[2024-01-24 13:37:26,133] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:26,135] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:26,136] [INFO] DQC Reference Directory: /var/lib/cwl/stg7ac54f5f-3cfa-4e3a-a5c4-5314c9149f4d/dqc_reference
[2024-01-24 13:37:27,392] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:27,395] [INFO] Task started: Prodigal
[2024-01-24 13:37:27,395] [INFO] Running command: gunzip -c /var/lib/cwl/stga1e25a8b-4c2a-44ee-8a25-636cea5e304b/GCF_013340765.1_NAS2_1.0_genomic.fna.gz | prodigal -d GCF_013340765.1_NAS2_1.0_genomic.fna/cds.fna -a GCF_013340765.1_NAS2_1.0_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:34,673] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:34,673] [INFO] Task started: HMMsearch
[2024-01-24 13:37:34,673] [INFO] Running command: hmmsearch --tblout GCF_013340765.1_NAS2_1.0_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7ac54f5f-3cfa-4e3a-a5c4-5314c9149f4d/dqc_reference/reference_markers.hmm GCF_013340765.1_NAS2_1.0_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:34,833] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:34,834] [WARNING] Found 1/6 markers. [/var/lib/cwl/stga1e25a8b-4c2a-44ee-8a25-636cea5e304b/GCF_013340765.1_NAS2_1.0_genomic.fna.gz]
[2024-01-24 13:37:34,853] [INFO] Query marker FASTA was written to GCF_013340765.1_NAS2_1.0_genomic.fna/markers.fasta
[2024-01-24 13:37:34,854] [INFO] Task started: Blastn
[2024-01-24 13:37:34,854] [INFO] Running command: blastn -query GCF_013340765.1_NAS2_1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ac54f5f-3cfa-4e3a-a5c4-5314c9149f4d/dqc_reference/reference_markers.fasta -out GCF_013340765.1_NAS2_1.0_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:35,293] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:35,296] [INFO] Selected 1 target genomes.
[2024-01-24 13:37:35,296] [INFO] Target genome list was writen to GCF_013340765.1_NAS2_1.0_genomic.fna/target_genomes.txt
[2024-01-24 13:37:35,297] [INFO] Task started: fastANI
[2024-01-24 13:37:35,297] [INFO] Running command: fastANI --query /var/lib/cwl/stga1e25a8b-4c2a-44ee-8a25-636cea5e304b/GCF_013340765.1_NAS2_1.0_genomic.fna.gz --refList GCF_013340765.1_NAS2_1.0_genomic.fna/target_genomes.txt --output GCF_013340765.1_NAS2_1.0_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:35,993] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:35,993] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7ac54f5f-3cfa-4e3a-a5c4-5314c9149f4d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:35,993] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7ac54f5f-3cfa-4e3a-a5c4-5314c9149f4d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:35,996] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:35,997] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:35,997] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Conexivisphaera calida	strain=NAS-02	GCA_013340765.1	1874277	1874277	type	True	100.0	531	531	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:37:35,998] [INFO] DFAST Taxonomy check result was written to GCF_013340765.1_NAS2_1.0_genomic.fna/tc_result.tsv
[2024-01-24 13:37:35,999] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:35,999] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:35,999] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7ac54f5f-3cfa-4e3a-a5c4-5314c9149f4d/dqc_reference/checkm_data
[2024-01-24 13:37:36,000] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:36,018] [INFO] Task started: CheckM
[2024-01-24 13:37:36,019] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013340765.1_NAS2_1.0_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013340765.1_NAS2_1.0_genomic.fna/checkm_input GCF_013340765.1_NAS2_1.0_genomic.fna/checkm_result
[2024-01-24 13:38:00,398] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:00,399] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.79%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:00,414] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:00,415] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:00,415] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013340765.1_NAS2_1.0_genomic.fna/markers.fasta)
[2024-01-24 13:38:00,415] [INFO] Task started: Blastn
[2024-01-24 13:38:00,415] [INFO] Running command: blastn -query GCF_013340765.1_NAS2_1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ac54f5f-3cfa-4e3a-a5c4-5314c9149f4d/dqc_reference/reference_markers_gtdb.fasta -out GCF_013340765.1_NAS2_1.0_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:00,831] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:00,834] [INFO] Selected 2 target genomes.
[2024-01-24 13:38:00,834] [INFO] Target genome list was writen to GCF_013340765.1_NAS2_1.0_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:00,838] [INFO] Task started: fastANI
[2024-01-24 13:38:00,838] [INFO] Running command: fastANI --query /var/lib/cwl/stga1e25a8b-4c2a-44ee-8a25-636cea5e304b/GCF_013340765.1_NAS2_1.0_genomic.fna.gz --refList GCF_013340765.1_NAS2_1.0_genomic.fna/target_genomes_gtdb.txt --output GCF_013340765.1_NAS2_1.0_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:01,713] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:01,716] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:01,716] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_013340765.1	s__Conexivisphaera calida	100.0	531	531	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Conexivisphaerales;f__Conexivisphaeraceae;g__Conexivisphaera	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_011054345.1	s__Conexivisphaera sp011054345	78.7439	219	531	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Conexivisphaerales;f__Conexivisphaeraceae;g__Conexivisphaera	95.0	97.80	97.80	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:01,718] [INFO] GTDB search result was written to GCF_013340765.1_NAS2_1.0_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:01,719] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:01,720] [INFO] DFAST_QC result json was written to GCF_013340765.1_NAS2_1.0_genomic.fna/dqc_result.json
[2024-01-24 13:38:01,720] [INFO] DFAST_QC completed!
[2024-01-24 13:38:01,720] [INFO] Total running time: 0h0m36s