[2024-01-25 18:50:05,607] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:50:05,609] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:50:05,609] [INFO] DQC Reference Directory: /var/lib/cwl/stgc9722310-8f04-4adc-aff2-b30f9b1f6cdf/dqc_reference
[2024-01-25 18:50:06,750] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:50:06,750] [INFO] Task started: Prodigal
[2024-01-25 18:50:06,750] [INFO] Running command: gunzip -c /var/lib/cwl/stgc7373a97-be1a-4c34-a530-89999e2d4494/GCF_024346675.1_ASM2434667v1_genomic.fna.gz | prodigal -d GCF_024346675.1_ASM2434667v1_genomic.fna/cds.fna -a GCF_024346675.1_ASM2434667v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:50:18,010] [INFO] Task succeeded: Prodigal
[2024-01-25 18:50:18,011] [INFO] Task started: HMMsearch
[2024-01-25 18:50:18,011] [INFO] Running command: hmmsearch --tblout GCF_024346675.1_ASM2434667v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc9722310-8f04-4adc-aff2-b30f9b1f6cdf/dqc_reference/reference_markers.hmm GCF_024346675.1_ASM2434667v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:50:18,287] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:50:18,288] [INFO] Found 6/6 markers.
[2024-01-25 18:50:18,332] [INFO] Query marker FASTA was written to GCF_024346675.1_ASM2434667v1_genomic.fna/markers.fasta
[2024-01-25 18:50:18,333] [INFO] Task started: Blastn
[2024-01-25 18:50:18,333] [INFO] Running command: blastn -query GCF_024346675.1_ASM2434667v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9722310-8f04-4adc-aff2-b30f9b1f6cdf/dqc_reference/reference_markers.fasta -out GCF_024346675.1_ASM2434667v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:50:19,069] [INFO] Task succeeded: Blastn
[2024-01-25 18:50:19,072] [INFO] Selected 8 target genomes.
[2024-01-25 18:50:19,072] [INFO] Target genome list was writen to GCF_024346675.1_ASM2434667v1_genomic.fna/target_genomes.txt
[2024-01-25 18:50:19,077] [INFO] Task started: fastANI
[2024-01-25 18:50:19,077] [INFO] Running command: fastANI --query /var/lib/cwl/stgc7373a97-be1a-4c34-a530-89999e2d4494/GCF_024346675.1_ASM2434667v1_genomic.fna.gz --refList GCF_024346675.1_ASM2434667v1_genomic.fna/target_genomes.txt --output GCF_024346675.1_ASM2434667v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:50:29,212] [INFO] Task succeeded: fastANI
[2024-01-25 18:50:29,213] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc9722310-8f04-4adc-aff2-b30f9b1f6cdf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:50:29,213] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc9722310-8f04-4adc-aff2-b30f9b1f6cdf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:50:29,219] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:50:29,219] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:50:29,220] [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 sanguinicancri	strain=CECT 7579	GCA_024346675.1	875932	875932	type	True	100.0	1845	1848	95	conclusive
Photobacterium sanguinicancri	strain=CAIM 1827	GCA_002265265.1	875932	875932	type	True	97.7107	1452	1848	95	conclusive
Photobacterium swingsii	strain=CECT 7576	GCA_024346715.1	680026	680026	type	True	86.5266	1546	1848	95	below_threshold
Photobacterium swingsii	strain=DSM 24669	GCA_003026435.1	680026	680026	type	True	86.3807	1533	1848	95	below_threshold
Photobacterium swingsii	strain=CAIM 1393	GCA_001077885.1	680026	680026	type	True	86.2503	1523	1848	95	below_threshold
Photobacterium toruni	strain=CECT 9189	GCA_024529955.1	1935446	1935446	type	True	80.0524	334	1848	95	below_threshold
Aliivibrio fischeri	strain=DSM 507	GCA_023983475.1	668	668	suspected-type	True	79.5932	243	1848	95	below_threshold
Photobacterium phosphoreum	strain=ATCC 11040	GCA_000949955.1	659	659	type	True	79.3043	324	1848	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:50:29,221] [INFO] DFAST Taxonomy check result was written to GCF_024346675.1_ASM2434667v1_genomic.fna/tc_result.tsv
[2024-01-25 18:50:29,221] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:50:29,221] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:50:29,222] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc9722310-8f04-4adc-aff2-b30f9b1f6cdf/dqc_reference/checkm_data
