[2024-01-25 18:59:20,672] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:59:20,674] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:59:20,674] [INFO] DQC Reference Directory: /var/lib/cwl/stgc321592c-6238-420f-9477-df9bc7996b77/dqc_reference
[2024-01-25 18:59:21,815] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:59:21,815] [INFO] Task started: Prodigal
[2024-01-25 18:59:21,815] [INFO] Running command: gunzip -c /var/lib/cwl/stg1196e514-3acb-4d91-94b1-2aa0a0d35c75/GCF_000367845.1_Adiv1.0_genomic.fna.gz | prodigal -d GCF_000367845.1_Adiv1.0_genomic.fna/cds.fna -a GCF_000367845.1_Adiv1.0_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:59:32,049] [INFO] Task succeeded: Prodigal
[2024-01-25 18:59:32,049] [INFO] Task started: HMMsearch
[2024-01-25 18:59:32,049] [INFO] Running command: hmmsearch --tblout GCF_000367845.1_Adiv1.0_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc321592c-6238-420f-9477-df9bc7996b77/dqc_reference/reference_markers.hmm GCF_000367845.1_Adiv1.0_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:59:32,261] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:59:32,262] [INFO] Found 6/6 markers.
[2024-01-25 18:59:32,292] [INFO] Query marker FASTA was written to GCF_000367845.1_Adiv1.0_genomic.fna/markers.fasta
[2024-01-25 18:59:32,293] [INFO] Task started: Blastn
[2024-01-25 18:59:32,293] [INFO] Running command: blastn -query GCF_000367845.1_Adiv1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stgc321592c-6238-420f-9477-df9bc7996b77/dqc_reference/reference_markers.fasta -out GCF_000367845.1_Adiv1.0_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:59:33,191] [INFO] Task succeeded: Blastn
[2024-01-25 18:59:33,194] [INFO] Selected 12 target genomes.
[2024-01-25 18:59:33,194] [INFO] Target genome list was writen to GCF_000367845.1_Adiv1.0_genomic.fna/target_genomes.txt
[2024-01-25 18:59:33,200] [INFO] Task started: fastANI
[2024-01-25 18:59:33,200] [INFO] Running command: fastANI --query /var/lib/cwl/stg1196e514-3acb-4d91-94b1-2aa0a0d35c75/GCF_000367845.1_Adiv1.0_genomic.fna.gz --refList GCF_000367845.1_Adiv1.0_genomic.fna/target_genomes.txt --output GCF_000367845.1_Adiv1.0_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:59:43,857] [INFO] Task succeeded: fastANI
[2024-01-25 18:59:43,858] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc321592c-6238-420f-9477-df9bc7996b77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:59:43,858] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc321592c-6238-420f-9477-df9bc7996b77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:59:43,866] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:59:43,866] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:59:43,866] [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
Aeromonas diversa	strain=2478-85	GCA_000367845.1	502790	502790	type	True	100.0	1290	1296	95	conclusive
Aeromonas diversa	strain=CECT 4254	GCA_000819805.1	502790	502790	type	True	99.9844	1286	1296	95	conclusive
Aeromonas schubertii	strain=ATCC 43700	GCA_001481395.1	652	652	type	True	90.4651	1111	1296	95	below_threshold
Aeromonas schubertii	strain=CECT 4240	GCA_000820105.2	652	652	type	True	90.4076	1097	1296	95	below_threshold
Aeromonas simiae	strain=CIP 107798	GCA_000820125.1	218936	218936	type	True	84.5164	863	1296	95	below_threshold
Aeromonas taiwanensis	strain=LMG 24683	GCA_000699185.1	633417	633417	type	True	82.8063	843	1296	95	below_threshold
Aeromonas sanarellii	strain=LMG 24682	GCA_000820085.1	633415	633415	type	True	82.7676	853	1296	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	76.9372	176	1296	95	below_threshold
Shewanella jiangmenensis	strain=JM162201	GCA_018596335.1	2837387	2837387	type	True	76.4736	138	1296	95	below_threshold
Alcanivorax marinus	strain=R8-12	GCA_025532125.1	1177169	1177169	type	True	76.4342	103	1296	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	76.3836	162	1296	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	76.3811	187	1296	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:59:43,869] [INFO] DFAST Taxonomy check result was written to GCF_000367845.1_Adiv1.0_genomic.fna/tc_result.tsv
