[2024-01-24 12:44:11,224] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:11,230] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:11,230] [INFO] DQC Reference Directory: /var/lib/cwl/stg55b82602-b597-4f18-9453-35120225d8b3/dqc_reference
[2024-01-24 12:44:12,587] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:12,587] [INFO] Task started: Prodigal
[2024-01-24 12:44:12,588] [INFO] Running command: gunzip -c /var/lib/cwl/stg8f4f300e-675d-4a62-84a1-e2c2d9969752/GCF_000819825.1_PRJEB7027_genomic.fna.gz | prodigal -d GCF_000819825.1_PRJEB7027_genomic.fna/cds.fna -a GCF_000819825.1_PRJEB7027_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:25,929] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:25,930] [INFO] Task started: HMMsearch
[2024-01-24 12:44:25,930] [INFO] Running command: hmmsearch --tblout GCF_000819825.1_PRJEB7027_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg55b82602-b597-4f18-9453-35120225d8b3/dqc_reference/reference_markers.hmm GCF_000819825.1_PRJEB7027_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:26,282] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:26,283] [INFO] Found 6/6 markers.
[2024-01-24 12:44:26,324] [INFO] Query marker FASTA was written to GCF_000819825.1_PRJEB7027_genomic.fna/markers.fasta
[2024-01-24 12:44:26,324] [INFO] Task started: Blastn
[2024-01-24 12:44:26,324] [INFO] Running command: blastn -query GCF_000819825.1_PRJEB7027_genomic.fna/markers.fasta -db /var/lib/cwl/stg55b82602-b597-4f18-9453-35120225d8b3/dqc_reference/reference_markers.fasta -out GCF_000819825.1_PRJEB7027_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:27,343] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:27,347] [INFO] Selected 17 target genomes.
[2024-01-24 12:44:27,348] [INFO] Target genome list was writen to GCF_000819825.1_PRJEB7027_genomic.fna/target_genomes.txt
[2024-01-24 12:44:27,362] [INFO] Task started: fastANI
[2024-01-24 12:44:27,363] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f4f300e-675d-4a62-84a1-e2c2d9969752/GCF_000819825.1_PRJEB7027_genomic.fna.gz --refList GCF_000819825.1_PRJEB7027_genomic.fna/target_genomes.txt --output GCF_000819825.1_PRJEB7027_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:44:43,606] [INFO] Task succeeded: fastANI
[2024-01-24 12:44:43,607] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg55b82602-b597-4f18-9453-35120225d8b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:44:43,607] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg55b82602-b597-4f18-9453-35120225d8b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:44:43,622] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:44:43,622] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:44:43,622] [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 encheleia	strain=CECT 4342	GCA_000819825.1	73010	73010	type	True	100.0	1472	1475	95	conclusive
Aeromonas encheleia	strain=NCTC12917	GCA_900637545.1	73010	73010	type	True	99.995	1475	1475	95	conclusive
Aeromonas aquatica	strain=AE235	GCA_000764655.1	558964	558964	type	True	91.5122	1248	1475	95	below_threshold
Aeromonas eucrenophila	strain=CECT 4224	GCA_000819865.1	649	649	type	True	90.0298	1288	1475	95	below_threshold
Aeromonas tecta	strain=CECT 7082	GCA_000820185.2	324617	324617	type	True	89.8033	1319	1475	95	below_threshold
Aeromonas media	strain=CECT 4232	GCA_000819985.1	651	651	type	True	89.6907	1164	1475	95	below_threshold
Aeromonas media	strain=ATCC 33907	GCA_018359985.1	651	651	type	True	89.6632	1199	1475	95	below_threshold
Aeromonas lusitana	strain=MDC 2473	GCA_002812985.1	931529	931529	type	True	89.2424	1276	1475	95	below_threshold
Aeromonas bestiarum	strain=CECT 4227	GCA_000819745.1	105751	105751	type	True	88.806	1228	1475	95	below_threshold
Aeromonas piscicola	strain=LMG 24783	GCA_000820005.1	600645	600645	type	True	88.2375	1233	1475	95	below_threshold
Aeromonas salmonicida subsp. masoucida	strain=NBRC 13784	GCA_000647955.1	197700	645	type	True	87.2198	1122	1475	95	below_threshold
Aeromonas salmonicida	strain=NCTC12959	GCA_900445115.1	645	645	type	True	87.0932	1194	1475	95	below_threshold
Pseudomonas mangiferae	strain=DMKU BBB3-04	GCA_007109405.1	2593654	2593654	type	True	76.6777	198	1475	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	76.4204	197	1475	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	76.231	110	1475	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	76.2131	113	1475	95	below_threshold