[2024-01-25 18:50:29,222] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:50:29,278] [INFO] Task started: CheckM
[2024-01-25 18:50:29,278] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024346675.1_ASM2434667v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024346675.1_ASM2434667v1_genomic.fna/checkm_input GCF_024346675.1_ASM2434667v1_genomic.fna/checkm_result
[2024-01-25 18:51:06,267] [INFO] Task succeeded: CheckM
[2024-01-25 18:51:06,268] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:51:06,292] [INFO] ===== Completeness check finished =====
[2024-01-25 18:51:06,292] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:51:06,292] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024346675.1_ASM2434667v1_genomic.fna/markers.fasta)
[2024-01-25 18:51:06,292] [INFO] Task started: Blastn
[2024-01-25 18:51:06,292] [INFO] Running command: blastn -query GCF_024346675.1_ASM2434667v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9722310-8f04-4adc-aff2-b30f9b1f6cdf/dqc_reference/reference_markers_gtdb.fasta -out GCF_024346675.1_ASM2434667v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:51:07,432] [INFO] Task succeeded: Blastn
[2024-01-25 18:51:07,435] [INFO] Selected 14 target genomes.
[2024-01-25 18:51:07,435] [INFO] Target genome list was writen to GCF_024346675.1_ASM2434667v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:51:07,439] [INFO] Task started: fastANI
[2024-01-25 18:51:07,439] [INFO] Running command: fastANI --query /var/lib/cwl/stgc7373a97-be1a-4c34-a530-89999e2d4494/GCF_024346675.1_ASM2434667v1_genomic.fna.gz --refList GCF_024346675.1_ASM2434667v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024346675.1_ASM2434667v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:51:22,845] [INFO] Task succeeded: fastANI
[2024-01-25 18:51:22,854] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:51:22,855] [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_002265265.1	s__Photobacterium sanguinicancri	97.7171	1450	1848	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	97.87	97.87	0.90	0.90	2	conclusive
GCF_001077885.1	s__Photobacterium swingsii	86.2502	1523	1848	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	99.98	99.98	1.00	1.00	2	-
GCF_001650345.1	s__Photobacterium jeanii	81.1813	954	1848	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004104355.1	s__Photobacterium chitinilyticum	80.0101	431	1848	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000196255.1	s__Photobacterium profundum_A	79.8936	548	1848	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.5718	N/A	N/A	N/A	N/A	1	-
GCF_001939735.1	s__Photobacterium proteolyticum	79.6232	417	1848	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003026215.1	s__Photobacterium indicum	79.5003	518	1848	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	79.4984	419	1848	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003026285.1	s__Photobacterium profundum	79.3899	519	1848	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	99.97	99.97	1.00	1.00	2	-
GCF_003026475.1	s__Photobacterium lipolyticum	79.3731	466	1848	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002954455.1	s__Photobacterium aquimaris	79.3123	317	1848	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	98.51	95.34	0.95	0.87	6	-
GCF_900185615.1	s__Photobacterium malacitanum	79.2925	322	1848	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	95.08	95.06	0.91	0.91	6	-
GCF_000331515.1	s__Photobacterium marinum	79.1791	385	1848	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	96.66	96.66	0.88	0.88	2	-
GCF_003026395.1	s__Photobacterium iliopiscarium	78.968	333	1848	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	99.31	98.95	0.95	0.91	7	-
--------------------------------------------------------------------------------
[2024-01-25 18:51:22,856] [INFO] GTDB search result was written to GCF_024346675.1_ASM2434667v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:51:22,857] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:51:22,859] [INFO] DFAST_QC result json was written to GCF_024346675.1_ASM2434667v1_genomic.fna/dqc_result.json
[2024-01-25 18:51:22,859] [INFO] DFAST_QC completed!
[2024-01-25 18:51:22,859] [INFO] Total running time: 0h1m17s