[2024-01-24 15:02:03,501] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:03,503] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:03,503] [INFO] DQC Reference Directory: /var/lib/cwl/stgae127df3-b186-46e2-9a38-345b6325488c/dqc_reference
[2024-01-24 15:02:06,125] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:06,127] [INFO] Task started: Prodigal
[2024-01-24 15:02:06,127] [INFO] Running command: gunzip -c /var/lib/cwl/stg061d47ad-df64-4a27-a953-38d0b2d9175f/GCF_900445175.1_49243_E02_genomic.fna.gz | prodigal -d GCF_900445175.1_49243_E02_genomic.fna/cds.fna -a GCF_900445175.1_49243_E02_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:23,327] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:23,328] [INFO] Task started: HMMsearch
[2024-01-24 15:02:23,328] [INFO] Running command: hmmsearch --tblout GCF_900445175.1_49243_E02_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgae127df3-b186-46e2-9a38-345b6325488c/dqc_reference/reference_markers.hmm GCF_900445175.1_49243_E02_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:23,654] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:23,656] [INFO] Found 6/6 markers.
[2024-01-24 15:02:23,699] [INFO] Query marker FASTA was written to GCF_900445175.1_49243_E02_genomic.fna/markers.fasta
[2024-01-24 15:02:23,699] [INFO] Task started: Blastn
[2024-01-24 15:02:23,699] [INFO] Running command: blastn -query GCF_900445175.1_49243_E02_genomic.fna/markers.fasta -db /var/lib/cwl/stgae127df3-b186-46e2-9a38-345b6325488c/dqc_reference/reference_markers.fasta -out GCF_900445175.1_49243_E02_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:24,774] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:24,777] [INFO] Selected 11 target genomes.
[2024-01-24 15:02:24,778] [INFO] Target genome list was writen to GCF_900445175.1_49243_E02_genomic.fna/target_genomes.txt
[2024-01-24 15:02:24,796] [INFO] Task started: fastANI
[2024-01-24 15:02:24,796] [INFO] Running command: fastANI --query /var/lib/cwl/stg061d47ad-df64-4a27-a953-38d0b2d9175f/GCF_900445175.1_49243_E02_genomic.fna.gz --refList GCF_900445175.1_49243_E02_genomic.fna/target_genomes.txt --output GCF_900445175.1_49243_E02_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:02:36,946] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:36,947] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgae127df3-b186-46e2-9a38-345b6325488c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:02:36,947] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgae127df3-b186-46e2-9a38-345b6325488c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:02:36,959] [INFO] Found 11 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 15:02:36,960] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:02:36,960] [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 hydrophila	strain=NCTC8049	GCA_900445175.1	644	644	type	True	100.0	1581	1583	95	conclusive
Aeromonas hydrophila subsp. hydrophila	strain=ATCC 7966	GCA_000014805.1	196023	644	type	True	99.9994	1580	1583	95	conclusive
Aeromonas hydrophila	strain=ATCC 7966	GCA_018360025.1	644	644	type	True	99.9882	1549	1583	95	conclusive
Aeromonas hydrophila	strain=ATCC 7966	GCA_001999685.1	644	644	type	True	99.9651	1508	1583	95	conclusive
Aeromonas hydrophila subsp. ranae	strain=CIP 107985	GCA_000820325.1	208958	644	type	True	96.8199	1392	1583	95	conclusive
Aeromonas caviae	strain=CECT 838	GCA_018360005.1	648	648	type	True	88.91	1226	1583	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	77.3568	292	1583	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	77.1701	229	1583	95	below_threshold
Pseudomonas songnenensis	strain=NEAU-ST5-5	GCA_003696315.1	1176259	1176259	type	True	76.8162	140	1583	95	below_threshold
Shewanella jiangmenensis	strain=JM162201	GCA_018596335.1	2837387	2837387	type	True	76.7643	180	1583	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	76.567	214	1583	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:02:36,961] [INFO] DFAST Taxonomy check result was written to GCF_900445175.1_49243_E02_genomic.fna/tc_result.tsv
[2024-01-24 15:02:36,962] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:02:36,962] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:02:36,962] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgae127df3-b186-46e2-9a38-345b6325488c/dqc_reference/checkm_data
