats = pd.DataFrame() for f in input: d = pd.read_csv(f, index_col=[0, 1], sep="\t") stats = stats.append(d) stats.to_csv(output[0], sep="\t") ``` ::: Por ahora está ejecutando y va más lejos que antes.... Pasó del Job 6. :nerd_face: **LO CONSEGUI!!!! Ahora tengo que entender los resultados... Se tardó como 10horas una muestra.** Pero creo que más no podría por espacio. Necesito usar el cluster. :helicopter: Escribir en el foro con la solución. ## Probar en cluster UAM: Script test metamobilepicker: ```bash=1 #!/bin/bash #SBATCH -p bioinfo #partition/queue name #SBATCH --job-name=metamobilepicker_test #Job name #SBATCH -n 20 #Run one thread #SBATCH -t 20:00:00 #Time limit hrs:min:sec #SBATCH --output=/home/proyectos/imdeaalim/ljmarcos/metamobile/log-%j.o #Log de salida #SBATCH --error=/home/proyectos/imdeaalim/ljmarcos/metamobile/log-%j.e #Log de errores #SBATCH --mail-user=judith.marcos@imdea.org #SBATCH --mail-type=ALL #SBATCH --mem=300G # Memory per CPU module load metamobilepicker/0.7.2 metamobilepicker run --test ``` Ejecutar `sbatch -A imdeaalim_serv -p bioinfo metamobile_test.sh ` ERROR Prueba test de nuevo: ```bash=1 #!/bin/bash #SBATCH -p bioinfo #partition/queue name #SBATCH --job-name=metamobilepicker_test #Job name #SBATCH -N 1 #SBATCH -n 16 #16 cores es el default de metamobile #SBATCH -t 5:00:00 #Time limit hrs:min:sec #SBATCH --output=/home/ljmarcos/metamobile/test/log-%j.o #Log de salida #SBATCH --error=/home/ljmarcos/metamobile/test/log-%j.e #Log de errores #SBATCH --mail-user=judith.marcos@imdea.org #SBATCH --mail-type=ALL module load metamobilepicker/0.7.2 metamobilepicker run --test ``` ERROR: Parece cosa de permisos. ``` Loading metamobilepicker/0.7.2 Loading requirement: go/1.20.2 singularity/3.11.1 Traceback (most recent call last): File "/usr/local/metamobilepicker/0.7.2/bin/snakemake", line 10, in <module> sys.exit(main()) File "/usr/local/metamobilepicker/0.7.2/lib/python3.10/site-packages/snakemake/__init__.py", line 2828, in main success = snakemake( File "/usr/local/metamobilepicker/0.7.2/lib/python3.10/site-packages/snakemake/__init__.py", line 534, in snakemake logger.setup_logfile() File "/usr/local/metamobilepicker/0.7.2/lib/python3.10/site-packages/snakemake/logging.py", line 316, in setup_logfile self.logfile_handler = _logging.FileHandler(self.logfile) File "/usr/local/metamobilepicker/0.7.2/lib/python3.10/logging/__init__.py", line 1169, in __init__ StreamHandler.__init__(self, self._open()) File "/usr/local/metamobilepicker/0.7.2/lib/python3.10/logging/__init__.py", line 1201, in _open return open_func(self.baseFilename, self.mode, PermissionError: [Errno 13] Permission denied: '/lustre/local/metamobilepicker/0.7.2/lib/python3.10/site-packages/MetaMobilePicker/.snakemake/log/2024-05-13T155842.992691.snakemake.log' [2024-05-13 15:58 CRITICAL] Command 'snakemake --use-conda --snakefile /lustre/local/metamobilepicker/0.7.2/lib/python3.10/site-packages/MetaMobilePicker/Snakefile --cores 16 --configfile /lustre/local/metamobilepicker/0.7.2/lib/python3.10/site-packages/MetaMobilePicker/config/test.yaml --rerun-incomplete --nolock --latency-wait 60 --directory /lustre/local/metamobilepicker/0.7.2/lib/python3.10/site-packages/MetaMobilePicker --use-singularity --singularity-prefix /lustre/local/metamobilepicker/0.7.2/lib/python3.10/site-packages/MetaMobilePicker/.snakemake --singularity-args '--home $PWD/.. --bind $TMPDIR,$PWD/..'' returned non-zero exit status 1. ``` :nerd_face: **Escribo al UCC** :::spoiler >Buenas tardes, > >Escribo porque estoy teniendo problemas para ejecutar metamobilepicker y creo que es por tema de permisos. El programa tiene una serie de scripts con snakemake y no puede escribir el el directorio > >/lustre/local/metamobilepicker/0.7.2/lib/python3.10/site-packages/MetaMobilePicker/.snakemake/log/ > >No sé si podriais otorgarme permiso de escritura para ese directorio o si podemos instalar el programa en un directorio donde si tenga permisos. > >Adjunto el log de error, para que verifiquen que el problema es el que creo y en caso que no sea así si me podeis ayudar a resolverlo. > >Gracias de antemano, > >Laura ::: PENDIENTE: Intentar con muestras: ```bash=1 #!