[2024-01-25 18:01:35,599] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:01:35,601] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:01:35,601] [INFO] DQC Reference Directory: /var/lib/cwl/stgc5b1ffab-9554-44dd-8745-636031b2e853/dqc_reference
[2024-01-25 18:01:36,749] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:01:36,750] [INFO] Task started: Prodigal
[2024-01-25 18:01:36,750] [INFO] Running command: gunzip -c /var/lib/cwl/stga8ae0175-cc54-487c-9482-251dcb3344ad/GCF_003025615.1_ASM302561v1_genomic.fna.gz | prodigal -d GCF_003025615.1_ASM302561v1_genomic.fna/cds.fna -a GCF_003025615.1_ASM302561v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:01:48,973] [INFO] Task succeeded: Prodigal
[2024-01-25 18:01:48,974] [INFO] Task started: HMMsearch
[2024-01-25 18:01:48,974] [INFO] Running command: hmmsearch --tblout GCF_003025615.1_ASM302561v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc5b1ffab-9554-44dd-8745-636031b2e853/dqc_reference/reference_markers.hmm GCF_003025615.1_ASM302561v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:01:49,276] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:01:49,277] [INFO] Found 6/6 markers.
[2024-01-25 18:01:49,324] [INFO] Query marker FASTA was written to GCF_003025615.1_ASM302561v1_genomic.fna/markers.fasta
[2024-01-25 18:01:49,324] [INFO] Task started: Blastn
[2024-01-25 18:01:49,324] [INFO] Running command: blastn -query GCF_003025615.1_ASM302561v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc5b1ffab-9554-44dd-8745-636031b2e853/dqc_reference/reference_markers.fasta -out GCF_003025615.1_ASM302561v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:01:50,058] [INFO] Task succeeded: Blastn
[2024-01-25 18:01:50,062] [INFO] Selected 20 target genomes.
[2024-01-25 18:01:50,063] [INFO] Target genome list was writen to GCF_003025615.1_ASM302561v1_genomic.fna/target_genomes.txt
[2024-01-25 18:01:50,105] [INFO] Task started: fastANI
[2024-01-25 18:01:50,105] [INFO] Running command: fastANI --query /var/lib/cwl/stga8ae0175-cc54-487c-9482-251dcb3344ad/GCF_003025615.1_ASM302561v1_genomic.fna.gz --refList GCF_003025615.1_ASM302561v1_genomic.fna/target_genomes.txt --output GCF_003025615.1_ASM302561v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:02:12,159] [INFO] Task succeeded: fastANI
[2024-01-25 18:02:12,160] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc5b1ffab-9554-44dd-8745-636031b2e853/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:02:12,161] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc5b1ffab-9554-44dd-8745-636031b2e853/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:02:12,173] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:02:12,173] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:02:12,173] [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 frigidiphilum	strain=JCM 12947	GCA_003025615.1	264736	264736	type	True	100.0	2074	2081	95	conclusive
Photobacterium indicum	strain=ATCC 19614	GCA_003026215.1	81447	81447	type	True	94.7011	1705	2081	95	below_threshold
Photobacterium lipolyticum	strain=DSM 16190	GCA_003026475.1	266810	266810	type	True	80.8034	622	2081	95	below_threshold
Photobacterium sanguinicancri	strain=CECT 7579	GCA_024346675.1	875932	875932	type	True	79.4934	507	2081	95	below_threshold
Photobacterium swingsii	strain=CECT 7576	GCA_024346715.1	680026	680026	type	True	79.4116	506	2081	95	below_threshold
Photobacterium swingsii	strain=CAIM 1393	GCA_001077885.1	680026	680026	type	True	79.341	490	2081	95	below_threshold
Photobacterium chitinilyticum	strain=BEI247	GCA_004104355.1	2485123	2485123	type	True	79.3025	515	2081	95	below_threshold
Photobacterium sanguinicancri	strain=CAIM 1827	GCA_002265265.1	875932	875932	type	True	79.2813	497	2081	95	below_threshold
Photobacterium toruni	strain=CECT 9189	GCA_024529955.1	1935446	1935446	type	True	79.0715	365	2081	95	below_threshold
Photobacterium phosphoreum	strain=ATCC 11040	GCA_000949955.1	659	659	type	True	79.0109	353	2081	95	below_threshold
Photobacterium piscicola	strain=type strain: NCCB 100098	GCA_900166965.1	1378299	1378299	type	True	78.9493	367	2081	95	below_threshold
Photobacterium alginatilyticum	strain=P03D4	GCA_009910675.1	1775171	1775171	type	True	78.9338	458	2081	95	below_threshold
Photobacterium toruni	strain=CECT 9189	GCA_900166975.1	1935446	1935446	type	True	78.9188	372	2081	95	below_threshold
Photobacterium angustum	strain=ATCC 25915	GCA_003026365.1	661	661	type	True	78.8892	401	2081	95	below_threshold
Photobacterium angustum	strain=ATCC 25915	GCA_000950005.1	661	661	type	True	78.8207	388	2081	95	below_threshold