[2024-01-24 15:02:36,963] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:02:37,010] [INFO] Task started: CheckM
[2024-01-24 15:02:37,010] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900445175.1_49243_E02_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900445175.1_49243_E02_genomic.fna/checkm_input GCF_900445175.1_49243_E02_genomic.fna/checkm_result
[2024-01-24 15:03:33,118] [INFO] Task succeeded: CheckM
[2024-01-24 15:03:33,119] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.48%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:03:33,140] [INFO] ===== Completeness check finished =====
[2024-01-24 15:03:33,140] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:03:33,141] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900445175.1_49243_E02_genomic.fna/markers.fasta)
[2024-01-24 15:03:33,141] [INFO] Task started: Blastn
[2024-01-24 15:03:33,141] [INFO] Running command: blastn -query GCF_900445175.1_49243_E02_genomic.fna/markers.fasta -db /var/lib/cwl/stgae127df3-b186-46e2-9a38-345b6325488c/dqc_reference/reference_markers_gtdb.fasta -out GCF_900445175.1_49243_E02_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:34,921] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:34,927] [INFO] Selected 14 target genomes.
[2024-01-24 15:03:34,927] [INFO] Target genome list was writen to GCF_900445175.1_49243_E02_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:03:34,941] [INFO] Task started: fastANI
[2024-01-24 15:03:34,941] [INFO] Running command: fastANI --query /var/lib/cwl/stg061d47ad-df64-4a27-a953-38d0b2d9175f/GCF_900445175.1_49243_E02_genomic.fna.gz --refList GCF_900445175.1_49243_E02_genomic.fna/target_genomes_gtdb.txt --output GCF_900445175.1_49243_E02_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:03:51,070] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:51,082] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:03:51,083] [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_000014805.1	s__Aeromonas hydrophila	99.9994	1580	1583	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.01	96.24	0.92	0.87	120	conclusive
GCF_000820305.1	s__Aeromonas dhakensis	93.9529	1362	1583	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.35	96.54	0.93	0.90	55	-
GCF_000819745.1	s__Aeromonas bestiarum	90.3632	1384	1583	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.5033	97.44	97.31	0.93	0.91	4	-
GCF_000820085.1	s__Aeromonas sanarellii	89.0935	1175	1583	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	89.0166	1187	1583	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.93	97.49	0.90	0.83	112	-
GCF_000820165.1	s__Aeromonas taiwanensis	88.8721	1148	1583	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	98.19	97.81	0.94	0.93	7	-
GCF_000764665.1	s__Aeromonas lacus	87.8323	1171	1583	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.8323	96.97	96.97	0.94	0.94	2	-
GCF_019048265.1	s__Aeromonas veronii_A	87.8078	1236	1583	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	96.07	95.82	0.91	0.90	4	-
GCF_000819955.1	s__Aeromonas jandaei	87.7955	1214	1583	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.8323	96.79	96.38	0.92	0.87	26	-
GCF_000819845.1	s__Aeromonas enteropelogenes	87.6805	1172	1583	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	97.20	96.87	0.93	0.91	7	-
GCF_000764645.1	s__Aeromonas finlandensis	87.6778	1089	1583	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204135.1	s__Aeromonas fluvialis_A	87.4995	1079	1583	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000819885.1	s__Aeromonas fluvialis	87.4737	1014	1583	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000819725.1	s__Aeromonas australiensis	87.1434	1067	1583	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 15:03:51,085] [INFO] GTDB search result was written to GCF_900445175.1_49243_E02_genomic.fna/result_gtdb.tsv
[2024-01-24 15:03:51,086] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:03:51,092] [INFO] DFAST_QC result json was written to GCF_900445175.1_49243_E02_genomic.fna/dqc_result.json
[2024-01-24 15:03:51,092] [INFO] DFAST_QC completed!
[2024-01-24 15:03:51,092] [INFO] Total running time: 0h1m48s