[2024-01-24 12:15:04,444] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:15:04,447] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:15:04,448] [INFO] DQC Reference Directory: /var/lib/cwl/stg1cd0af88-4831-4362-bb3c-a518a8845437/dqc_reference
[2024-01-24 12:15:05,784] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:15:05,785] [INFO] Task started: Prodigal
[2024-01-24 12:15:05,785] [INFO] Running command: gunzip -c /var/lib/cwl/stgd22c4247-9ca8-4849-878c-aaf8575e03c4/GCF_003026475.1_ASM302647v1_genomic.fna.gz | prodigal -d GCF_003026475.1_ASM302647v1_genomic.fna/cds.fna -a GCF_003026475.1_ASM302647v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:18,312] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:18,312] [INFO] Task started: HMMsearch
[2024-01-24 12:15:18,312] [INFO] Running command: hmmsearch --tblout GCF_003026475.1_ASM302647v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1cd0af88-4831-4362-bb3c-a518a8845437/dqc_reference/reference_markers.hmm GCF_003026475.1_ASM302647v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:18,621] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:18,623] [INFO] Found 6/6 markers.
[2024-01-24 12:15:18,669] [INFO] Query marker FASTA was written to GCF_003026475.1_ASM302647v1_genomic.fna/markers.fasta
[2024-01-24 12:15:18,669] [INFO] Task started: Blastn
[2024-01-24 12:15:18,670] [INFO] Running command: blastn -query GCF_003026475.1_ASM302647v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1cd0af88-4831-4362-bb3c-a518a8845437/dqc_reference/reference_markers.fasta -out GCF_003026475.1_ASM302647v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:19,457] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:19,461] [INFO] Selected 19 target genomes.
[2024-01-24 12:15:19,461] [INFO] Target genome list was writen to GCF_003026475.1_ASM302647v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:19,472] [INFO] Task started: fastANI
[2024-01-24 12:15:19,473] [INFO] Running command: fastANI --query /var/lib/cwl/stgd22c4247-9ca8-4849-878c-aaf8575e03c4/GCF_003026475.1_ASM302647v1_genomic.fna.gz --refList GCF_003026475.1_ASM302647v1_genomic.fna/target_genomes.txt --output GCF_003026475.1_ASM302647v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:37,101] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:37,102] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1cd0af88-4831-4362-bb3c-a518a8845437/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:37,102] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1cd0af88-4831-4362-bb3c-a518a8845437/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:37,120] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:15:37,120] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:37,120] [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 lipolyticum	strain=DSM 16190	GCA_003026475.1	266810	266810	type	True	100.0	1622	1624	95	conclusive
Photobacterium frigidiphilum	strain=JCM 12947	GCA_003025615.1	264736	264736	type	True	80.6362	648	1624	95	below_threshold
Photobacterium indicum	strain=ATCC 19614	GCA_003026215.1	81447	81447	type	True	80.4297	612	1624	95	below_threshold
Photobacterium alginatilyticum	strain=P03D4	GCA_009910675.1	1775171	1775171	type	True	80.1656	591	1624	95	below_threshold
Photobacterium chitinilyticum	strain=BEI247	GCA_004104355.1	2485123	2485123	type	True	80.1107	637	1624	95	below_threshold
Photobacterium proteolyticum	strain=13-12	GCA_001939735.1	1903952	1903952	type	True	79.9573	607	1624	95	below_threshold
Photobacterium sanguinicancri	strain=CECT 7579	GCA_024346675.1	875932	875932	type	True	79.6361	452	1624	95	below_threshold
Photobacterium swingsii	strain=DSM 24669	GCA_003026435.1	680026	680026	type	True	79.6265	435	1624	95	below_threshold
Photobacterium swingsii	strain=CECT 7576	GCA_024346715.1	680026	680026	type	True	79.6122	445	1624	95	below_threshold
Photobacterium sanctipauli	strain=A-394	GCA_000730475.1	1342794	1342794	type	True	79.4661	334	1624	95	below_threshold
Photobacterium sanctipauli	strain=DSM 100436	GCA_003026495.1	1342794	1342794	type	True	79.4496	444	1624	95	below_threshold
Photobacterium rosenbergii	strain=DSM 19138	GCA_003026455.1	294936	294936	type	True	79.4238	422	1624	95	below_threshold
Photobacterium swingsii	strain=CAIM 1393	GCA_001077885.1	680026	680026	type	True	79.4225	433	1624	95	below_threshold
Photobacterium sanguinicancri	strain=CAIM 1827	GCA_002265265.1	875932	875932	type	True	79.4077	422	1624	95	below_threshold
Photobacterium aphoticum	strain=DSM 25995	GCA_003025575.1	754436	754436	type	True	79.2161	397	1624	95	below_threshold
Photobacterium toruni	strain=CECT 9189	GCA_024529955.1	1935446	1935446	type	True	78.7778	289	1624	95	below_threshold
Photobacterium phosphoreum	strain=ATCC 11040	GCA_000949955.1	659	659	type	True	78.5528	299	1624	95	below_threshold
Photobacterium salinisoli	strain=LAM9072	GCA_003614885.1	1616783	1616783	type	True	78.1795	277	1624	95	below_threshold
