[2024-01-24 14:15:02,181] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:15:02,183] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:15:02,183] [INFO] DQC Reference Directory: /var/lib/cwl/stgf26272a3-f6ca-4ff5-ac08-50396803adea/dqc_reference
[2024-01-24 14:15:03,622] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:15:03,623] [INFO] Task started: Prodigal
[2024-01-24 14:15:03,624] [INFO] Running command: gunzip -c /var/lib/cwl/stg7b46060f-ae03-44e7-aef4-d5e3ce610e24/GCF_018359985.1_ASM1835998v1_genomic.fna.gz | prodigal -d GCF_018359985.1_ASM1835998v1_genomic.fna/cds.fna -a GCF_018359985.1_ASM1835998v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:15:17,553] [INFO] Task succeeded: Prodigal
[2024-01-24 14:15:17,553] [INFO] Task started: HMMsearch
[2024-01-24 14:15:17,553] [INFO] Running command: hmmsearch --tblout GCF_018359985.1_ASM1835998v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf26272a3-f6ca-4ff5-ac08-50396803adea/dqc_reference/reference_markers.hmm GCF_018359985.1_ASM1835998v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:15:17,874] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:15:17,875] [INFO] Found 6/6 markers.
[2024-01-24 14:15:17,920] [INFO] Query marker FASTA was written to GCF_018359985.1_ASM1835998v1_genomic.fna/markers.fasta
[2024-01-24 14:15:17,921] [INFO] Task started: Blastn
[2024-01-24 14:15:17,921] [INFO] Running command: blastn -query GCF_018359985.1_ASM1835998v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf26272a3-f6ca-4ff5-ac08-50396803adea/dqc_reference/reference_markers.fasta -out GCF_018359985.1_ASM1835998v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:18,996] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:19,004] [INFO] Selected 21 target genomes.
[2024-01-24 14:15:19,004] [INFO] Target genome list was writen to GCF_018359985.1_ASM1835998v1_genomic.fna/target_genomes.txt
[2024-01-24 14:15:19,013] [INFO] Task started: fastANI
[2024-01-24 14:15:19,014] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b46060f-ae03-44e7-aef4-d5e3ce610e24/GCF_018359985.1_ASM1835998v1_genomic.fna.gz --refList GCF_018359985.1_ASM1835998v1_genomic.fna/target_genomes.txt --output GCF_018359985.1_ASM1835998v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:40,248] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:40,248] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf26272a3-f6ca-4ff5-ac08-50396803adea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:40,249] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf26272a3-f6ca-4ff5-ac08-50396803adea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:40,272] [INFO] Found 21 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:15:40,272] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:15:40,272] [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 media	strain=ATCC 33907	GCA_018359985.1	651	651	type	True	100.0	1405	1412	95	conclusive
Aeromonas media	strain=CECT 4232	GCA_000819985.1	651	651	type	True	99.9546	1355	1412	95	conclusive
Aeromonas sanarellii	strain=LMG 24682	GCA_000820085.1	633415	633415	type	True	90.6944	1199	1412	95	below_threshold
Aeromonas caviae	strain=CECT 838	GCA_018360005.1	648	648	type	True	90.044	1213	1412	95	below_threshold
Aeromonas caviae	strain=CECT 838	GCA_000819785.1	648	648	type	True	89.9696	1201	1412	95	below_threshold
Aeromonas encheleia	strain=NCTC12917	GCA_900637545.1	73010	73010	type	True	89.6408	1197	1412	95	below_threshold
Aeromonas encheleia	strain=CECT 4342	GCA_000819825.1	73010	73010	type	True	89.6302	1198	1412	95	below_threshold
Aeromonas aquatica	strain=AE235	GCA_000764655.1	558964	558964	type	True	89.3744	1164	1412	95	below_threshold
Aeromonas eucrenophila	strain=CECT 4224	GCA_000819865.1	649	649	type	True	89.0598	1198	1412	95	below_threshold
Aeromonas lusitana	strain=MDC 2473	GCA_002812985.1	931529	931529	type	True	88.7918	1161	1412	95	below_threshold
Aeromonas hydrophila	strain=ATCC 7966	GCA_018360025.1	644	644	type	True	88.6931	1165	1412	95	below_threshold
Aeromonas hydrophila subsp. hydrophila	strain=ATCC 7966	GCA_000014805.1	196023	644	type	True	88.5879	1175	1412	95	below_threshold
Aeromonas hydrophila	strain=NCTC8049	GCA_900445175.1	644	644	type	True	88.5581	1173	1412	95	below_threshold
Aeromonas bestiarum	strain=CECT 4227	GCA_000819745.1	105751	105751	type	True	88.5466	1174	1412	95	below_threshold
Aeromonas bivalvium	strain=CECT 7113	GCA_000819765.1	440079	440079	type	True	87.3122	1079	1412	95	below_threshold
