[2024-01-25 20:01:35,562] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:01:35,564] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:01:35,564] [INFO] DQC Reference Directory: /var/lib/cwl/stga3ae9c11-e441-4715-8382-88a4c23222c2/dqc_reference
[2024-01-25 20:01:36,843] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:01:36,844] [INFO] Task started: Prodigal
[2024-01-25 20:01:36,844] [INFO] Running command: gunzip -c /var/lib/cwl/stg2277670e-930d-4aad-9ab2-68bff0cf3d56/GCF_003025575.1_ASM302557v1_genomic.fna.gz | prodigal -d GCF_003025575.1_ASM302557v1_genomic.fna/cds.fna -a GCF_003025575.1_ASM302557v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:01:49,754] [INFO] Task succeeded: Prodigal
[2024-01-25 20:01:49,754] [INFO] Task started: HMMsearch
[2024-01-25 20:01:49,754] [INFO] Running command: hmmsearch --tblout GCF_003025575.1_ASM302557v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga3ae9c11-e441-4715-8382-88a4c23222c2/dqc_reference/reference_markers.hmm GCF_003025575.1_ASM302557v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:01:50,016] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:01:50,017] [INFO] Found 6/6 markers.
[2024-01-25 20:01:50,058] [INFO] Query marker FASTA was written to GCF_003025575.1_ASM302557v1_genomic.fna/markers.fasta
[2024-01-25 20:01:50,058] [INFO] Task started: Blastn
[2024-01-25 20:01:50,058] [INFO] Running command: blastn -query GCF_003025575.1_ASM302557v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga3ae9c11-e441-4715-8382-88a4c23222c2/dqc_reference/reference_markers.fasta -out GCF_003025575.1_ASM302557v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:01:50,879] [INFO] Task succeeded: Blastn
[2024-01-25 20:01:50,882] [INFO] Selected 15 target genomes.
[2024-01-25 20:01:50,882] [INFO] Target genome list was writen to GCF_003025575.1_ASM302557v1_genomic.fna/target_genomes.txt
[2024-01-25 20:01:50,902] [INFO] Task started: fastANI
[2024-01-25 20:01:50,902] [INFO] Running command: fastANI --query /var/lib/cwl/stg2277670e-930d-4aad-9ab2-68bff0cf3d56/GCF_003025575.1_ASM302557v1_genomic.fna.gz --refList GCF_003025575.1_ASM302557v1_genomic.fna/target_genomes.txt --output GCF_003025575.1_ASM302557v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:02:05,072] [INFO] Task succeeded: fastANI
[2024-01-25 20:02:05,072] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga3ae9c11-e441-4715-8382-88a4c23222c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:02:05,072] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga3ae9c11-e441-4715-8382-88a4c23222c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:02:05,083] [INFO] Found 15 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 20:02:05,083] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:02:05,084] [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 aphoticum	strain=DSM 25995	GCA_003025575.1	754436	754436	type	True	100.0	1617	1625	95	conclusive
Photobacterium aphoticum	strain=KCTC 23057	GCA_014652075.1	754436	754436	type	True	99.9839	1615	1625	95	conclusive
Photobacterium aphoticum	strain=DSM 25995	GCA_001029435.1	754436	754436	type	True	99.9806	1601	1625	95	conclusive
Photobacterium aquae	strain=CGMCC 1.12159	GCA_001029445.1	1195763	1195763	type	True	80.597	557	1625	95	below_threshold
Photobacterium gaetbulicola	strain=DSM 26887	GCA_003025515.1	1295392	1295392	type	True	80.4415	585	1625	95	below_threshold
Photobacterium gaetbulicola	strain=Gung47	GCA_000940995.1	1295392	1295392	type	True	80.4156	599	1625	95	below_threshold
Photobacterium ganghwense	strain=JCM 12487	GCA_003025595.1	320778	320778	type	True	80.0716	568	1625	95	below_threshold
Photobacterium ganghwense	strain=DSM 22954	GCA_001029455.1	320778	320778	type	True	79.9369	577	1625	95	below_threshold
Photobacterium marinum	strain=AK15	GCA_000331515.1	1056511	1056511	type	True	79.8707	444	1625	95	below_threshold
Photobacterium jeanii	strain=R-40508	GCA_001650345.1	858640	858640	type	True	79.6442	424	1625	95	below_threshold
Photobacterium swingsii	strain=CECT 7576	GCA_024346715.1	680026	680026	type	True	79.3714	391	1625	95	below_threshold
Photobacterium sanguinicancri	strain=CECT 7579	GCA_024346675.1	875932	875932	type	True	79.1559	365	1625	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	78.5562	184	1625	95	below_threshold
