[2024-01-25 18:15:35,592] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:15:35,593] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:15:35,593] [INFO] DQC Reference Directory: /var/lib/cwl/stg0c97958c-773e-42c1-92bc-d87bc0df4fac/dqc_reference
[2024-01-25 18:15:36,740] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:15:36,740] [INFO] Task started: Prodigal
[2024-01-25 18:15:36,741] [INFO] Running command: gunzip -c /var/lib/cwl/stg12940f3d-d789-4e56-9c11-0e2b92556349/GCF_000331515.1_Photobacterium_marinum_AK15_genomic.fna.gz | prodigal -d GCF_000331515.1_Photobacterium_marinum_AK15_genomic.fna/cds.fna -a GCF_000331515.1_Photobacterium_marinum_AK15_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:15:48,872] [INFO] Task succeeded: Prodigal
[2024-01-25 18:15:48,872] [INFO] Task started: HMMsearch
[2024-01-25 18:15:48,873] [INFO] Running command: hmmsearch --tblout GCF_000331515.1_Photobacterium_marinum_AK15_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0c97958c-773e-42c1-92bc-d87bc0df4fac/dqc_reference/reference_markers.hmm GCF_000331515.1_Photobacterium_marinum_AK15_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:15:49,200] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:15:49,201] [INFO] Found 6/6 markers.
[2024-01-25 18:15:49,243] [INFO] Query marker FASTA was written to GCF_000331515.1_Photobacterium_marinum_AK15_genomic.fna/markers.fasta
[2024-01-25 18:15:49,243] [INFO] Task started: Blastn
[2024-01-25 18:15:49,243] [INFO] Running command: blastn -query GCF_000331515.1_Photobacterium_marinum_AK15_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c97958c-773e-42c1-92bc-d87bc0df4fac/dqc_reference/reference_markers.fasta -out GCF_000331515.1_Photobacterium_marinum_AK15_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:15:50,052] [INFO] Task succeeded: Blastn
[2024-01-25 18:15:50,054] [INFO] Selected 19 target genomes.
[2024-01-25 18:15:50,055] [INFO] Target genome list was writen to GCF_000331515.1_Photobacterium_marinum_AK15_genomic.fna/target_genomes.txt
[2024-01-25 18:15:50,066] [INFO] Task started: fastANI
[2024-01-25 18:15:50,066] [INFO] Running command: fastANI --query /var/lib/cwl/stg12940f3d-d789-4e56-9c11-0e2b92556349/GCF_000331515.1_Photobacterium_marinum_AK15_genomic.fna.gz --refList GCF_000331515.1_Photobacterium_marinum_AK15_genomic.fna/target_genomes.txt --output GCF_000331515.1_Photobacterium_marinum_AK15_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:16:08,748] [INFO] Task succeeded: fastANI
[2024-01-25 18:16:08,748] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0c97958c-773e-42c1-92bc-d87bc0df4fac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:16:08,749] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0c97958c-773e-42c1-92bc-d87bc0df4fac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:16:08,760] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:16:08,760] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:16:08,761] [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
Photobacterium marinum	strain=AK15	GCA_000331515.1	1056511	1056511	type	True	100.0	1803	1809	95	conclusive
Photobacterium proteolyticum	strain=13-12	GCA_001939735.1	1903952	1903952	type	True	80.7604	757	1809	95	below_threshold
Photobacterium alginatilyticum	strain=P03D4	GCA_009910675.1	1775171	1775171	type	True	80.713	774	1809	95	below_threshold
Photobacterium chitinilyticum	strain=BEI247	GCA_004104355.1	2485123	2485123	type	True	80.3227	763	1809	95	below_threshold
Photobacterium sanctipauli	strain=A-394	GCA_000730475.1	1342794	1342794	type	True	80.1908	388	1809	95	below_threshold
Photobacterium sanctipauli	strain=DSM 100436	GCA_003026495.1	1342794	1342794	type	True	80.185	511	1809	95	below_threshold
Photobacterium gaetbulicola	strain=Gung47	GCA_000940995.1	1295392	1295392	type	True	80.0841	525	1809	95	below_threshold
Photobacterium gaetbulicola	strain=DSM 26887	GCA_003025515.1	1295392	1295392	type	True	80.0631	525	1809	95	below_threshold
Photobacterium rosenbergii	strain=DSM 19138	GCA_003026455.1	294936	294936	type	True	79.9884	517	1809	95	below_threshold
Photobacterium aphoticum	strain=DSM 25995	GCA_003025575.1	754436	754436	type	True	79.8311	450	1809	95	below_threshold
Photobacterium ganghwense	strain=JCM 12487	GCA_003025595.1	320778	320778	type	True	79.809	513	1809	95	below_threshold
Photobacterium ganghwense	strain=DSM 22954	GCA_001029455.1	320778	320778	type	True	79.7931	512	1809	95	below_threshold
Photobacterium aphoticum	strain=DSM 25995	GCA_001029435.1	754436	754436	type	True	79.7172	485	1809	95	below_threshold
Photobacterium aquae	strain=CGMCC 1.12159	GCA_001029445.1	1195763	1195763	type	True	79.3335	485	1809	95	below_threshold
Photobacterium swingsii	strain=CECT 7576	GCA_024346715.1	680026	680026	type	True	79.1691	395	1809	95	below_threshold
Photobacterium sanguinicancri	strain=CECT 7579	GCA_024346675.1	875932	875932	type	True	79.0034	403	1809	95	below_threshold
