[2023-06-08 07:24:04,356] [INFO] DFAST_QC pipeline started.
[2023-06-08 07:24:04,373] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 07:24:04,373] [INFO] DQC Reference Directory: /var/lib/cwl/stgcf440e08-18e7-417b-acad-17eed26f9ea1/dqc_reference
[2023-06-08 07:24:06,263] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 07:24:06,264] [INFO] Task started: Prodigal
[2023-06-08 07:24:06,265] [INFO] Running command: gunzip -c /var/lib/cwl/stg57cfd14e-12f2-4cc7-9650-f6e6349e3561/GCA_902521925.1_AG-894-P15_genomic.fna.gz | prodigal -d GCA_902521925.1_AG-894-P15_genomic.fna/cds.fna -a GCA_902521925.1_AG-894-P15_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 07:24:07,206] [INFO] Task succeeded: Prodigal
[2023-06-08 07:24:07,206] [INFO] Task started: HMMsearch
[2023-06-08 07:24:07,206] [INFO] Running command: hmmsearch --tblout GCA_902521925.1_AG-894-P15_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcf440e08-18e7-417b-acad-17eed26f9ea1/dqc_reference/reference_markers.hmm GCA_902521925.1_AG-894-P15_genomic.fna/protein.faa > /dev/null
[2023-06-08 07:24:07,362] [INFO] Task succeeded: HMMsearch
[2023-06-08 07:24:07,364] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg57cfd14e-12f2-4cc7-9650-f6e6349e3561/GCA_902521925.1_AG-894-P15_genomic.fna.gz]
[2023-06-08 07:24:07,376] [INFO] Query marker FASTA was written to GCA_902521925.1_AG-894-P15_genomic.fna/markers.fasta
[2023-06-08 07:24:07,376] [INFO] Task started: Blastn
[2023-06-08 07:24:07,377] [INFO] Running command: blastn -query GCA_902521925.1_AG-894-P15_genomic.fna/markers.fasta -db /var/lib/cwl/stgcf440e08-18e7-417b-acad-17eed26f9ea1/dqc_reference/reference_markers.fasta -out GCA_902521925.1_AG-894-P15_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 07:24:09,601] [INFO] Task succeeded: Blastn
[2023-06-08 07:24:09,605] [INFO] Selected 5 target genomes.
[2023-06-08 07:24:09,605] [INFO] Target genome list was writen to GCA_902521925.1_AG-894-P15_genomic.fna/target_genomes.txt
[2023-06-08 07:24:09,606] [INFO] Task started: fastANI
[2023-06-08 07:24:09,606] [INFO] Running command: fastANI --query /var/lib/cwl/stg57cfd14e-12f2-4cc7-9650-f6e6349e3561/GCA_902521925.1_AG-894-P15_genomic.fna.gz --refList GCA_902521925.1_AG-894-P15_genomic.fna/target_genomes.txt --output GCA_902521925.1_AG-894-P15_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 07:24:11,112] [INFO] Task succeeded: fastANI
[2023-06-08 07:24:11,113] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcf440e08-18e7-417b-acad-17eed26f9ea1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 07:24:11,114] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcf440e08-18e7-417b-acad-17eed26f9ea1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 07:24:11,116] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 07:24:11,116] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 07:24:11,116] [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
--------------------------------------------------------------------------------
[2023-06-08 07:24:11,118] [INFO] DFAST Taxonomy check result was written to GCA_902521925.1_AG-894-P15_genomic.fna/tc_result.tsv
[2023-06-08 07:24:11,119] [INFO] ===== Taxonomy check completed =====
[2023-06-08 07:24:11,119] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 07:24:11,119] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcf440e08-18e7-417b-acad-17eed26f9ea1/dqc_reference/checkm_data
[2023-06-08 07:24:11,124] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 07:24:11,131] [INFO] Task started: CheckM
[2023-06-08 07:24:11,132] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902521925.1_AG-894-P15_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902521925.1_AG-894-P15_genomic.fna/checkm_input GCA_902521925.1_AG-894-P15_genomic.fna/checkm_result
[2023-06-08 07:24:23,665] [INFO] Task succeeded: CheckM
[2023-06-08 07:24:23,667] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 37.50%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 07:24:23,686] [INFO] ===== Completeness check finished =====
[2023-06-08 07:24:23,686] [INFO] ===== Start GTDB Search =====
[2023-06-08 07:24:23,686] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902521925.1_AG-894-P15_genomic.fna/markers.fasta)
[2023-06-08 07:24:23,687] [INFO] Task started: Blastn
[2023-06-08 07:24:23,687] [INFO] Running command: blastn -query GCA_902521925.1_AG-894-P15_genomic.fna/markers.fasta -db /var/lib/cwl/stgcf440e08-18e7-417b-acad-17eed26f9ea1/dqc_reference/reference_markers_gtdb.fasta -out GCA_902521925.1_AG-894-P15_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 07:24:24,236] [INFO] Task succeeded: Blastn
[2023-06-08 07:24:24,241] [INFO] Selected 5 target genomes.
[2023-06-08 07:24:24,242] [INFO] Target genome list was writen to GCA_902521925.1_AG-894-P15_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 07:24:24,243] [INFO] Task started: fastANI
[2023-06-08 07:24:24,244] [INFO] Running command: fastANI --query /var/lib/cwl/stg57cfd14e-12f2-4cc7-9650-f6e6349e3561/GCA_902521925.1_AG-894-P15_genomic.fna.gz --refList GCA_902521925.1_AG-894-P15_genomic.fna/target_genomes_gtdb.txt --output GCA_902521925.1_AG-894-P15_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 07:24:25,250] [INFO] Task succeeded: fastANI
[2023-06-08 07:24:25,258] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 07:24:25,259] [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_001179985.1	s__Pelagibacter ubique_J	95.4407	80	97	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902622545.1	s__Pelagibacter sp902622545	90.7853	86	97	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	99.84	99.73	0.95	0.94	4	-
GCA_902600485.1	s__Pelagibacter sp902600485	90.2819	71	97	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	95.74	95.74	0.88	0.88	2	-
GCA_902610315.1	s__Pelagibacter sp902610315	90.1239	74	97	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 07:24:25,261] [INFO] GTDB search result was written to GCA_902521925.1_AG-894-P15_genomic.fna/result_gtdb.tsv
[2023-06-08 07:24:25,261] [INFO] ===== GTDB Search completed =====
[2023-06-08 07:24:25,264] [INFO] DFAST_QC result json was written to GCA_902521925.1_AG-894-P15_genomic.fna/dqc_result.json
[2023-06-08 07:24:25,264] [INFO] DFAST_QC completed!
[2023-06-08 07:24:25,265] [INFO] Total running time: 0h0m21s