Aeromonas finlandensis	strain=4287D	GCA_000764645.1	1543375	1543375	type	True	86.1864	981	1412	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	76.626	211	1412	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	76.3859	177	1412	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	76.2281	182	1412	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	76.221	146	1412	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	75.6811	103	1412	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:40,274] [INFO] DFAST Taxonomy check result was written to GCF_018359985.1_ASM1835998v1_genomic.fna/tc_result.tsv
[2024-01-24 14:15:40,274] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:40,275] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:40,275] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf26272a3-f6ca-4ff5-ac08-50396803adea/dqc_reference/checkm_data
[2024-01-24 14:15:40,276] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:40,322] [INFO] Task started: CheckM
[2024-01-24 14:15:40,322] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018359985.1_ASM1835998v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018359985.1_ASM1835998v1_genomic.fna/checkm_input GCF_018359985.1_ASM1835998v1_genomic.fna/checkm_result
[2024-01-24 14:16:21,569] [INFO] Task succeeded: CheckM
[2024-01-24 14:16:21,570] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.48%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:16:21,588] [INFO] ===== Completeness check finished =====
[2024-01-24 14:16:21,589] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:16:21,589] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018359985.1_ASM1835998v1_genomic.fna/markers.fasta)
[2024-01-24 14:16:21,589] [INFO] Task started: Blastn
[2024-01-24 14:16:21,590] [INFO] Running command: blastn -query GCF_018359985.1_ASM1835998v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf26272a3-f6ca-4ff5-ac08-50396803adea/dqc_reference/reference_markers_gtdb.fasta -out GCF_018359985.1_ASM1835998v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:16:23,349] [INFO] Task succeeded: Blastn
[2024-01-24 14:16:23,354] [INFO] Selected 14 target genomes.
[2024-01-24 14:16:23,354] [INFO] Target genome list was writen to GCF_018359985.1_ASM1835998v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:16:23,363] [INFO] Task started: fastANI
[2024-01-24 14:16:23,364] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b46060f-ae03-44e7-aef4-d5e3ce610e24/GCF_018359985.1_ASM1835998v1_genomic.fna.gz --refList GCF_018359985.1_ASM1835998v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018359985.1_ASM1835998v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:16:38,547] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:38,566] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:16:38,566] [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_000819985.1	s__Aeromonas media	99.9546	1355	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.95	97.16	0.92	0.87	16	conclusive
GCF_010974825.1	s__Aeromonas rivipollensis	94.1012	1240	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.26	95.18	0.91	0.86	15	-
GCF_000820085.1	s__Aeromonas sanarellii	90.6944	1199	1412	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	89.9696	1201	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.93	97.49	0.90	0.83	112	-
GCF_900637545.1	s__Aeromonas encheleia	89.6516	1196	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	98.38	97.80	0.95	0.91	5	-
GCF_000764655.1	s__Aeromonas aquatica	89.3674	1165	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000819865.1	s__Aeromonas eucrenophila	89.054	1199	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002812985.1	s__Aeromonas lusitana	88.7935	1161	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000014805.1	s__Aeromonas hydrophila	88.5879	1175	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.01	96.24	0.92	0.87	120	-
GCF_000819745.1	s__Aeromonas bestiarum	88.5466	1174	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.5033	97.44	97.31	0.93	0.91	4	-
GCF_000820305.1	s__Aeromonas dhakensis	88.3959	1140	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.35	96.54	0.93	0.90	55	-
GCF_000819765.1	s__Aeromonas bivalvium	87.3067	1080	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	98.28	98.27	0.92	0.92	5	-
GCF_000819685.1	s__Aeromonas allosaccharophila	86.4659	1055	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	96.32	95.53	0.87	0.85	15	-
GCF_000764645.1	s__Aeromonas finlandensis	86.2006	979	1412	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 14:16:38,567] [INFO] GTDB search result was written to GCF_018359985.1_ASM1835998v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:16:38,568] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:16:38,572] [INFO] DFAST_QC result json was written to GCF_018359985.1_ASM1835998v1_genomic.fna/dqc_result.json
[2024-01-24 14:16:38,572] [INFO] DFAST_QC completed!
[2024-01-24 14:16:38,572] [INFO] Total running time: 0h1m36s