[2024-01-25 18:59:43,869] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:59:43,869] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:59:43,870] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc321592c-6238-420f-9477-df9bc7996b77/dqc_reference/checkm_data
[2024-01-25 18:59:43,870] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:59:43,913] [INFO] Task started: CheckM
[2024-01-25 18:59:43,913] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000367845.1_Adiv1.0_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000367845.1_Adiv1.0_genomic.fna/checkm_input GCF_000367845.1_Adiv1.0_genomic.fna/checkm_result
[2024-01-25 19:00:15,857] [INFO] Task succeeded: CheckM
[2024-01-25 19:00:15,859] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:00:15,882] [INFO] ===== Completeness check finished =====
[2024-01-25 19:00:15,882] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:00:15,884] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000367845.1_Adiv1.0_genomic.fna/markers.fasta)
[2024-01-25 19:00:15,884] [INFO] Task started: Blastn
[2024-01-25 19:00:15,884] [INFO] Running command: blastn -query GCF_000367845.1_Adiv1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stgc321592c-6238-420f-9477-df9bc7996b77/dqc_reference/reference_markers_gtdb.fasta -out GCF_000367845.1_Adiv1.0_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:00:17,518] [INFO] Task succeeded: Blastn
[2024-01-25 19:00:17,521] [INFO] Selected 12 target genomes.
[2024-01-25 19:00:17,521] [INFO] Target genome list was writen to GCF_000367845.1_Adiv1.0_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:00:17,531] [INFO] Task started: fastANI
[2024-01-25 19:00:17,531] [INFO] Running command: fastANI --query /var/lib/cwl/stg1196e514-3acb-4d91-94b1-2aa0a0d35c75/GCF_000367845.1_Adiv1.0_genomic.fna.gz --refList GCF_000367845.1_Adiv1.0_genomic.fna/target_genomes_gtdb.txt --output GCF_000367845.1_Adiv1.0_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:00:29,182] [INFO] Task succeeded: fastANI
[2024-01-25 19:00:29,190] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:00:29,190] [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_000819805.1	s__Aeromonas diversa	99.9844	1286	1296	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	99.98	99.98	0.99	0.99	2	conclusive
GCF_000820105.1	s__Aeromonas schubertii	90.4114	1097	1296	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	99.15	98.66	0.97	0.94	4	-
GCF_000820125.1	s__Aeromonas simiae	84.5201	862	1296	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	96.54	96.54	0.89	0.89	2	-
GCF_000820305.1	s__Aeromonas dhakensis	83.0445	910	1296	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.35	96.54	0.93	0.90	55	-
GCF_000820165.1	s__Aeromonas taiwanensis	82.8619	854	1296	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	98.19	97.81	0.94	0.93	7	-
GCF_000820085.1	s__Aeromonas sanarellii	82.7822	851	1296	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	98.21	98.21	0.95	0.95	3	-
GCF_000014805.1	s__Aeromonas hydrophila	82.6473	887	1296	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.01	96.24	0.92	0.87	120	-
GCF_010974825.1	s__Aeromonas rivipollensis	82.3761	829	1296	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.26	95.18	0.91	0.86	15	-
GCF_000819785.1	s__Aeromonas caviae	82.3717	844	1296	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.93	97.49	0.90	0.83	112	-
GCF_000819985.1	s__Aeromonas media	82.2969	816	1296	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.95	97.16	0.92	0.87	16	-
GCF_000819765.1	s__Aeromonas bivalvium	82.2829	819	1296	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	98.28	98.27	0.92	0.92	5	-
GCF_900156095.1	s__Aeromonas sp900156095	81.2686	701	1296	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:00:29,196] [INFO] GTDB search result was written to GCF_000367845.1_Adiv1.0_genomic.fna/result_gtdb.tsv
[2024-01-25 19:00:29,198] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:00:29,201] [INFO] DFAST_QC result json was written to GCF_000367845.1_Adiv1.0_genomic.fna/dqc_result.json
[2024-01-25 19:00:29,201] [INFO] DFAST_QC completed!
[2024-01-25 19:00:29,201] [INFO] Total running time: 0h1m9s