[2024-01-24 12:14:35,265] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:35,267] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:35,267] [INFO] DQC Reference Directory: /var/lib/cwl/stg0bcb52a6-6537-4e38-a174-661bcf920857/dqc_reference
[2024-01-24 12:14:36,636] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:36,637] [INFO] Task started: Prodigal
[2024-01-24 12:14:36,638] [INFO] Running command: gunzip -c /var/lib/cwl/stg5957edfc-5dd8-4d79-907b-a06ff465a907/GCF_000820165.1_PRJEB7041_genomic.fna.gz | prodigal -d GCF_000820165.1_PRJEB7041_genomic.fna/cds.fna -a GCF_000820165.1_PRJEB7041_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:49,251] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:49,252] [INFO] Task started: HMMsearch
[2024-01-24 12:14:49,252] [INFO] Running command: hmmsearch --tblout GCF_000820165.1_PRJEB7041_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0bcb52a6-6537-4e38-a174-661bcf920857/dqc_reference/reference_markers.hmm GCF_000820165.1_PRJEB7041_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:49,592] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:49,594] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5957edfc-5dd8-4d79-907b-a06ff465a907/GCF_000820165.1_PRJEB7041_genomic.fna.gz]
[2024-01-24 12:14:49,643] [INFO] Query marker FASTA was written to GCF_000820165.1_PRJEB7041_genomic.fna/markers.fasta
[2024-01-24 12:14:49,644] [INFO] Task started: Blastn
[2024-01-24 12:14:49,644] [INFO] Running command: blastn -query GCF_000820165.1_PRJEB7041_genomic.fna/markers.fasta -db /var/lib/cwl/stg0bcb52a6-6537-4e38-a174-661bcf920857/dqc_reference/reference_markers.fasta -out GCF_000820165.1_PRJEB7041_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:50,659] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:50,663] [INFO] Selected 14 target genomes.
[2024-01-24 12:14:50,664] [INFO] Target genome list was writen to GCF_000820165.1_PRJEB7041_genomic.fna/target_genomes.txt
[2024-01-24 12:14:50,668] [INFO] Task started: fastANI
[2024-01-24 12:14:50,668] [INFO] Running command: fastANI --query /var/lib/cwl/stg5957edfc-5dd8-4d79-907b-a06ff465a907/GCF_000820165.1_PRJEB7041_genomic.fna.gz --refList GCF_000820165.1_PRJEB7041_genomic.fna/target_genomes.txt --output GCF_000820165.1_PRJEB7041_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:03,854] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:03,854] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0bcb52a6-6537-4e38-a174-661bcf920857/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:03,855] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0bcb52a6-6537-4e38-a174-661bcf920857/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:03,869] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:15:03,869] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:03,869] [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 taiwanensis	strain=LMG 24683	GCA_000820165.1	633417	633417	type	True	100.0	1361	1366	95	conclusive
Aeromonas taiwanensis	strain=LMG 24683	GCA_000699185.1	633417	633417	type	True	99.9248	1303	1366	95	conclusive
Aeromonas sanarellii	strain=LMG 24682	GCA_000820085.1	633415	633415	type	True	92.0348	1153	1366	95	below_threshold
Aeromonas caviae	strain=NCTC12244	GCA_900476005.1	648	648	type	True	91.048	1222	1366	95	below_threshold
Aeromonas caviae	strain=CECT 838	GCA_000819785.1	648	648	type	True	91.0247	1184	1366	95	below_threshold
Aeromonas caviae	strain=CECT 838	GCA_018360005.1	648	648	type	True	91.0111	1209	1366	95	below_threshold
Aeromonas dhakensis	strain=CIP 107500	GCA_000820305.1	196024	196024	type	True	89.2955	1146	1366	95	below_threshold
Aeromonas lusitana	strain=MDC 2473	GCA_002812985.1	931529	931529	type	True	88.2692	1149	1366	95	below_threshold
Aeromonas bivalvium	strain=CECT 7113	GCA_000819765.1	440079	440079	type	True	86.8271	1088	1366	95	below_threshold
Shewanella jiangmenensis	strain=JM162201	GCA_018596335.1	2837387	2837387	type	True	76.482	151	1366	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	76.4318	198	1366	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	76.3662	202	1366	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	76.3365	198	1366	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	76.2873	114	1366	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:03,871] [INFO] DFAST Taxonomy check result was written to GCF_000820165.1_PRJEB7041_genomic.fna/tc_result.tsv
