[2024-01-24 13:57:43,123] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:43,124] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:43,125] [INFO] DQC Reference Directory: /var/lib/cwl/stg5f19eea7-9c52-4ec2-9dcd-449bd2e75fb8/dqc_reference
[2024-01-24 13:57:44,478] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:44,480] [INFO] Task started: Prodigal
[2024-01-24 13:57:44,480] [INFO] Running command: gunzip -c /var/lib/cwl/stgaf49e88b-fee0-4fce-8234-707e9a99078e/GCF_000950005.1_CFSAN029433_01.0_genomic.fna.gz | prodigal -d GCF_000950005.1_CFSAN029433_01.0_genomic.fna/cds.fna -a GCF_000950005.1_CFSAN029433_01.0_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:54,816] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:54,816] [INFO] Task started: HMMsearch
[2024-01-24 13:57:54,816] [INFO] Running command: hmmsearch --tblout GCF_000950005.1_CFSAN029433_01.0_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5f19eea7-9c52-4ec2-9dcd-449bd2e75fb8/dqc_reference/reference_markers.hmm GCF_000950005.1_CFSAN029433_01.0_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:55,157] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:55,158] [INFO] Found 6/6 markers.
[2024-01-24 13:57:55,202] [INFO] Query marker FASTA was written to GCF_000950005.1_CFSAN029433_01.0_genomic.fna/markers.fasta
[2024-01-24 13:57:55,203] [INFO] Task started: Blastn
[2024-01-24 13:57:55,203] [INFO] Running command: blastn -query GCF_000950005.1_CFSAN029433_01.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f19eea7-9c52-4ec2-9dcd-449bd2e75fb8/dqc_reference/reference_markers.fasta -out GCF_000950005.1_CFSAN029433_01.0_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:56,074] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:56,078] [INFO] Selected 16 target genomes.
[2024-01-24 13:57:56,078] [INFO] Target genome list was writen to GCF_000950005.1_CFSAN029433_01.0_genomic.fna/target_genomes.txt
[2024-01-24 13:57:56,084] [INFO] Task started: fastANI
[2024-01-24 13:57:56,085] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf49e88b-fee0-4fce-8234-707e9a99078e/GCF_000950005.1_CFSAN029433_01.0_genomic.fna.gz --refList GCF_000950005.1_CFSAN029433_01.0_genomic.fna/target_genomes.txt --output GCF_000950005.1_CFSAN029433_01.0_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:11,240] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:11,241] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5f19eea7-9c52-4ec2-9dcd-449bd2e75fb8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:11,241] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5f19eea7-9c52-4ec2-9dcd-449bd2e75fb8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:11,258] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:58:11,258] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:11,259] [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 angustum	strain=ATCC 25915	GCA_000950005.1	661	661	type	True	100.0	1595	1595	95	conclusive
Photobacterium angustum	strain=ATCC 25915	GCA_003026365.1	661	661	type	True	99.9849	1580	1595	95	conclusive
Photobacterium leiognathi	strain=ATCC 25521	GCA_003026235.1	553611	553611	type	True	84.6008	1105	1595	95	below_threshold
Photobacterium leiognathi	strain=ATCC 25521	GCA_000950415.1	553611	553611	type	True	84.5998	1079	1595	95	below_threshold
Photobacterium lucens	strain=CAIM 1937	GCA_009873615.1	2562949	2562949	type	True	84.1517	933	1595	95	below_threshold
Photobacterium aquimaris	strain=GCSL-P109	GCA_001676085.1	512643	512643	suspected-type	True	80.6483	616	1595	95	below_threshold
Photobacterium aquimaris	strain=DSM 23343	GCA_003025415.1	512643	512643	suspected-type	True	80.6316	630	1595	95	below_threshold
Photobacterium kishitanii	strain=ATCC:BAA-1194	GCA_003026355.1	318456	318456	type	True	80.54	626	1595	95	below_threshold
Photobacterium andalusiense	strain=CECT 9192	GCA_900185625.1	2204296	2204296	type	True	80.5013	611	1595	95	below_threshold
Photobacterium toruni	strain=CECT 9189	GCA_024529955.1	1935446	1935446	type	True	80.4559	581	1595	95	below_threshold
Photobacterium kishitanii	strain=ATCC BAA-1194	GCA_000950095.1	318456	318456	type	True	80.4262	640	1595	95	below_threshold
Photobacterium kishitanii	strain=pjapo.1.1	GCA_003025975.1	318456	318456	type	True	80.3618	639	1595	95	below_threshold
