[2024-01-24 12:23:03,094] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:03,095] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:03,095] [INFO] DQC Reference Directory: /var/lib/cwl/stg7a58de49-becf-4fa2-a672-bf38282459de/dqc_reference
[2024-01-24 12:23:04,265] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:04,266] [INFO] Task started: Prodigal
[2024-01-24 12:23:04,266] [INFO] Running command: gunzip -c /var/lib/cwl/stgb6f00336-6a79-42ae-9ebd-1ff41054dc6c/GCF_014202415.1_ASM1420241v1_genomic.fna.gz | prodigal -d GCF_014202415.1_ASM1420241v1_genomic.fna/cds.fna -a GCF_014202415.1_ASM1420241v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:11,962] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:11,962] [INFO] Task started: HMMsearch
[2024-01-24 12:23:11,962] [INFO] Running command: hmmsearch --tblout GCF_014202415.1_ASM1420241v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7a58de49-becf-4fa2-a672-bf38282459de/dqc_reference/reference_markers.hmm GCF_014202415.1_ASM1420241v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:12,169] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:12,170] [INFO] Found 6/6 markers.
[2024-01-24 12:23:12,201] [INFO] Query marker FASTA was written to GCF_014202415.1_ASM1420241v1_genomic.fna/markers.fasta
[2024-01-24 12:23:12,201] [INFO] Task started: Blastn
[2024-01-24 12:23:12,201] [INFO] Running command: blastn -query GCF_014202415.1_ASM1420241v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a58de49-becf-4fa2-a672-bf38282459de/dqc_reference/reference_markers.fasta -out GCF_014202415.1_ASM1420241v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:12,953] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:12,956] [INFO] Selected 20 target genomes.
[2024-01-24 12:23:12,956] [INFO] Target genome list was writen to GCF_014202415.1_ASM1420241v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:12,963] [INFO] Task started: fastANI
[2024-01-24 12:23:12,964] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6f00336-6a79-42ae-9ebd-1ff41054dc6c/GCF_014202415.1_ASM1420241v1_genomic.fna.gz --refList GCF_014202415.1_ASM1420241v1_genomic.fna/target_genomes.txt --output GCF_014202415.1_ASM1420241v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:25,979] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:25,979] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7a58de49-becf-4fa2-a672-bf38282459de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:25,979] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7a58de49-becf-4fa2-a672-bf38282459de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:25,989] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:23:25,989] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:25,989] [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
Tolumonas osonensis	strain=DSM 22975	GCA_014202415.1	675874	675874	type	True	100.0	1079	1080	95	conclusive
Tolumonas auensis	strain=DSM 9187	GCA_000023065.1	43948	43948	type	True	85.0941	827	1080	95	below_threshold
Tolumonas lignilytica	strain=BRL6-1	GCA_000527035.1	1283284	1283284	type	True	82.0806	614	1080	95	below_threshold
Plesiomonas shigelloides	strain=NCTC10360	GCA_900087055.1	703	703	type	True	77.5965	87	1080	95	below_threshold
Shigella sonnei	strain=ATCC 29930	GCA_002950395.1	624	624	type	True	77.3567	106	1080	95	below_threshold
Aeromonas veronii	strain=CECT 4257	GCA_000820225.1	654	654	type	True	77.3416	127	1080	95	below_threshold
Aeromonas lacus	strain=AE122	GCA_000764665.1	558884	558884	type	True	77.2352	124	1080	95	below_threshold
Aeromonas veronii	strain=ATCC 35624	GCA_018359905.1	654	654	type	True	77.1968	124	1080	95	below_threshold
Escherichia coli	strain=DSM 30083	GCA_024519395.1	562	562	neotype	True	77.1456	104	1080	95	below_threshold
Leclercia pneumoniae	strain=49125	GCA_017348915.1	2815358	2815358	type	True	77.1196	88	1080	95	below_threshold
Leclercia pneumoniae	strain=49125	GCA_018987305.1	2815358	2815358	type	True	77.0036	88	1080	95	below_threshold
Aeromonas dhakensis	strain=CIP 107500	GCA_000820305.1	196024	196024	type	True	76.9991	107	1080	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	76.9717	107	1080	95	below_threshold
Grimontia hollisae	strain=CIP 101886	GCA_000176515.1	673	673	type	True	76.969	65	1080	95	below_threshold
Dongshaea marina	strain=DM2	GCA_003072645.1	2047966	2047966	type	True	76.7742	54	1080	95	below_threshold
Zobellella endophytica	strain=59N8	GCA_003012775.1	2116700	2116700	type	True	76.6669	73	1080	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:25,991] [INFO] DFAST Taxonomy check result was written to GCF_014202415.1_ASM1420241v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:25,991] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:25,992] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:25,992] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7a58de49-becf-4fa2-a672-bf38282459de/dqc_reference/checkm_data
[2024-01-24 12:23:25,992] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:26,027] [INFO] Task started: CheckM
[2024-01-24 12:23:26,027] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014202415.1_ASM1420241v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014202415.1_ASM1420241v1_genomic.fna/checkm_input GCF_014202415.1_ASM1420241v1_genomic.fna/checkm_result
[2024-01-24 12:23:52,553] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:52,554] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:52,571] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:52,571] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:52,571] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014202415.1_ASM1420241v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:52,572] [INFO] Task started: Blastn
[2024-01-24 12:23:52,572] [INFO] Running command: blastn -query GCF_014202415.1_ASM1420241v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a58de49-becf-4fa2-a672-bf38282459de/dqc_reference/reference_markers_gtdb.fasta -out GCF_014202415.1_ASM1420241v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:53,769] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:53,772] [INFO] Selected 9 target genomes.
[2024-01-24 12:23:53,772] [INFO] Target genome list was writen to GCF_014202415.1_ASM1420241v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:53,778] [INFO] Task started: fastANI
[2024-01-24 12:23:53,778] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6f00336-6a79-42ae-9ebd-1ff41054dc6c/GCF_014202415.1_ASM1420241v1_genomic.fna.gz --refList GCF_014202415.1_ASM1420241v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014202415.1_ASM1420241v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:00,177] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:00,183] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:24:00,183] [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_014202415.1	s__Tolumonas osonensis	100.0	1079	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Tolumonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000023065.1	s__Tolumonas auensis	85.0798	828	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Tolumonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008015085.1	s__Tolumonas sp008015085	82.7262	355	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Tolumonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000527035.1	s__Tolumonas lignilytica	82.0839	614	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Tolumonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903931645.1	s__Tolumonas sp903931645	81.1685	356	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Tolumonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003251455.1	s__Tolumonas sp003251455	79.0821	268	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Tolumonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900087055.1	s__Plesiomonas shigelloides	77.6253	87	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Plesiomonas	95.0	97.46	97.09	0.91	0.86	29	-
GCF_900156095.1	s__Aeromonas sp900156095	77.2868	117	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000176515.1	s__Enterovibrio hollisae	76.9722	65	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Enterovibrio	95.0	99.40	99.22	0.97	0.96	10	-
--------------------------------------------------------------------------------
[2024-01-24 12:24:00,185] [INFO] GTDB search result was written to GCF_014202415.1_ASM1420241v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:00,185] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:00,188] [INFO] DFAST_QC result json was written to GCF_014202415.1_ASM1420241v1_genomic.fna/dqc_result.json
[2024-01-24 12:24:00,188] [INFO] DFAST_QC completed!
[2024-01-24 12:24:00,189] [INFO] Total running time: 0h0m57s