[2024-01-24 15:19:52,319] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:19:52,323] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:19:52,323] [INFO] DQC Reference Directory: /var/lib/cwl/stg985f29a7-2ee6-492c-92bf-f307e707e5cb/dqc_reference
[2024-01-24 15:19:53,632] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:19:53,632] [INFO] Task started: Prodigal
[2024-01-24 15:19:53,633] [INFO] Running command: gunzip -c /var/lib/cwl/stgdfa35253-a0d6-4326-abc1-11006c639463/GCF_900637545.1_51438_G01_genomic.fna.gz | prodigal -d GCF_900637545.1_51438_G01_genomic.fna/cds.fna -a GCF_900637545.1_51438_G01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:20:08,817] [INFO] Task succeeded: Prodigal
[2024-01-24 15:20:08,817] [INFO] Task started: HMMsearch
[2024-01-24 15:20:08,817] [INFO] Running command: hmmsearch --tblout GCF_900637545.1_51438_G01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg985f29a7-2ee6-492c-92bf-f307e707e5cb/dqc_reference/reference_markers.hmm GCF_900637545.1_51438_G01_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:20:09,184] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:20:09,186] [INFO] Found 6/6 markers.
[2024-01-24 15:20:09,235] [INFO] Query marker FASTA was written to GCF_900637545.1_51438_G01_genomic.fna/markers.fasta
[2024-01-24 15:20:09,236] [INFO] Task started: Blastn
[2024-01-24 15:20:09,236] [INFO] Running command: blastn -query GCF_900637545.1_51438_G01_genomic.fna/markers.fasta -db /var/lib/cwl/stg985f29a7-2ee6-492c-92bf-f307e707e5cb/dqc_reference/reference_markers.fasta -out GCF_900637545.1_51438_G01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:20:10,244] [INFO] Task succeeded: Blastn
[2024-01-24 15:20:10,249] [INFO] Selected 17 target genomes.
[2024-01-24 15:20:10,250] [INFO] Target genome list was writen to GCF_900637545.1_51438_G01_genomic.fna/target_genomes.txt
[2024-01-24 15:20:10,257] [INFO] Task started: fastANI
[2024-01-24 15:20:10,258] [INFO] Running command: fastANI --query /var/lib/cwl/stgdfa35253-a0d6-4326-abc1-11006c639463/GCF_900637545.1_51438_G01_genomic.fna.gz --refList GCF_900637545.1_51438_G01_genomic.fna/target_genomes.txt --output GCF_900637545.1_51438_G01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:20:28,627] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:28,628] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg985f29a7-2ee6-492c-92bf-f307e707e5cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:20:28,629] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg985f29a7-2ee6-492c-92bf-f307e707e5cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:20:28,648] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:20:28,648] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:20:28,648] [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=NCTC12917	GCA_900637545.1	73010	73010	type	True	100.0	1511	1514	95	conclusive
Aeromonas encheleia	strain=CECT 4342	GCA_000819825.1	73010	73010	type	True	99.9784	1473	1514	95	conclusive
Aeromonas aquatica	strain=AE235	GCA_000764655.1	558964	558964	type	True	91.4503	1253	1514	95	below_threshold
Aeromonas eucrenophila	strain=CECT 4224	GCA_000819865.1	649	649	type	True	90.0365	1301	1514	95	below_threshold
Aeromonas tecta	strain=CECT 7082	GCA_000820185.2	324617	324617	type	True	89.7201	1318	1514	95	below_threshold
Aeromonas media	strain=CECT 4232	GCA_000819985.1	651	651	type	True	89.6329	1170	1514	95	below_threshold
Aeromonas media	strain=ATCC 33907	GCA_018359985.1	651	651	type	True	89.6319	1191	1514	95	below_threshold
Aeromonas lusitana	strain=MDC 2473	GCA_002812985.1	931529	931529	type	True	89.2192	1283	1514	95	below_threshold
Aeromonas bestiarum	strain=CECT 4227	GCA_000819745.1	105751	105751	type	True	88.8656	1236	1514	95	below_threshold
Aeromonas piscicola	strain=LMG 24783	GCA_000820005.1	600645	600645	type	True	88.2673	1236	1514	95	below_threshold
Aeromonas salmonicida	strain=NCTC12959	GCA_900445115.1	645	645	type	True	87.2052	1208	1514	95	below_threshold
Aeromonas salmonicida subsp. masoucida	strain=NBRC 13784	GCA_000647955.1	197700	645	type	True	87.1661	1132	1514	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	77.0974	194	1514	95	below_threshold
