[2024-01-24 13:36:39,981] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:39,983] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:39,983] [INFO] DQC Reference Directory: /var/lib/cwl/stg15739040-1f9b-4d57-8f0c-a9a7e9a1869f/dqc_reference
[2024-01-24 13:36:41,183] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:41,184] [INFO] Task started: Prodigal
[2024-01-24 13:36:41,184] [INFO] Running command: gunzip -c /var/lib/cwl/stg815ddf3b-e542-4285-abc7-338a0de68234/GCF_014653175.1_ASM1465317v1_genomic.fna.gz | prodigal -d GCF_014653175.1_ASM1465317v1_genomic.fna/cds.fna -a GCF_014653175.1_ASM1465317v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:00,172] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:00,173] [INFO] Task started: HMMsearch
[2024-01-24 13:37:00,173] [INFO] Running command: hmmsearch --tblout GCF_014653175.1_ASM1465317v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg15739040-1f9b-4d57-8f0c-a9a7e9a1869f/dqc_reference/reference_markers.hmm GCF_014653175.1_ASM1465317v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:00,423] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:00,425] [INFO] Found 6/6 markers.
[2024-01-24 13:37:00,461] [INFO] Query marker FASTA was written to GCF_014653175.1_ASM1465317v1_genomic.fna/markers.fasta
[2024-01-24 13:37:00,462] [INFO] Task started: Blastn
[2024-01-24 13:37:00,462] [INFO] Running command: blastn -query GCF_014653175.1_ASM1465317v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg15739040-1f9b-4d57-8f0c-a9a7e9a1869f/dqc_reference/reference_markers.fasta -out GCF_014653175.1_ASM1465317v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:01,061] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:01,065] [INFO] Selected 19 target genomes.
[2024-01-24 13:37:01,065] [INFO] Target genome list was writen to GCF_014653175.1_ASM1465317v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:01,072] [INFO] Task started: fastANI
[2024-01-24 13:37:01,072] [INFO] Running command: fastANI --query /var/lib/cwl/stg815ddf3b-e542-4285-abc7-338a0de68234/GCF_014653175.1_ASM1465317v1_genomic.fna.gz --refList GCF_014653175.1_ASM1465317v1_genomic.fna/target_genomes.txt --output GCF_014653175.1_ASM1465317v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:15,848] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:15,848] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg15739040-1f9b-4d57-8f0c-a9a7e9a1869f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:15,848] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg15739040-1f9b-4d57-8f0c-a9a7e9a1869f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:15,856] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:15,857] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:15,857] [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
Roseivirga thermotolerans	strain=CGMCC 1.15111	GCA_014653175.1	1758176	1758176	type	True	100.0	1396	1398	95	conclusive
Roseivirga spongicola	strain=UST030701-084	GCA_001592965.1	333140	333140	type	True	79.0694	392	1398	95	below_threshold
Roseivirga pacifica	strain=CGMCC 1.12402	GCA_900111145.1	1267423	1267423	type	True	77.0932	210	1398	95	below_threshold
Roseivirga pacifica	strain=DSM 100771	GCA_003633845.1	1267423	1267423	type	True	77.0821	203	1398	95	below_threshold
Roseivirga misakiensis	strain=SK-8	GCA_001747105.1	1563681	1563681	type	True	76.7893	100	1398	95	below_threshold
Roseivirga ehrenbergii	strain=DSM 102268	GCA_004340805.1	279360	279360	type	True	76.4426	126	1398	95	below_threshold
Roseivirga ehrenbergii	strain=KMM 6017	GCA_001593005.1	279360	279360	type	True	76.4216	126	1398	95	below_threshold
Roseivirga seohaensis subsp. aquiponti	strain=D-25	GCA_001267955.1	1566026	1914963	type	True	76.4078	121	1398	95	below_threshold
Roseivirga seohaensis	strain=SW-152	GCA_001592945.1	1914963	1914963	type	True	76.3951	131	1398	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:15,859] [INFO] DFAST Taxonomy check result was written to GCF_014653175.1_ASM1465317v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:15,859] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:15,859] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:15,860] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg15739040-1f9b-4d57-8f0c-a9a7e9a1869f/dqc_reference/checkm_data
[2024-01-24 13:37:15,861] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:15,904] [INFO] Task started: CheckM
[2024-01-24 13:37:15,904] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014653175.1_ASM1465317v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014653175.1_ASM1465317v1_genomic.fna/checkm_input GCF_014653175.1_ASM1465317v1_genomic.fna/checkm_result
[2024-01-24 13:38:14,440] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:14,441] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:14,458] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:14,458] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:14,459] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014653175.1_ASM1465317v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:14,459] [INFO] Task started: Blastn
[2024-01-24 13:38:14,459] [INFO] Running command: blastn -query GCF_014653175.1_ASM1465317v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg15739040-1f9b-4d57-8f0c-a9a7e9a1869f/dqc_reference/reference_markers_gtdb.fasta -out GCF_014653175.1_ASM1465317v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:15,277] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:15,280] [INFO] Selected 17 target genomes.
[2024-01-24 13:38:15,280] [INFO] Target genome list was writen to GCF_014653175.1_ASM1465317v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:15,309] [INFO] Task started: fastANI
[2024-01-24 13:38:15,310] [INFO] Running command: fastANI --query /var/lib/cwl/stg815ddf3b-e542-4285-abc7-338a0de68234/GCF_014653175.1_ASM1465317v1_genomic.fna.gz --refList GCF_014653175.1_ASM1465317v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014653175.1_ASM1465317v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:27,105] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:27,112] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:27,112] [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_014653175.1	s__Fabibacter thermotolerans	100.0	1396	1398	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	98.67	98.61	0.92	0.91	4	conclusive
GCF_001592965.1	s__Fabibacter spongicola	79.0634	393	1398	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	97.73	96.54	0.93	0.88	5	-
GCA_013373005.1	s__Fabibacter sp013373005	78.101	321	1398	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111145.1	s__Fabibacter pacificus	77.0932	210	1398	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001747095.1	s__Fabibacter sp001747095	76.9879	134	1398	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002427755.1	s__Fabibacter sp002427755	76.6146	112	1398	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001593005.1	s__Roseivirga ehrenbergii	76.4216	126	1398	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Roseivirga	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001592945.1	s__Roseivirga seohaensis	76.3951	131	1398	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Roseivirga	95.0	97.29	97.29	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:27,114] [INFO] GTDB search result was written to GCF_014653175.1_ASM1465317v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:27,115] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:27,118] [INFO] DFAST_QC result json was written to GCF_014653175.1_ASM1465317v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:27,118] [INFO] DFAST_QC completed!
[2024-01-24 13:38:27,118] [INFO] Total running time: 0h1m47s