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[billytaj]

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[yeolex]

Hi, please help us. We are running the MetarproTutorial but we don't get it. We suspected the pipeline/Metapro.py has more comands than config_mouse_tutorial.ini because the script python3 pipeline/MetaPro.py -c $config -s $read1 -o $output --tutorial quality recognize all the paths of databases and files, but is doesn't found Labels and others. When we run the pipeline obtain this messages:

CHECKING CONFIG
USING CONFIG /MetaPro_docker_tutorial/config_mouse_tutorial.ini
target_rank found! using: genus
AdapterRemoval_minlength found! using: 30
Show_unclassified found! using: No
bypass_log_name no inner section found. using default bypass_log.txt
debug_stop_flag no inner section found. using default none
num_threads no inner section found. using default 12
taxa_existence_cutoff no inner section found. using default 0.1
DNA_DB_mode no inner section found. using default chocophlan
RPKM_cutoff found! using: 0.01
BWA_cigar_cutoff found! using: 90
BLAT_identity_cutoff found! using: 85
BLAT_length_cutoff found! using: 0.65
BLAT_score_cutoff found! using: 60
DIAMOND_identity_cutoff found! using: 85
DIAMOND_length_cutoff found! using: 0.65
DIAMOND_score_cutoff found! using: 60
BWA_mem_footprint no inner section found. using default 5
BLAT_mem_footprint no inner section found. using default 5
DMD_mem_footprint no inner section found. using default 10
BWA_mem_threshold found! using: 60
BLAT_mem_threshold found! using: 60
DIAMOND_mem_threshold found! using: 60
DETECT_mem_threshold found! using: 60
Infernal_mem_threshold found! using: 60
Barrnap_mem_threshold found! using: 60
BWA_pp_mem_threshold found! using: 60
BLAT_pp_mem_threshold found! using: 60
DIAMOND_pp_mem_threshold found! using: 60
GA_final_merge_mem_threshold no inner section found. using default 5
TA_mem_threshold found! using: 60
repop_mem_threshold no inner section found. using default 50
EC_mem_threshold no inner section found. using default 5
BWA_job_limit found! using: 10
BLAT_job_limit found! using: 10
DIAMOND_job_limit found! using: 10
DETECT_job_limit found! using: 10
Infernal_job_limit found! using: 10
Barrnap_job_limit found! using: 10
BWA_pp_job_limit found! using: 10
BLAT_pp_job_limit found! using: 10
DIAMOND_pp_job_limit found! using: 10
GA_final_merge_job_limit no inner section found. using default 9
TA_job_limit no inner section found. using default 9
repop_job_limit no inner section found. using default 1
EC_job_limit no inner section found. using default 9
Centrifuge_job_limit no inner section found. using default 1
Infernal_job_delay no inner section found. using default 5
Barrnap_job_delay no inner section found. using default 5
BWA_job_delay found! using: 5
BLAT_job_delay found! using: 0.005
DIAMOND_job_delay found! using: 5
DETECT_job_delay no inner section found. using default 5
BWA_pp_job_delay found! using: 5
BLAT_pp_job_delay found! using: 0.05
DIAMOND_pp_job_delay found! using: 5
GA_final_merge_job_delay no inner section found. using default 5
TA_job_delay found! using: 10
repop_job_delay no inner section found. using default 10
EC_job_delay no inner section found. using default 1
keep_all found! using: yes
keep_quality found! using: no
keep_host found! using: no
keep_vector found! using: no
keep_rRNA found! using: no
keep_repop found! using: no
keep_assemble_contigs found! using: no
keep_GA_BWA found! using: no
keep_GA_BLAT found! using: no
keep_GA_DIAMOND found! using: no
keep_GA_final found! using: no
keep_TA found! using: no
keep_EC found! using: no
keep_outputs found! using: no
filter_stringency found! using: high
GA_chunk_size found! using: 50000
EC_chunk_size no inner section found. using default 50000
rRNA_chunk_size found! using: 50000
Labels no section found, using default: quality_filter
Labels no section found, using default: host_filter
Labels no section found, using default: vector_filter
Labels no section found, using default: rRNA_filter
Labels no section found, using default: rRNA_filter_split
Labels no section found, using default: rRNA_filter_convert
Labels no section found, using default: rRNA_filter_barrnap
Labels no section found, using default: rRNA_filter_barrnap_merge
Labels no section found, using default: rRNA_filter_barrnap_pp
Labels no section found, using default: rRNA_filter_infernal
Labels no section found, using default: rRNA_filter_infernal_prep
Labels no section found, using default: rRNA_filter_splitter
Labels no section found, using default: rRNA_filter_post
Labels no section found, using default: duplicate_repopulation
Labels no section found, using default: assemble_contigs
