[2024-01-24 12:05:26,606] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:05:26,607] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:05:26,608] [INFO] DQC Reference Directory: /var/lib/cwl/stga8a51ad8-b14e-4d9b-a500-3eb31254956d/dqc_reference
[2024-01-24 12:05:30,676] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:05:30,678] [INFO] Task started: Prodigal
[2024-01-24 12:05:30,678] [INFO] Running command: gunzip -c /var/lib/cwl/stg5a770ee2-d622-416e-9ea8-e0283542a653/GCF_003025415.1_ASM302541v1_genomic.fna.gz | prodigal -d GCF_003025415.1_ASM302541v1_genomic.fna/cds.fna -a GCF_003025415.1_ASM302541v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:05:39,776] [INFO] Task succeeded: Prodigal
[2024-01-24 12:05:39,777] [INFO] Task started: HMMsearch
[2024-01-24 12:05:39,777] [INFO] Running command: hmmsearch --tblout GCF_003025415.1_ASM302541v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga8a51ad8-b14e-4d9b-a500-3eb31254956d/dqc_reference/reference_markers.hmm GCF_003025415.1_ASM302541v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:05:40,070] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:05:40,072] [INFO] Found 6/6 markers.
[2024-01-24 12:05:40,126] [INFO] Query marker FASTA was written to GCF_003025415.1_ASM302541v1_genomic.fna/markers.fasta
[2024-01-24 12:05:40,126] [INFO] Task started: Blastn
[2024-01-24 12:05:40,126] [INFO] Running command: blastn -query GCF_003025415.1_ASM302541v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga8a51ad8-b14e-4d9b-a500-3eb31254956d/dqc_reference/reference_markers.fasta -out GCF_003025415.1_ASM302541v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:05:40,958] [INFO] Task succeeded: Blastn
[2024-01-24 12:05:40,961] [INFO] Selected 12 target genomes.
[2024-01-24 12:05:40,961] [INFO] Target genome list was writen to GCF_003025415.1_ASM302541v1_genomic.fna/target_genomes.txt
[2024-01-24 12:05:40,967] [INFO] Task started: fastANI
[2024-01-24 12:05:40,967] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a770ee2-d622-416e-9ea8-e0283542a653/GCF_003025415.1_ASM302541v1_genomic.fna.gz --refList GCF_003025415.1_ASM302541v1_genomic.fna/target_genomes.txt --output GCF_003025415.1_ASM302541v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:05:52,710] [INFO] Task succeeded: fastANI
[2024-01-24 12:05:52,710] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga8a51ad8-b14e-4d9b-a500-3eb31254956d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:05:52,711] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga8a51ad8-b14e-4d9b-a500-3eb31254956d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:05:52,721] [INFO] Found 12 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 12:05:52,721] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:05:52,721] [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 aquimaris	strain=DSM 23343	GCA_003025415.1	512643	512643	suspected-type	True	100.0	1437	1441	95	inconclusive
Photobacterium aquimaris	strain=GCSL-P109	GCA_001676085.1	512643	512643	suspected-type	True	99.9744	1424	1441	95	inconclusive
Photobacterium aquimaris	strain=LC2-065	GCA_002954455.1	512643	512643	suspected-type	True	99.9626	1439	1441	95	inconclusive
Photobacterium andalusiense	strain=CECT 9192	GCA_900185625.1	2204296	2204296	type	True	95.5551	1231	1441	95	inconclusive
Photobacterium malacitanum	strain=CECT 9190	GCA_900185615.1	2204294	2204294	type	True	93.0449	1248	1441	95	below_threshold
Photobacterium phosphoreum	strain=ATCC 11040	GCA_000949955.1	659	659	type	True	86.4484	1149	1441	95	below_threshold
Photobacterium toruni	strain=CECT 9189	GCA_024529955.1	1935446	1935446	type	True	85.7196	1054	1441	95	below_threshold
Photobacterium iliopiscarium	strain=ATCC 51760	GCA_003026395.1	56192	56192	type	True	85.1159	1059	1441	95	below_threshold
Photobacterium iliopiscarium	strain=ATCC 51760	GCA_000950265.1	56192	56192	type	True	84.9597	1061	1441	95	below_threshold
Photobacterium sanguinicancri	strain=CECT 7579	GCA_024346675.1	875932	875932	type	True	79.0743	333	1441	95	below_threshold
Vibrio toranzoniae	strain=CECT 7225	GCA_024347655.1	1194427	1194427	type	True	78.4194	162	1441	95	below_threshold