Vibrio cortegadensis	strain=CECT 7227	GCA_024347395.1	1328770	1328770	type	True	78.2467	203	2081	95	below_threshold
Vibrio chagasii	strain=LMG 21353	GCA_024347355.1	170679	170679	suspected-type	True	77.9486	195	2081	95	below_threshold
Vibrio chagasii	strain=LMG 21353	GCA_005281815.1	170679	170679	suspected-type	True	77.9336	186	2081	95	below_threshold
Vibrio chagasii	strain=CCUG 48643	GCA_008801295.1	170679	170679	suspected-type	True	77.8302	182	2081	95	below_threshold
Vibrio nitrifigilis	strain=NFV-1	GCA_015686695.1	2789781	2789781	type	True	77.3702	132	2081	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:02:12,175] [INFO] DFAST Taxonomy check result was written to GCF_003025615.1_ASM302561v1_genomic.fna/tc_result.tsv
[2024-01-25 18:02:12,175] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:02:12,175] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:02:12,175] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc5b1ffab-9554-44dd-8745-636031b2e853/dqc_reference/checkm_data
[2024-01-25 18:02:12,176] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:02:12,239] [INFO] Task started: CheckM
[2024-01-25 18:02:12,239] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003025615.1_ASM302561v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003025615.1_ASM302561v1_genomic.fna/checkm_input GCF_003025615.1_ASM302561v1_genomic.fna/checkm_result
[2024-01-25 18:02:50,684] [INFO] Task succeeded: CheckM
[2024-01-25 18:02:50,685] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:02:50,703] [INFO] ===== Completeness check finished =====
[2024-01-25 18:02:50,703] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:02:50,704] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003025615.1_ASM302561v1_genomic.fna/markers.fasta)
[2024-01-25 18:02:50,704] [INFO] Task started: Blastn
[2024-01-25 18:02:50,704] [INFO] Running command: blastn -query GCF_003025615.1_ASM302561v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc5b1ffab-9554-44dd-8745-636031b2e853/dqc_reference/reference_markers_gtdb.fasta -out GCF_003025615.1_ASM302561v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:02:51,831] [INFO] Task succeeded: Blastn
[2024-01-25 18:02:51,834] [INFO] Selected 10 target genomes.
[2024-01-25 18:02:51,834] [INFO] Target genome list was writen to GCF_003025615.1_ASM302561v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:02:51,847] [INFO] Task started: fastANI
[2024-01-25 18:02:51,847] [INFO] Running command: fastANI --query /var/lib/cwl/stga8ae0175-cc54-487c-9482-251dcb3344ad/GCF_003025615.1_ASM302561v1_genomic.fna.gz --refList GCF_003025615.1_ASM302561v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003025615.1_ASM302561v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:03:04,284] [INFO] Task succeeded: fastANI
[2024-01-25 18:03:04,291] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:03:04,292] [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_003025615.1	s__Photobacterium frigidiphilum	100.0	2074	2081	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.5718	N/A	N/A	N/A	N/A	1	conclusive
GCF_000196255.1	s__Photobacterium profundum_A	95.5437	1715	2081	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	94.6894	1706	2081	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	93.619	1664	2081	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	80.8486	614	2081	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002265265.1	s__Photobacterium sanguinicancri	79.3048	496	2081	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	97.87	97.87	0.90	0.90	2	-
GCF_003026355.1	s__Photobacterium kishitanii	79.1793	353	2081	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	98.67	97.61	0.95	0.91	24	-
GCF_900166975.1	s__Photobacterium toruni	78.9354	369	2081	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153325.1	s__Photobacterium sp000153325	78.594	397	2081	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005281815.1	s__Vibrio chagasii	77.9231	188	2081	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.30	95.30	0.86	0.82	10	-
--------------------------------------------------------------------------------
[2024-01-25 18:03:04,293] [INFO] GTDB search result was written to GCF_003025615.1_ASM302561v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:03:04,293] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:03:04,296] [INFO] DFAST_QC result json was written to GCF_003025615.1_ASM302561v1_genomic.fna/dqc_result.json
[2024-01-25 18:03:04,296] [INFO] DFAST_QC completed!
[2024-01-25 18:03:04,297] [INFO] Total running time: 0h1m29s