Labels no section found, using default: destroy_contigs
Labels no section found, using default: GA_pre_scan
Labels no section found, using default: GA_split
Labels no section found, using default: GA_BWA
Labels no section found, using default: GA_BWA_pp
Labels no section found, using default: GA_BWA_merge
Labels no section found, using default: GA_BLAT
Labels no section found, using default: GA_BLAT_cleanup
Labels no section found, using default: GA_BLAT_cat
Labels no section found, using default: GA_BLAT_pp
Labels no section found, using default: GA_BLAT_merge
Labels no section found, using default: GA_DMD
Labels no section found, using default: GA_DMD_pp
Labels no section found, using default: GA_final_merge
Labels no section found, using default: taxonomic_annotation
Labels no section found, using default: enzyme_annotation
Labels no section found, using default: enzyme_annotation_detect
Labels no section found, using default: enzyme_annotation_priam
Labels no section found, using default: enzyme_annotation_priam_split
Labels no section found, using default: enzyme_annotation_priam_cat
Labels no section found, using default: enzyme_annotation_DMD
Labels no section found, using default: enzyme_annotation_pp
Labels no section found, using default: outputs
Labels no section found, using default: output_copy_gene_map
Labels no section found, using default: output_clean_ec
Labels no section found, using default: output_copy_taxa
Labels no section found, using default: output_network_generation
Labels no section found, using default: output_unique_hosts_singletons
Labels no section found, using default: output_unique_hosts_pair_1
Labels no section found, using default: output_unique_hosts_pair_2
Labels no section found, using default: output_unique_vectors_singletons
Labels no section found, using default: output_unique_vectors_pair_1
Labels no section found, using default: output_unique_vectors_pair_2
Labels no section found, using default: output_combine_hosts
Labels no section found, using default: output_per_read_scores
Labels no section found, using default: output_contig_stats
Labels no section found, using default: output_ec_heatmap
Labels no section found, using default: output_taxa_groupby
Labels no section found, using default: output_read_count
UniVec_Core found! using: /MetaPro_docker_tutorial/databases//UniVec_Core.fasta
Adapter found! using: /MetaPro_docker_tutorial/databases//TruSeq3-PE-2.fa
Host found! using: /MetaPro_docker_tutorial/databases//Mouse_cds.fasta
Rfam found! using: /MetaPro_docker_tutorial/databases//Rfam/Rfam.cm
DNA_DB no inner section found. using default /project/j/jparkin/Lab_Databases/ChocoPhlAn/ChocoPhlAn.fasta
source_taxa_db no inner section found. using default /project/j/jparkin/Lab_Databases/family_llbs
Prot_DB no inner section found. using default /project/j/jparkin/Lab_Databases/nr/nr
Prot_DB_reads no inner section found. using default /project/j/jparkin/Lab_Databases/nr/nr
accession2taxid no inner section found. using default /project/j/jparkin/Lab_Databases/accession2taxid/accession2taxid
nodes found! using: /MetaPro_docker_tutorial/databases//nodes.dmp
names found! using: /MetaPro_docker_tutorial/databases//names.dmp
Kaiju_db no inner section found. using default /project/j/jparkin/Lab_Databases/kaiju_db/kaiju_db_nr.fmi
Centrifuge_db no inner section found. using default /project/j/jparkin/Lab_Databases/centrifuge_db/nt
SWISS_PROT no inner section found. using default /project/j/jparkin/Lab_Databases/swiss_prot_db/swiss_prot_db
SWISS_PROT_map no inner section found. using default /project/j/jparkin/Lab_Databases/swiss_prot_db/SwissProt_EC_Mapping.tsv
PriamDB no inner section found. using default /project/j/jparkin/Lab_Databases/PRIAM_db/
DetectDB no inner section found. using default /project/j/jparkin/Lab_Databases/DETECTv2
WEVOTEDB no inner section found. using default /project/j/jparkin/Lab_Databases/WEVOTE_db/
EC_pathway no inner section found. using default /project/j/jparkin/Lab_Databases/EC_pathway.txt
path_to_superpath found! using: /pipeline/custom_databases/pathway_to_superpathway.csv
MetaGeneMark_model found! using: /pipeline_tools/mgm/MetaGeneMark_v1.mod
enzyme_db found! using: /pipeline/custom_databases/FREQ_EC_pairs_3_mai_2020.txt
taxid_tree no inner section found. using default /pipeline/custom_databases/taxid_trees/family_tree.tsv
kraken2_db no inner section found. using default /pipeline/custom_databases/kraken2_db
dir name: /project/j/jparkin/Lab_Databases/nr
file name: nr
/project/j/jparkin/Lab_Databases/nr/nr
file does not exists

We now that are so many steps with a # , so we think that some errors like nr files does not exists would not matter.

thank's