Vibrio algicola	strain=SM1977	GCA_009601765.2	2662262	2662262	type	True	77.8903	172	1441	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:05:52,727] [INFO] DFAST Taxonomy check result was written to GCF_003025415.1_ASM302541v1_genomic.fna/tc_result.tsv
[2024-01-24 12:05:52,727] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:05:52,728] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:05:52,728] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga8a51ad8-b14e-4d9b-a500-3eb31254956d/dqc_reference/checkm_data
[2024-01-24 12:05:52,729] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:05:52,777] [INFO] Task started: CheckM
[2024-01-24 12:05:52,777] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003025415.1_ASM302541v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003025415.1_ASM302541v1_genomic.fna/checkm_input GCF_003025415.1_ASM302541v1_genomic.fna/checkm_result
[2024-01-24 12:06:25,294] [INFO] Task succeeded: CheckM
[2024-01-24 12:06:25,295] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:06:25,320] [INFO] ===== Completeness check finished =====
[2024-01-24 12:06:25,320] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:06:25,320] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003025415.1_ASM302541v1_genomic.fna/markers.fasta)
[2024-01-24 12:06:25,321] [INFO] Task started: Blastn
[2024-01-24 12:06:25,321] [INFO] Running command: blastn -query GCF_003025415.1_ASM302541v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga8a51ad8-b14e-4d9b-a500-3eb31254956d/dqc_reference/reference_markers_gtdb.fasta -out GCF_003025415.1_ASM302541v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:26,476] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:26,479] [INFO] Selected 8 target genomes.
[2024-01-24 12:06:26,479] [INFO] Target genome list was writen to GCF_003025415.1_ASM302541v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:06:26,487] [INFO] Task started: fastANI
[2024-01-24 12:06:26,487] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a770ee2-d622-416e-9ea8-e0283542a653/GCF_003025415.1_ASM302541v1_genomic.fna.gz --refList GCF_003025415.1_ASM302541v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003025415.1_ASM302541v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:06:36,244] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:36,258] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:06:36,258] [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_002954455.1	s__Photobacterium aquimaris	99.9626	1439	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	98.51	95.34	0.95	0.87	6	conclusive
GCF_900185615.1	s__Photobacterium malacitanum	93.0579	1247	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	95.08	95.06	0.91	0.91	6	-
GCF_003026355.1	s__Photobacterium kishitanii	86.6061	1168	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	98.67	97.61	0.95	0.91	24	-
GCF_002954725.1	s__Photobacterium phosphoreum	86.4538	1184	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	98.41	96.65	0.93	0.88	23	-
GCF_900166975.1	s__Photobacterium toruni	85.8433	1032	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002849605.1	s__Photobacterium carnosum	85.5464	1065	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	98.77	98.77	0.93	0.93	2	-
GCF_900166965.1	s__Photobacterium piscicola	85.178	1088	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	98.92	98.92	0.94	0.94	2	-
GCF_003026395.1	s__Photobacterium iliopiscarium	85.1062	1060	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	99.31	98.95	0.95	0.91	7	-
--------------------------------------------------------------------------------
[2024-01-24 12:06:36,260] [INFO] GTDB search result was written to GCF_003025415.1_ASM302541v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:06:36,261] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:06:36,264] [INFO] DFAST_QC result json was written to GCF_003025415.1_ASM302541v1_genomic.fna/dqc_result.json
[2024-01-24 12:06:36,264] [INFO] DFAST_QC completed!
[2024-01-24 12:06:36,265] [INFO] Total running time: 0h1m10s