/bin/bash #SBATCH -p bioinfo #partition/queue name #SBATCH --job-name=woltka #Job name #SBATCH -N 1 #Un nodo #SBATCH -n 40 #Veinte cores #SBATCH -t 8:00:00 #Time limit hrs:min:sec #SBATCH --output=/home/ljmarcos/woltka/log-%j.o #Log de salida #SBATCH --error=/home/ljmarcos/woltka/log-%j.e #Log de errores #SBATCH --mail-user=judith.marcos@imdea.org #SBATCH --mail-type=END,FAIL module load metamobilepicker/0.7.2 metamobilepicker config --samples sample_meta.txt --output V1_783_config.yaml --outdir out_meta metamobilepicker run -c V1_783_config.yaml ``` Creo que va a petar porque puse 40 cores y usa solo 16, debo indicar con-C en metamobile ### Prueba script implementando archivos temp para evitar problemas de espacio ```bash=1 #!/bin/bash #SBATCH -p bioinfo #partition/queue name #SBATCH --job-name=metamobile1 #Job name #SBATCH -N 1 #Un nodo #SBATCH -n 16 #Lo que tiene por default metamobile #SBATCH -t 20:00:00 #Time limit hrs:min:sec #SBATCH --output=/home/ljmarcos/metamobile/log-%j.o #Log de salida #SBATCH --error=/home/ljmarcos/metamobile/log-%j.e #Log de errores #SBATCH --mail-user=judith.marcos@alimentacion.imdea.org #SBATCH --mail-type=END,FAIL # Copiar a temporal los ficheros de entrada necesarios para metamobile mkdir /temporal/$SLURM_JOB_USER/$SLURM_JOB_ID cp -r clean_data /temporal/$SLURM_JOB_USER/$SLURM_JOB_ID cd /temporal/$SLURM_JOB_USER/$SLURM_JOB_ID mkdir /temporal/$SLURM_JOB_USER/$SLURM_JOB_ID/output # Ejecutar el comando Metamobile metamobilepicker config --samples clean_data/samples.txt --output V1_783config.yaml --outdir /temporal/$SLURM_JOB_USER/$SLURM_JOB_ID/output metamobilepicker run -c V1_783config.yaml # Mover a imdeaalim los resultados del cálculo. mv -r /temporal/$SLURM_JOB_USER/$SLURM_JOB_ID/output /lustre/NodoBIO/imdeaalim/ljmarcos/output ``` #!/bin/bash #SBATCH -p bioinfo #partition/queue name #SBATCH --job-name=metamobile1 #Job name #SBATCH -N 1 #Un nodo #SBATCH -n 4 #Lo que tiene por default metamobile #SBATCH -t 1:00:00 #Time limit hrs:min:sec #SBATCH --output=/home/ljmarcos/metamobile/log-%j.o #Log de salida #SBATCH --error=/home/ljmarcos/metamobile/log-%j.e #Log de errores #SBATCH --mail-user=judith.marcos@alimentacion.imdea.org #SBATCH --mail-type=END,FAIL git clone https://github.com/Microbial-Ecology-Group/AMRplusplus.git Esto funcionó: ``` #!/bin/bash #SBATCH -p bioinfo #partition/queue name #SBATCH --job-name=metamobile1 #Job name #SBATCH -N 1 #Un nodo #SBATCH -n 16 #Lo que tiene por default metamobile #SBATCH -t 20:00:00 #Time limit hrs:min:sec #SBATCH --output=/home/ljmarcos/metamobile/log-%j.o #Log de salida #SBATCH --error=/home/ljmarcos/metamobile/log-%j.e #Log de errores #SBATCH --mail-user=judith.marcos@alimentacion.imdea.org #SBATCH --mail-type=END,FAIL # Copiar a temporal los ficheros de entrada necesarios para metamobile mkdir /temporal/$SLURM_JOB_USER/$SLURM_JOB_ID cp -r data /temporal/$SLURM_JOB_USER/$SLURM_JOB_ID cd /temporal/$SLURM_JOB_USER/$SLURM_JOB_ID mkdir output # Ejecutar el comando Metamobile module load metamobilepicker/0.7.2 metamobilepicker config --samples data/sample.txt --output V1_783config.yaml --outdir output metamobilepicker run -c V1_783config.yaml # Mover a imdeaalim los resultados del cálculo. mv output /lustre/NodoBIO/imdeaalim/ljmarcos/output ```