[2024-01-24 13:32:43,016] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:43,019] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:43,019] [INFO] DQC Reference Directory: /var/lib/cwl/stg0ba022a9-64d3-4f0c-9871-f806a15ae379/dqc_reference
[2024-01-24 13:32:44,495] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:44,496] [INFO] Task started: Prodigal
[2024-01-24 13:32:44,496] [INFO] Running command: gunzip -c /var/lib/cwl/stg09566c12-cdbb-4c9b-b125-8d2e30ea0a88/GCF_900177375.1_IMG-taxon_2708742538_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900177375.1_IMG-taxon_2708742538_annotated_assembly_genomic.fna/cds.fna -a GCF_900177375.1_IMG-taxon_2708742538_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:54,193] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:54,194] [INFO] Task started: HMMsearch
[2024-01-24 13:32:54,194] [INFO] Running command: hmmsearch --tblout GCF_900177375.1_IMG-taxon_2708742538_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0ba022a9-64d3-4f0c-9871-f806a15ae379/dqc_reference/reference_markers.hmm GCF_900177375.1_IMG-taxon_2708742538_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:54,539] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:54,541] [INFO] Found 6/6 markers.
[2024-01-24 13:32:54,601] [INFO] Query marker FASTA was written to GCF_900177375.1_IMG-taxon_2708742538_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:32:54,601] [INFO] Task started: Blastn
[2024-01-24 13:32:54,601] [INFO] Running command: blastn -query GCF_900177375.1_IMG-taxon_2708742538_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ba022a9-64d3-4f0c-9871-f806a15ae379/dqc_reference/reference_markers.fasta -out GCF_900177375.1_IMG-taxon_2708742538_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:55,250] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:55,253] [INFO] Selected 10 target genomes.
[2024-01-24 13:32:55,254] [INFO] Target genome list was writen to GCF_900177375.1_IMG-taxon_2708742538_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:32:55,258] [INFO] Task started: fastANI
[2024-01-24 13:32:55,258] [INFO] Running command: fastANI --query /var/lib/cwl/stg09566c12-cdbb-4c9b-b125-8d2e30ea0a88/GCF_900177375.1_IMG-taxon_2708742538_annotated_assembly_genomic.fna.gz --refList GCF_900177375.1_IMG-taxon_2708742538_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900177375.1_IMG-taxon_2708742538_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:02,036] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:02,037] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0ba022a9-64d3-4f0c-9871-f806a15ae379/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:02,037] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0ba022a9-64d3-4f0c-9871-f806a15ae379/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:02,043] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:33:02,044] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:33:02,044] [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
Maridesulfovibrio frigidus	strain=DSM 17176	GCA_000711735.1	340956	340956	type	True	79.7288	509	1314	95	below_threshold
Maridesulfovibrio hydrothermalis	strain=DSM 14728	GCA_000425245.1	191026	191026	type	True	78.1209	307	1314	95	below_threshold
Maridesulfovibrio hydrothermalis	strain=AM13	GCA_000331025.1	191026	191026	type	True	77.9679	320	1314	95	below_threshold
Maridesulfovibrio zosterae	strain=DSM 11974	GCA_000425265.1	82171	82171	type	True	77.8219	309	1314	95	below_threshold
Maridesulfovibrio salexigens	strain=DSM 2638	GCA_000023445.1	880	880	type	True	77.4971	247	1314	95	below_threshold
Maridesulfovibrio bastinii	strain=DSM 16055	GCA_000429985.1	47157	47157	type	True	77.0086	158	1314	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:02,045] [INFO] DFAST Taxonomy check result was written to GCF_900177375.1_IMG-taxon_2708742538_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:33:02,045] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:02,046] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:02,046] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0ba022a9-64d3-4f0c-9871-f806a15ae379/dqc_reference/checkm_data
[2024-01-24 13:33:02,047] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:02,086] [INFO] Task started: CheckM
[2024-01-24 13:33:02,086] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900177375.1_IMG-taxon_2708742538_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900177375.1_IMG-taxon_2708742538_annotated_assembly_genomic.fna/checkm_input GCF_900177375.1_IMG-taxon_2708742538_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:33:35,653] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:35,654] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:35,673] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:35,674] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:35,674] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900177375.1_IMG-taxon_2708742538_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:33:35,674] [INFO] Task started: Blastn
[2024-01-24 13:33:35,675] [INFO] Running command: blastn -query GCF_900177375.1_IMG-taxon_2708742538_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ba022a9-64d3-4f0c-9871-f806a15ae379/dqc_reference/reference_markers_gtdb.fasta -out GCF_900177375.1_IMG-taxon_2708742538_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:36,522] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:36,527] [INFO] Selected 8 target genomes.
[2024-01-24 13:33:36,527] [INFO] Target genome list was writen to GCF_900177375.1_IMG-taxon_2708742538_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:36,538] [INFO] Task started: fastANI
[2024-01-24 13:33:36,538] [INFO] Running command: fastANI --query /var/lib/cwl/stg09566c12-cdbb-4c9b-b125-8d2e30ea0a88/GCF_900177375.1_IMG-taxon_2708742538_annotated_assembly_genomic.fna.gz --refList GCF_900177375.1_IMG-taxon_2708742538_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900177375.1_IMG-taxon_2708742538_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:44,016] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:44,025] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:44,026] [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_900177375.1	s__Maridesulfovibrio gilichinskyi	100.0	1314	1314	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Maridesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_006210265.1	s__Maridesulfovibrio sp006210265	88.3203	1092	1314	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Maridesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101105.1	s__Maridesulfovibrio ferrireducens	82.4007	845	1314	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Maridesulfovibrio	95.0	95.27	95.27	0.87	0.87	2	-
GCF_000711735.1	s__Maridesulfovibrio frigidus	79.7189	510	1314	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Maridesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000331025.1	s__Maridesulfovibrio hydrothermalis	77.9815	318	1314	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Maridesulfovibrio	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000425265.1	s__Maridesulfovibrio zosterae	77.8218	309	1314	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Maridesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010470665.1	s__Maridesulfovibrio sp010470665	77.6809	237	1314	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Maridesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000023445.1	s__Maridesulfovibrio salexigens	77.5154	245	1314	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Maridesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:44,028] [INFO] GTDB search result was written to GCF_900177375.1_IMG-taxon_2708742538_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:44,028] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:44,032] [INFO] DFAST_QC result json was written to GCF_900177375.1_IMG-taxon_2708742538_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:33:44,033] [INFO] DFAST_QC completed!
[2024-01-24 13:33:44,033] [INFO] Total running time: 0h1m1s