Vibrio panuliri	strain=LBS 2	GCA_008830195.1	1381081	1381081	type	True	78.5455	188	1625	95	below_threshold
Photobacterium salinisoli	strain=LAM9072	GCA_003614885.1	1616783	1616783	type	True	78.3482	296	1625	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:02:05,086] [INFO] DFAST Taxonomy check result was written to GCF_003025575.1_ASM302557v1_genomic.fna/tc_result.tsv
[2024-01-25 20:02:05,087] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:02:05,087] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:02:05,087] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga3ae9c11-e441-4715-8382-88a4c23222c2/dqc_reference/checkm_data
[2024-01-25 20:02:05,088] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:02:05,162] [INFO] Task started: CheckM
[2024-01-25 20:02:05,162] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003025575.1_ASM302557v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003025575.1_ASM302557v1_genomic.fna/checkm_input GCF_003025575.1_ASM302557v1_genomic.fna/checkm_result
[2024-01-25 20:02:46,259] [INFO] Task succeeded: CheckM
[2024-01-25 20:02:46,260] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:02:46,280] [INFO] ===== Completeness check finished =====
[2024-01-25 20:02:46,281] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:02:46,281] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003025575.1_ASM302557v1_genomic.fna/markers.fasta)
[2024-01-25 20:02:46,281] [INFO] Task started: Blastn
[2024-01-25 20:02:46,282] [INFO] Running command: blastn -query GCF_003025575.1_ASM302557v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga3ae9c11-e441-4715-8382-88a4c23222c2/dqc_reference/reference_markers_gtdb.fasta -out GCF_003025575.1_ASM302557v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:02:47,554] [INFO] Task succeeded: Blastn
[2024-01-25 20:02:47,558] [INFO] Selected 11 target genomes.
[2024-01-25 20:02:47,558] [INFO] Target genome list was writen to GCF_003025575.1_ASM302557v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:02:47,566] [INFO] Task started: fastANI
[2024-01-25 20:02:47,566] [INFO] Running command: fastANI --query /var/lib/cwl/stg2277670e-930d-4aad-9ab2-68bff0cf3d56/GCF_003025575.1_ASM302557v1_genomic.fna.gz --refList GCF_003025575.1_ASM302557v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003025575.1_ASM302557v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:03:00,694] [INFO] Task succeeded: fastANI
[2024-01-25 20:03:00,702] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:03:00,702] [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_001029435.1	s__Photobacterium aphoticum	99.9806	1601	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	99.09	97.29	0.97	0.93	4	conclusive
GCF_001029445.1	s__Photobacterium aquae	80.597	557	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003026455.1	s__Photobacterium rosenbergii	80.5462	571	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	95.32	95.32	0.83	0.83	2	-
GCF_003026495.1	s__Photobacterium sanctipauli	80.4484	549	1625	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	80.4139	601	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	97.90	95.81	0.93	0.87	3	-
GCF_003025555.1	s__Photobacterium lutimaris	80.2229	583	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009910675.1	s__Photobacterium alginatilyticum	80.0841	462	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003025595.1	s__Photobacterium ganghwense	80.0761	567	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	99.50	98.82	0.97	0.96	4	-
GCF_000331515.1	s__Photobacterium marinum	79.8688	444	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	96.66	96.66	0.88	0.88	2	-
GCF_001939735.1	s__Photobacterium proteolyticum	79.84	473	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650345.1	s__Photobacterium jeanii	79.6416	425	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:03:00,703] [INFO] GTDB search result was written to GCF_003025575.1_ASM302557v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:03:00,704] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:03:00,735] [INFO] DFAST_QC result json was written to GCF_003025575.1_ASM302557v1_genomic.fna/dqc_result.json
[2024-01-25 20:03:00,735] [INFO] DFAST_QC completed!
[2024-01-25 20:03:00,735] [INFO] Total running time: 0h1m25s