Pseudomonas mangiferae	strain=DMKU BBB3-04	GCA_007109405.1	2593654	2593654	type	True	76.6203	210	1514	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	76.3663	114	1514	95	below_threshold
Shewanella insulae	strain=JBTF-M18	GCA_009831655.1	2681496	2681496	type	True	76.2604	130	1514	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	76.1453	130	1514	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:20:28,650] [INFO] DFAST Taxonomy check result was written to GCF_900637545.1_51438_G01_genomic.fna/tc_result.tsv
[2024-01-24 15:20:28,651] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:20:28,651] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:20:28,652] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg985f29a7-2ee6-492c-92bf-f307e707e5cb/dqc_reference/checkm_data
[2024-01-24 15:20:28,654] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:20:28,704] [INFO] Task started: CheckM
[2024-01-24 15:20:28,704] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900637545.1_51438_G01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900637545.1_51438_G01_genomic.fna/checkm_input GCF_900637545.1_51438_G01_genomic.fna/checkm_result
[2024-01-24 15:21:14,135] [INFO] Task succeeded: CheckM
[2024-01-24 15:21:14,137] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.10%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:21:14,158] [INFO] ===== Completeness check finished =====
[2024-01-24 15:21:14,158] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:21:14,158] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900637545.1_51438_G01_genomic.fna/markers.fasta)
[2024-01-24 15:21:14,159] [INFO] Task started: Blastn
[2024-01-24 15:21:14,159] [INFO] Running command: blastn -query GCF_900637545.1_51438_G01_genomic.fna/markers.fasta -db /var/lib/cwl/stg985f29a7-2ee6-492c-92bf-f307e707e5cb/dqc_reference/reference_markers_gtdb.fasta -out GCF_900637545.1_51438_G01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:21:15,841] [INFO] Task succeeded: Blastn
[2024-01-24 15:21:15,845] [INFO] Selected 12 target genomes.
[2024-01-24 15:21:15,845] [INFO] Target genome list was writen to GCF_900637545.1_51438_G01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:21:15,854] [INFO] Task started: fastANI
[2024-01-24 15:21:15,854] [INFO] Running command: fastANI --query /var/lib/cwl/stgdfa35253-a0d6-4326-abc1-11006c639463/GCF_900637545.1_51438_G01_genomic.fna.gz --refList GCF_900637545.1_51438_G01_genomic.fna/target_genomes_gtdb.txt --output GCF_900637545.1_51438_G01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:21:29,981] [INFO] Task succeeded: fastANI
[2024-01-24 15:21:29,996] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:21:29,996] [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_900637545.1	s__Aeromonas encheleia	100.0	1512	1514	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	91.4401	1254	1514	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	90.2053	1261	1514	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	90.014	1303	1514	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	89.7201	1318	1514	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	89.6329	1170	1514	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	89.2156	1283	1514	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	88.8725	1235	1514	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	88.2633	1237	1514	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	87.1066	1170	1514	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	85.4647	1099	1514	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	84.4461	956	1514	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 15:21:30,000] [INFO] GTDB search result was written to GCF_900637545.1_51438_G01_genomic.fna/result_gtdb.tsv
[2024-01-24 15:21:30,000] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:21:30,006] [INFO] DFAST_QC result json was written to GCF_900637545.1_51438_G01_genomic.fna/dqc_result.json
[2024-01-24 15:21:30,007] [INFO] DFAST_QC completed!
[2024-01-24 15:21:30,007] [INFO] Total running time: 0h1m38s