[2024-01-24 12:15:03,872] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:03,872] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:03,872] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0bcb52a6-6537-4e38-a174-661bcf920857/dqc_reference/checkm_data
[2024-01-24 12:15:03,874] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:03,921] [INFO] Task started: CheckM
[2024-01-24 12:15:03,921] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000820165.1_PRJEB7041_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000820165.1_PRJEB7041_genomic.fna/checkm_input GCF_000820165.1_PRJEB7041_genomic.fna/checkm_result
[2024-01-24 12:15:44,522] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:44,523] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.31%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:44,541] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:44,541] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:44,541] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000820165.1_PRJEB7041_genomic.fna/markers.fasta)
[2024-01-24 12:15:44,542] [INFO] Task started: Blastn
[2024-01-24 12:15:44,542] [INFO] Running command: blastn -query GCF_000820165.1_PRJEB7041_genomic.fna/markers.fasta -db /var/lib/cwl/stg0bcb52a6-6537-4e38-a174-661bcf920857/dqc_reference/reference_markers_gtdb.fasta -out GCF_000820165.1_PRJEB7041_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:46,071] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:46,075] [INFO] Selected 9 target genomes.
[2024-01-24 12:15:46,075] [INFO] Target genome list was writen to GCF_000820165.1_PRJEB7041_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:46,080] [INFO] Task started: fastANI
[2024-01-24 12:15:46,080] [INFO] Running command: fastANI --query /var/lib/cwl/stg5957edfc-5dd8-4d79-907b-a06ff465a907/GCF_000820165.1_PRJEB7041_genomic.fna.gz --refList GCF_000820165.1_PRJEB7041_genomic.fna/target_genomes_gtdb.txt --output GCF_000820165.1_PRJEB7041_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:55,982] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:55,996] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:55,996] [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_000820165.1	s__Aeromonas taiwanensis	100.0	1361	1366	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	98.19	97.81	0.94	0.93	7	conclusive
GCF_000820085.1	s__Aeromonas sanarellii	92.0348	1153	1366	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	98.21	98.21	0.95	0.95	3	-
GCF_000819785.1	s__Aeromonas caviae	91.0211	1184	1366	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.93	97.49	0.90	0.83	112	-
GCF_000820305.1	s__Aeromonas dhakensis	89.2938	1146	1366	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.35	96.54	0.93	0.90	55	-
GCF_000014805.1	s__Aeromonas hydrophila	88.8618	1150	1366	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.01	96.24	0.92	0.87	120	-
GCF_002812985.1	s__Aeromonas lusitana	88.2742	1148	1366	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000819845.1	s__Aeromonas enteropelogenes	87.3096	1061	1366	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.20	96.87	0.93	0.91	7	-
GCF_000819765.1	s__Aeromonas bivalvium	86.8299	1088	1366	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	98.28	98.27	0.92	0.92	5	-
GCF_000819955.1	s__Aeromonas jandaei	85.8556	1022	1366	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.8323	96.79	96.38	0.92	0.87	26	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:55,997] [INFO] GTDB search result was written to GCF_000820165.1_PRJEB7041_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:55,998] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:56,001] [INFO] DFAST_QC result json was written to GCF_000820165.1_PRJEB7041_genomic.fna/dqc_result.json
[2024-01-24 12:15:56,001] [INFO] DFAST_QC completed!
[2024-01-24 12:15:56,002] [INFO] Total running time: 0h1m21s