[2024-01-24 10:47:24,301] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:24,305] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:24,306] [INFO] DQC Reference Directory: /var/lib/cwl/stgc9105ea3-d766-4f67-91d4-25e046befaa0/dqc_reference
[2024-01-24 10:47:26,304] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:26,305] [INFO] Task started: Prodigal
[2024-01-24 10:47:26,305] [INFO] Running command: gunzip -c /var/lib/cwl/stg54bcc0c2-1bc9-48c1-84c0-0e9b5d09fe1e/GCF_900018365.1_IMG-taxon_2615840617_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900018365.1_IMG-taxon_2615840617_annotated_assembly_genomic.fna/cds.fna -a GCF_900018365.1_IMG-taxon_2615840617_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:32,870] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:32,871] [INFO] Task started: HMMsearch
[2024-01-24 10:47:32,871] [INFO] Running command: hmmsearch --tblout GCF_900018365.1_IMG-taxon_2615840617_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc9105ea3-d766-4f67-91d4-25e046befaa0/dqc_reference/reference_markers.hmm GCF_900018365.1_IMG-taxon_2615840617_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:33,107] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:33,110] [INFO] Found 6/6 markers.
[2024-01-24 10:47:33,136] [INFO] Query marker FASTA was written to GCF_900018365.1_IMG-taxon_2615840617_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 10:47:33,136] [INFO] Task started: Blastn
[2024-01-24 10:47:33,136] [INFO] Running command: blastn -query GCF_900018365.1_IMG-taxon_2615840617_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9105ea3-d766-4f67-91d4-25e046befaa0/dqc_reference/reference_markers.fasta -out GCF_900018365.1_IMG-taxon_2615840617_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:33,730] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:33,734] [INFO] Selected 16 target genomes.
[2024-01-24 10:47:33,734] [INFO] Target genome list was writen to GCF_900018365.1_IMG-taxon_2615840617_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 10:47:33,750] [INFO] Task started: fastANI
[2024-01-24 10:47:33,751] [INFO] Running command: fastANI --query /var/lib/cwl/stg54bcc0c2-1bc9-48c1-84c0-0e9b5d09fe1e/GCF_900018365.1_IMG-taxon_2615840617_annotated_assembly_genomic.fna.gz --refList GCF_900018365.1_IMG-taxon_2615840617_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900018365.1_IMG-taxon_2615840617_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:43,408] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:43,409] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc9105ea3-d766-4f67-91d4-25e046befaa0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:43,409] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc9105ea3-d766-4f67-91d4-25e046befaa0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:43,417] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:47:43,417] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:43,417] [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
Apibacter mensalis	strain=R-53146	GCA_900018365.1	1586267	1586267	type	True	100.0	751	755	95	conclusive
Apibacter mensalis	strain=R-53146	GCA_001418685.1	1586267	1586267	type	True	100.0	751	755	95	conclusive
Apibacter raozihei	strain=HY041	GCA_004014855.1	2500547	2500547	type	True	77.6038	200	755	95	below_threshold
Apibacter adventoris	strain=wkB301	GCA_002964975.1	1679466	1679466	type	True	77.4825	253	755	95	below_threshold
Apibacter muscae	strain=G8	GCA_007845635.1	2509004	2509004	type	True	77.1227	151	755	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:43,418] [INFO] DFAST Taxonomy check result was written to GCF_900018365.1_IMG-taxon_2615840617_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 10:47:43,419] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:43,419] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:43,419] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc9105ea3-d766-4f67-91d4-25e046befaa0/dqc_reference/checkm_data
[2024-01-24 10:47:43,420] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:43,450] [INFO] Task started: CheckM
[2024-01-24 10:47:43,451] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900018365.1_IMG-taxon_2615840617_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900018365.1_IMG-taxon_2615840617_annotated_assembly_genomic.fna/checkm_input GCF_900018365.1_IMG-taxon_2615840617_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 10:48:08,737] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:08,738] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:08,757] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:08,757] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:08,758] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900018365.1_IMG-taxon_2615840617_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 10:48:08,758] [INFO] Task started: Blastn
[2024-01-24 10:48:08,758] [INFO] Running command: blastn -query GCF_900018365.1_IMG-taxon_2615840617_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9105ea3-d766-4f67-91d4-25e046befaa0/dqc_reference/reference_markers_gtdb.fasta -out GCF_900018365.1_IMG-taxon_2615840617_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:09,668] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:09,671] [INFO] Selected 17 target genomes.
[2024-01-24 10:48:09,671] [INFO] Target genome list was writen to GCF_900018365.1_IMG-taxon_2615840617_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:09,684] [INFO] Task started: fastANI
[2024-01-24 10:48:09,685] [INFO] Running command: fastANI --query /var/lib/cwl/stg54bcc0c2-1bc9-48c1-84c0-0e9b5d09fe1e/GCF_900018365.1_IMG-taxon_2615840617_annotated_assembly_genomic.fna.gz --refList GCF_900018365.1_IMG-taxon_2615840617_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900018365.1_IMG-taxon_2615840617_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:19,262] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:19,269] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:19,269] [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_001418685.1	s__Apibacter mensalis	100.0	752	755	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Apibacter	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_011082725.1	s__Apibacter sp002964915	84.7882	617	755	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Apibacter	95.0	97.29	96.74	0.93	0.90	15	-
GCF_004014855.1	s__Apibacter raozihei	77.6358	198	755	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Apibacter	95.0	98.39	98.39	0.93	0.93	2	-
GCF_002964975.1	s__Apibacter adventoris	77.4703	254	755	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Apibacter	95.0	98.15	98.15	0.92	0.92	2	-
GCF_007845635.1	s__Apibacter muscae	77.1768	148	755	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Apibacter	95.0	97.91	97.54	0.94	0.93	3	-
GCF_003710065.1	s__Chryseobacterium nematophagum_B	76.141	51	755	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	95.50	95.50	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:19,271] [INFO] GTDB search result was written to GCF_900018365.1_IMG-taxon_2615840617_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:19,271] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:19,273] [INFO] DFAST_QC result json was written to GCF_900018365.1_IMG-taxon_2615840617_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 10:48:19,273] [INFO] DFAST_QC completed!
[2024-01-24 10:48:19,273] [INFO] Total running time: 0h0m55s