[2024-01-24 14:55:50,412] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:50,416] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:50,416] [INFO] DQC Reference Directory: /var/lib/cwl/stg4c13a872-c091-41b5-82c6-fa2d5a348c39/dqc_reference
[2024-01-24 14:55:51,724] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:51,725] [INFO] Task started: Prodigal
[2024-01-24 14:55:51,725] [INFO] Running command: gunzip -c /var/lib/cwl/stg6e3d6961-7f43-4430-bbe4-53af6ecdceb8/GCF_902167245.1_DSV_KAUST_v1_genomic.fna.gz | prodigal -d GCF_902167245.1_DSV_KAUST_v1_genomic.fna/cds.fna -a GCF_902167245.1_DSV_KAUST_v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:56:04,925] [INFO] Task succeeded: Prodigal
[2024-01-24 14:56:04,925] [INFO] Task started: HMMsearch
[2024-01-24 14:56:04,925] [INFO] Running command: hmmsearch --tblout GCF_902167245.1_DSV_KAUST_v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4c13a872-c091-41b5-82c6-fa2d5a348c39/dqc_reference/reference_markers.hmm GCF_902167245.1_DSV_KAUST_v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:56:05,215] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:56:05,217] [INFO] Found 6/6 markers.
[2024-01-24 14:56:05,251] [INFO] Query marker FASTA was written to GCF_902167245.1_DSV_KAUST_v1_genomic.fna/markers.fasta
[2024-01-24 14:56:05,251] [INFO] Task started: Blastn
[2024-01-24 14:56:05,252] [INFO] Running command: blastn -query GCF_902167245.1_DSV_KAUST_v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c13a872-c091-41b5-82c6-fa2d5a348c39/dqc_reference/reference_markers.fasta -out GCF_902167245.1_DSV_KAUST_v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:05,891] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:05,895] [INFO] Selected 5 target genomes.
[2024-01-24 14:56:05,895] [INFO] Target genome list was writen to GCF_902167245.1_DSV_KAUST_v1_genomic.fna/target_genomes.txt
[2024-01-24 14:56:05,898] [INFO] Task started: fastANI
[2024-01-24 14:56:05,899] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e3d6961-7f43-4430-bbe4-53af6ecdceb8/GCF_902167245.1_DSV_KAUST_v1_genomic.fna.gz --refList GCF_902167245.1_DSV_KAUST_v1_genomic.fna/target_genomes.txt --output GCF_902167245.1_DSV_KAUST_v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:56:10,164] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:10,165] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4c13a872-c091-41b5-82c6-fa2d5a348c39/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:56:10,166] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4c13a872-c091-41b5-82c6-fa2d5a348c39/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:56:10,178] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:56:10,179] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:56:10,179] [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
Desulfovibrio vulgaris	strain=Hildenborough	GCA_902167245.1	881	881	type	True	100.0	1242	1242	95	conclusive
Desulfovibrio vulgaris	strain=Hildenborough	GCA_000195755.1	881	881	type	True	99.4452	1194	1242	95	conclusive
Cupidesulfovibrio oxamicus	strain=NCIMB 9442	GCA_015731765.1	32016	32016	type	True	79.5285	404	1242	95	below_threshold
Cupidesulfovibrio liaohensis	strain=XJ01	GCA_011682075.1	2604158	2604158	type	True	79.395	430	1242	95	below_threshold
Cupidesulfovibrio termitidis	strain=HI1	GCA_000504305.1	42252	42252	type	True	79.3848	495	1242	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:56:10,181] [INFO] DFAST Taxonomy check result was written to GCF_902167245.1_DSV_KAUST_v1_genomic.fna/tc_result.tsv
[2024-01-24 14:56:10,181] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:56:10,181] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:56:10,182] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4c13a872-c091-41b5-82c6-fa2d5a348c39/dqc_reference/checkm_data
[2024-01-24 14:56:10,183] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:56:10,220] [INFO] Task started: CheckM
[2024-01-24 14:56:10,220] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902167245.1_DSV_KAUST_v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902167245.1_DSV_KAUST_v1_genomic.fna/checkm_input GCF_902167245.1_DSV_KAUST_v1_genomic.fna/checkm_result
[2024-01-24 14:56:55,929] [INFO] Task succeeded: CheckM
[2024-01-24 14:56:55,931] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:56:55,947] [INFO] ===== Completeness check finished =====
[2024-01-24 14:56:55,948] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:56:55,948] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902167245.1_DSV_KAUST_v1_genomic.fna/markers.fasta)
[2024-01-24 14:56:55,949] [INFO] Task started: Blastn
[2024-01-24 14:56:55,949] [INFO] Running command: blastn -query GCF_902167245.1_DSV_KAUST_v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c13a872-c091-41b5-82c6-fa2d5a348c39/dqc_reference/reference_markers_gtdb.fasta -out GCF_902167245.1_DSV_KAUST_v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:56,880] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:56,883] [INFO] Selected 10 target genomes.
[2024-01-24 14:56:56,884] [INFO] Target genome list was writen to GCF_902167245.1_DSV_KAUST_v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:56:56,896] [INFO] Task started: fastANI
[2024-01-24 14:56:56,896] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e3d6961-7f43-4430-bbe4-53af6ecdceb8/GCF_902167245.1_DSV_KAUST_v1_genomic.fna.gz --refList GCF_902167245.1_DSV_KAUST_v1_genomic.fna/target_genomes_gtdb.txt --output GCF_902167245.1_DSV_KAUST_v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:57:05,644] [INFO] Task succeeded: fastANI
[2024-01-24 14:57:05,651] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:57:05,651] [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_000195755.1	s__Nitratidesulfovibrio vulgaris	99.4447	1193	1242	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Nitratidesulfovibrio	95.0	99.25	98.85	0.97	0.94	6	conclusive
GCF_015731765.1	s__Cupidesulfovibrio oxamicus	79.5143	404	1242	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Cupidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000021385.1	s__Cupidesulfovibrio vulgaris_A	79.4166	531	1242	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Cupidesulfovibrio	95.0	97.08	97.08	0.92	0.92	2	-
GCF_000226255.1	s__Cupidesulfovibrio sp000226255	79.3905	515	1242	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Cupidesulfovibrio	95.0	96.66	96.06	0.89	0.84	6	-
GCF_011682075.1	s__Cupidesulfovibrio liaohensis	79.3865	429	1242	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Cupidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000504305.1	s__Cupidesulfovibrio termitidis	79.3791	494	1242	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Cupidesulfovibrio	95.0	98.21	98.21	0.92	0.92	2	-
GCA_009712225.1	s__Desulfovibrio sp009712225	77.1428	116	1242	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:57:05,656] [INFO] GTDB search result was written to GCF_902167245.1_DSV_KAUST_v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:57:05,657] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:57:05,659] [INFO] DFAST_QC result json was written to GCF_902167245.1_DSV_KAUST_v1_genomic.fna/dqc_result.json
[2024-01-24 14:57:05,659] [INFO] DFAST_QC completed!
[2024-01-24 14:57:05,659] [INFO] Total running time: 0h1m15s