Photobacterium phosphoreum	strain=ATCC 11040	GCA_000949955.1	659	659	type	True	80.2317	578	1595	95	below_threshold
Photobacterium sanguinicancri	strain=CECT 7579	GCA_024346675.1	875932	875932	type	True	79.2568	375	1595	95	below_threshold
Aliivibrio fischeri	strain=DSM 507	GCA_023983475.1	668	668	suspected-type	True	78.1776	241	1595	95	below_threshold
Vibrio nitrifigilis	strain=NFV-1	GCA_015686695.1	2789781	2789781	type	True	77.8451	151	1595	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:11,261] [INFO] DFAST Taxonomy check result was written to GCF_000950005.1_CFSAN029433_01.0_genomic.fna/tc_result.tsv
[2024-01-24 13:58:11,261] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:11,262] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:11,262] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5f19eea7-9c52-4ec2-9dcd-449bd2e75fb8/dqc_reference/checkm_data
[2024-01-24 13:58:11,264] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:11,318] [INFO] Task started: CheckM
[2024-01-24 13:58:11,319] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000950005.1_CFSAN029433_01.0_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000950005.1_CFSAN029433_01.0_genomic.fna/checkm_input GCF_000950005.1_CFSAN029433_01.0_genomic.fna/checkm_result
[2024-01-24 13:58:48,119] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:48,120] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:48,136] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:48,137] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:48,137] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000950005.1_CFSAN029433_01.0_genomic.fna/markers.fasta)
[2024-01-24 13:58:48,137] [INFO] Task started: Blastn
[2024-01-24 13:58:48,138] [INFO] Running command: blastn -query GCF_000950005.1_CFSAN029433_01.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f19eea7-9c52-4ec2-9dcd-449bd2e75fb8/dqc_reference/reference_markers_gtdb.fasta -out GCF_000950005.1_CFSAN029433_01.0_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:49,341] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:49,349] [INFO] Selected 9 target genomes.
[2024-01-24 13:58:49,349] [INFO] Target genome list was writen to GCF_000950005.1_CFSAN029433_01.0_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:49,364] [INFO] Task started: fastANI
[2024-01-24 13:58:49,364] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf49e88b-fee0-4fce-8234-707e9a99078e/GCF_000950005.1_CFSAN029433_01.0_genomic.fna.gz --refList GCF_000950005.1_CFSAN029433_01.0_genomic.fna/target_genomes_gtdb.txt --output GCF_000950005.1_CFSAN029433_01.0_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:59,088] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:59,102] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:59,102] [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_003026365.1	s__Photobacterium angustum	99.9849	1580	1595	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	97.76	95.45	0.92	0.87	27	conclusive
GCF_003026105.1	s__Photobacterium sp003026105	94.1624	1347	1595	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	99.17	99.06	0.96	0.95	8	-
GCF_000153325.1	s__Photobacterium sp000153325	93.3902	1381	1595	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000950415.1	s__Photobacterium leiognathi	84.5848	1082	1595	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	84.1333	935	1595	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	98.83	97.58	0.96	0.94	5	-
GCF_002954455.1	s__Photobacterium aquimaris	80.6929	634	1595	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	80.5844	603	1595	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	80.5218	630	1595	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	80.3511	587	1595	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:59,104] [INFO] GTDB search result was written to GCF_000950005.1_CFSAN029433_01.0_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:59,105] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:59,108] [INFO] DFAST_QC result json was written to GCF_000950005.1_CFSAN029433_01.0_genomic.fna/dqc_result.json
[2024-01-24 13:58:59,108] [INFO] DFAST_QC completed!
[2024-01-24 13:58:59,109] [INFO] Total running time: 0h1m16s