Aliivibrio fischeri	strain=DSM 507	GCA_023983475.1	668	668	suspected-type	True	77.6237	161	1624	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:37,121] [INFO] DFAST Taxonomy check result was written to GCF_003026475.1_ASM302647v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:37,122] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:37,122] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:37,122] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1cd0af88-4831-4362-bb3c-a518a8845437/dqc_reference/checkm_data
[2024-01-24 12:15:37,123] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:37,170] [INFO] Task started: CheckM
[2024-01-24 12:15:37,170] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003026475.1_ASM302647v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003026475.1_ASM302647v1_genomic.fna/checkm_input GCF_003026475.1_ASM302647v1_genomic.fna/checkm_result
[2024-01-24 12:16:16,389] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:16,390] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:16,414] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:16,415] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:16,415] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003026475.1_ASM302647v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:16,415] [INFO] Task started: Blastn
[2024-01-24 12:16:16,416] [INFO] Running command: blastn -query GCF_003026475.1_ASM302647v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1cd0af88-4831-4362-bb3c-a518a8845437/dqc_reference/reference_markers_gtdb.fasta -out GCF_003026475.1_ASM302647v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:17,408] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:17,413] [INFO] Selected 18 target genomes.
[2024-01-24 12:16:17,413] [INFO] Target genome list was writen to GCF_003026475.1_ASM302647v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:17,426] [INFO] Task started: fastANI
[2024-01-24 12:16:17,427] [INFO] Running command: fastANI --query /var/lib/cwl/stgd22c4247-9ca8-4849-878c-aaf8575e03c4/GCF_003026475.1_ASM302647v1_genomic.fna.gz --refList GCF_003026475.1_ASM302647v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003026475.1_ASM302647v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:35,136] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:35,163] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:35,163] [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_003026475.1	s__Photobacterium lipolyticum	100.0	1622	1624	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003025615.1	s__Photobacterium frigidiphilum	80.668	644	1624	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.5718	N/A	N/A	N/A	N/A	1	-
GCF_000196255.1	s__Photobacterium profundum_A	80.5974	639	1624	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.5718	N/A	N/A	N/A	N/A	1	-
GCF_003026215.1	s__Photobacterium indicum	80.4691	606	1624	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	80.3628	598	1624	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	99.97	99.97	1.00	1.00	2	-
GCF_009910675.1	s__Photobacterium alginatilyticum	80.1486	595	1624	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	80.107	637	1624	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001939735.1	s__Photobacterium proteolyticum	79.9697	608	1624	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	79.4497	445	1624	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	79.4287	421	1624	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	95.32	95.32	0.83	0.83	2	-
GCF_002265265.1	s__Photobacterium sanguinicancri	79.4193	424	1624	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	97.87	97.87	0.90	0.90	2	-
GCF_001077885.1	s__Photobacterium swingsii	79.4166	434	1624	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	79.1954	428	1624	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000331515.1	s__Photobacterium marinum	79.1763	530	1624	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	96.66	96.66	0.88	0.88	2	-
GCF_001029435.1	s__Photobacterium aphoticum	79.1019	424	1624	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	99.09	97.29	0.97	0.93	4	-
GCF_000950415.1	s__Photobacterium leiognathi	78.9893	328	1624	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	97.11	96.59	0.91	0.88	15	-
GCF_009873615.1	s__Photobacterium lucens	78.98	324	1624	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	98.83	97.58	0.96	0.94	5	-
GCF_900185615.1	s__Photobacterium malacitanum	78.7313	297	1624	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	95.08	95.06	0.91	0.91	6	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:35,165] [INFO] GTDB search result was written to GCF_003026475.1_ASM302647v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:35,165] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:35,174] [INFO] DFAST_QC result json was written to GCF_003026475.1_ASM302647v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:35,174] [INFO] DFAST_QC completed!
[2024-01-24 12:16:35,174] [INFO] Total running time: 0h1m31s