Photobacterium galatheae	strain=DSM 100496	GCA_023653475.1	1654360	1654360	type	True	78.5606	354	1809	95	below_threshold
Vibrio albus	strain=E4404	GCA_003144035.1	2200953	2200953	type	True	78.5371	158	1809	95	below_threshold
Photobacterium salinisoli	strain=LAM9072	GCA_003614885.1	1616783	1616783	type	True	78.2396	342	1809	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:16:08,762] [INFO] DFAST Taxonomy check result was written to GCF_000331515.1_Photobacterium_marinum_AK15_genomic.fna/tc_result.tsv
[2024-01-25 18:16:08,763] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:16:08,763] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:16:08,763] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0c97958c-773e-42c1-92bc-d87bc0df4fac/dqc_reference/checkm_data
[2024-01-25 18:16:08,764] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:16:08,820] [INFO] Task started: CheckM
[2024-01-25 18:16:08,820] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000331515.1_Photobacterium_marinum_AK15_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000331515.1_Photobacterium_marinum_AK15_genomic.fna/checkm_input GCF_000331515.1_Photobacterium_marinum_AK15_genomic.fna/checkm_result
[2024-01-25 18:16:47,607] [INFO] Task succeeded: CheckM
[2024-01-25 18:16:47,608] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:16:47,623] [INFO] ===== Completeness check finished =====
[2024-01-25 18:16:47,623] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:16:47,623] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000331515.1_Photobacterium_marinum_AK15_genomic.fna/markers.fasta)
[2024-01-25 18:16:47,624] [INFO] Task started: Blastn
[2024-01-25 18:16:47,624] [INFO] Running command: blastn -query GCF_000331515.1_Photobacterium_marinum_AK15_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c97958c-773e-42c1-92bc-d87bc0df4fac/dqc_reference/reference_markers_gtdb.fasta -out GCF_000331515.1_Photobacterium_marinum_AK15_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:16:48,862] [INFO] Task succeeded: Blastn
[2024-01-25 18:16:48,864] [INFO] Selected 12 target genomes.
[2024-01-25 18:16:48,864] [INFO] Target genome list was writen to GCF_000331515.1_Photobacterium_marinum_AK15_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:16:48,897] [INFO] Task started: fastANI
[2024-01-25 18:16:48,897] [INFO] Running command: fastANI --query /var/lib/cwl/stg12940f3d-d789-4e56-9c11-0e2b92556349/GCF_000331515.1_Photobacterium_marinum_AK15_genomic.fna.gz --refList GCF_000331515.1_Photobacterium_marinum_AK15_genomic.fna/target_genomes_gtdb.txt --output GCF_000331515.1_Photobacterium_marinum_AK15_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:17:02,787] [INFO] Task succeeded: fastANI
[2024-01-25 18:17:02,794] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:17:02,795] [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_000331515.1	s__Photobacterium marinum	100.0	1803	1809	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	96.66	96.66	0.88	0.88	2	conclusive
GCF_001939735.1	s__Photobacterium proteolyticum	80.7516	758	1809	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009910675.1	s__Photobacterium alginatilyticum	80.7313	772	1809	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004104355.1	s__Photobacterium chitinilyticum	80.3183	764	1809	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003026495.1	s__Photobacterium sanctipauli	80.2022	510	1809	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000940995.1	s__Photobacterium gaetbulicola	80.0803	524	1809	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	97.90	95.81	0.93	0.87	3	-
GCF_003026455.1	s__Photobacterium rosenbergii	79.9889	518	1809	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	95.32	95.32	0.83	0.83	2	-
GCF_003025555.1	s__Photobacterium lutimaris	79.8609	500	1809	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003025595.1	s__Photobacterium ganghwense	79.8036	514	1809	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	99.50	98.82	0.97	0.96	4	-
GCF_001029435.1	s__Photobacterium aphoticum	79.7172	485	1809	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	99.09	97.29	0.97	0.93	4	-
GCF_001029445.1	s__Photobacterium aquae	79.3258	487	1809	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003614885.1	s__Photobacterium sp003614885	78.2288	343	1809	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:17:02,796] [INFO] GTDB search result was written to GCF_000331515.1_Photobacterium_marinum_AK15_genomic.fna/result_gtdb.tsv
[2024-01-25 18:17:02,797] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:17:02,800] [INFO] DFAST_QC result json was written to GCF_000331515.1_Photobacterium_marinum_AK15_genomic.fna/dqc_result.json
[2024-01-25 18:17:02,800] [INFO] DFAST_QC completed!
[2024-01-25 18:17:02,800] [INFO] Total running time: 0h1m27s