Shewanella insulae	strain=JBTF-M18	GCA_009831655.1	2681496	2681496	type	True	76.136	123	1475	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:44:43,625] [INFO] DFAST Taxonomy check result was written to GCF_000819825.1_PRJEB7027_genomic.fna/tc_result.tsv
[2024-01-24 12:44:43,626] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:44:43,626] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:44:43,627] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg55b82602-b597-4f18-9453-35120225d8b3/dqc_reference/checkm_data
[2024-01-24 12:44:43,628] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:44:43,673] [INFO] Task started: CheckM
[2024-01-24 12:44:43,674] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000819825.1_PRJEB7027_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000819825.1_PRJEB7027_genomic.fna/checkm_input GCF_000819825.1_PRJEB7027_genomic.fna/checkm_result
[2024-01-24 12:45:25,459] [INFO] Task succeeded: CheckM
[2024-01-24 12:45:25,460] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.10%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:45:25,483] [INFO] ===== Completeness check finished =====
[2024-01-24 12:45:25,483] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:45:25,483] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000819825.1_PRJEB7027_genomic.fna/markers.fasta)
[2024-01-24 12:45:25,484] [INFO] Task started: Blastn
[2024-01-24 12:45:25,484] [INFO] Running command: blastn -query GCF_000819825.1_PRJEB7027_genomic.fna/markers.fasta -db /var/lib/cwl/stg55b82602-b597-4f18-9453-35120225d8b3/dqc_reference/reference_markers_gtdb.fasta -out GCF_000819825.1_PRJEB7027_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:27,108] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:27,112] [INFO] Selected 12 target genomes.
[2024-01-24 12:45:27,112] [INFO] Target genome list was writen to GCF_000819825.1_PRJEB7027_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:45:27,132] [INFO] Task started: fastANI
[2024-01-24 12:45:27,132] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f4f300e-675d-4a62-84a1-e2c2d9969752/GCF_000819825.1_PRJEB7027_genomic.fna.gz --refList GCF_000819825.1_PRJEB7027_genomic.fna/target_genomes_gtdb.txt --output GCF_000819825.1_PRJEB7027_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:45:40,331] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:40,346] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:45:40,346] [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_900637545.1	s__Aeromonas encheleia	99.995	1475	1475	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	98.38	97.80	0.95	0.91	5	conclusive
GCF_000764655.1	s__Aeromonas aquatica	91.5122	1248	1475	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010974825.1	s__Aeromonas rivipollensis	90.1947	1264	1475	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.26	95.18	0.91	0.86	15	-
GCF_000819865.1	s__Aeromonas eucrenophila	90.0298	1288	1475	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000820185.1	s__Aeromonas tecta	89.8033	1319	1475	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000819985.1	s__Aeromonas media	89.6907	1164	1475	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.95	97.16	0.92	0.87	16	-
GCF_002812985.1	s__Aeromonas lusitana	89.2424	1276	1475	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000819745.1	s__Aeromonas bestiarum	88.8057	1227	1475	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.5033	97.44	97.31	0.93	0.91	4	-
GCF_000820005.1	s__Aeromonas piscicola	88.2375	1233	1475	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.5033	97.81	97.81	0.93	0.93	2	-
GCF_001643305.1	s__Aeromonas salmonicida	87.1696	1150	1475	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	99.08	96.89	0.95	0.86	74	-
GCF_000820045.1	s__Aeromonas rivuli	85.4369	1098	1475	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000388115.1	s__Aeromonas molluscorum	84.3809	949	1475	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:45:40,348] [INFO] GTDB search result was written to GCF_000819825.1_PRJEB7027_genomic.fna/result_gtdb.tsv
[2024-01-24 12:45:40,348] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:45:40,352] [INFO] DFAST_QC result json was written to GCF_000819825.1_PRJEB7027_genomic.fna/dqc_result.json
[2024-01-24 12:45:40,352] [INFO] DFAST_QC completed!
[2024-01-24 12:45:40,352] [INFO] Total running time: 0h1m29s