[2024-01-25 17:41:20,596] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:41:20,598] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:41:20,598] [INFO] DQC Reference Directory: /var/lib/cwl/stg439a1a55-52e9-4f2e-8023-9dfb96157392/dqc_reference
[2024-01-25 17:41:21,731] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:41:21,732] [INFO] Task started: Prodigal
[2024-01-25 17:41:21,732] [INFO] Running command: gunzip -c /var/lib/cwl/stgfe29729a-e985-47c9-bf27-e064472d70c6/GCF_003346865.1_ASM334686v1_genomic.fna.gz | prodigal -d GCF_003346865.1_ASM334686v1_genomic.fna/cds.fna -a GCF_003346865.1_ASM334686v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:41:26,979] [INFO] Task succeeded: Prodigal
[2024-01-25 17:41:26,979] [INFO] Task started: HMMsearch
[2024-01-25 17:41:26,979] [INFO] Running command: hmmsearch --tblout GCF_003346865.1_ASM334686v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg439a1a55-52e9-4f2e-8023-9dfb96157392/dqc_reference/reference_markers.hmm GCF_003346865.1_ASM334686v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:41:27,206] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:41:27,207] [INFO] Found 6/6 markers.
[2024-01-25 17:41:27,235] [INFO] Query marker FASTA was written to GCF_003346865.1_ASM334686v1_genomic.fna/markers.fasta
[2024-01-25 17:41:27,235] [INFO] Task started: Blastn
[2024-01-25 17:41:27,235] [INFO] Running command: blastn -query GCF_003346865.1_ASM334686v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg439a1a55-52e9-4f2e-8023-9dfb96157392/dqc_reference/reference_markers.fasta -out GCF_003346865.1_ASM334686v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:41:27,767] [INFO] Task succeeded: Blastn
[2024-01-25 17:41:27,770] [INFO] Selected 13 target genomes.
[2024-01-25 17:41:27,770] [INFO] Target genome list was writen to GCF_003346865.1_ASM334686v1_genomic.fna/target_genomes.txt
[2024-01-25 17:41:27,778] [INFO] Task started: fastANI
[2024-01-25 17:41:27,778] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe29729a-e985-47c9-bf27-e064472d70c6/GCF_003346865.1_ASM334686v1_genomic.fna.gz --refList GCF_003346865.1_ASM334686v1_genomic.fna/target_genomes.txt --output GCF_003346865.1_ASM334686v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:41:35,458] [INFO] Task succeeded: fastANI
[2024-01-25 17:41:35,459] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg439a1a55-52e9-4f2e-8023-9dfb96157392/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:41:35,459] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg439a1a55-52e9-4f2e-8023-9dfb96157392/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:41:35,463] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:41:35,463] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:41:35,463] [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
Halobacteriovorax vibrionivorans	strain=BL9	GCA_003346865.1	2152716	2152716	type	True	100.0	1044	1044	95	conclusive
Halobacteriovorax marinus	strain=SJ	GCA_000210915.2	97084	97084	type	True	77.1645	92	1044	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:41:35,465] [INFO] DFAST Taxonomy check result was written to GCF_003346865.1_ASM334686v1_genomic.fna/tc_result.tsv
[2024-01-25 17:41:35,466] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:41:35,466] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:41:35,466] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg439a1a55-52e9-4f2e-8023-9dfb96157392/dqc_reference/checkm_data
[2024-01-25 17:41:35,467] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:41:35,501] [INFO] Task started: CheckM
[2024-01-25 17:41:35,501] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003346865.1_ASM334686v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003346865.1_ASM334686v1_genomic.fna/checkm_input GCF_003346865.1_ASM334686v1_genomic.fna/checkm_result
[2024-01-25 17:41:57,146] [INFO] Task succeeded: CheckM
[2024-01-25 17:41:57,147] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:41:57,177] [INFO] ===== Completeness check finished =====
[2024-01-25 17:41:57,177] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:41:57,177] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003346865.1_ASM334686v1_genomic.fna/markers.fasta)
[2024-01-25 17:41:57,178] [INFO] Task started: Blastn
[2024-01-25 17:41:57,178] [INFO] Running command: blastn -query GCF_003346865.1_ASM334686v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg439a1a55-52e9-4f2e-8023-9dfb96157392/dqc_reference/reference_markers_gtdb.fasta -out GCF_003346865.1_ASM334686v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:41:58,029] [INFO] Task succeeded: Blastn
[2024-01-25 17:41:58,032] [INFO] Selected 11 target genomes.
[2024-01-25 17:41:58,032] [INFO] Target genome list was writen to GCF_003346865.1_ASM334686v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:41:58,047] [INFO] Task started: fastANI
[2024-01-25 17:41:58,048] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe29729a-e985-47c9-bf27-e064472d70c6/GCF_003346865.1_ASM334686v1_genomic.fna.gz --refList GCF_003346865.1_ASM334686v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003346865.1_ASM334686v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:42:05,422] [INFO] Task succeeded: fastANI
[2024-01-25 17:42:05,428] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:42:05,429] [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_003612895.1	s__DB6-IX sp003612895	98.6334	998	1044	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__DB6-IX	95.0	98.61	98.58	0.96	0.96	3	conclusive
GCF_002903145.1	s__DB6-IX sp002903145	80.7627	589	1044	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__DB6-IX	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000443995.1	s__DB6-IX sp000443995	80.7072	575	1044	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__DB6-IX	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000447755.1	s__BSW11-IV sp000447755	77.575	94	1044	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__BSW11-IV	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000447775.1	s__DB6-IX sp000447775	77.4508	138	1044	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__DB6-IX	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000447795.1	s__DB6-IX sp000447795	77.4256	144	1044	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__DB6-IX	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001874305.1	s__DB6-IX sp001874305	77.3836	156	1044	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__DB6-IX	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004006665.1	s__Halobacteriovorax sp004006665	76.7872	73	1044	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__Halobacteriovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002338505.1	s__DB6-IX sp002338505	76.6809	93	1044	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__DB6-IX	95.0	99.70	99.70	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:42:05,430] [INFO] GTDB search result was written to GCF_003346865.1_ASM334686v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:42:05,431] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:42:05,433] [INFO] DFAST_QC result json was written to GCF_003346865.1_ASM334686v1_genomic.fna/dqc_result.json
[2024-01-25 17:42:05,433] [INFO] DFAST_QC completed!
[2024-01-25 17:42:05,433] [INFO] Total running time: 0h0m45s