[2024-01-25 18:15:20,702] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:15:20,703] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:15:20,704] [INFO] DQC Reference Directory: /var/lib/cwl/stg23d069c0-df0d-409b-9b1b-057459fd8535/dqc_reference
[2024-01-25 18:15:21,845] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:15:21,845] [INFO] Task started: Prodigal
[2024-01-25 18:15:21,846] [INFO] Running command: gunzip -c /var/lib/cwl/stg6b4c98bc-f303-4a27-82ca-21c9b414506e/GCF_014174395.1_ASM1417439v1_genomic.fna.gz | prodigal -d GCF_014174395.1_ASM1417439v1_genomic.fna/cds.fna -a GCF_014174395.1_ASM1417439v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:15:33,131] [INFO] Task succeeded: Prodigal
[2024-01-25 18:15:33,132] [INFO] Task started: HMMsearch
[2024-01-25 18:15:33,132] [INFO] Running command: hmmsearch --tblout GCF_014174395.1_ASM1417439v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg23d069c0-df0d-409b-9b1b-057459fd8535/dqc_reference/reference_markers.hmm GCF_014174395.1_ASM1417439v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:15:33,394] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:15:33,395] [INFO] Found 6/6 markers.
[2024-01-25 18:15:33,436] [INFO] Query marker FASTA was written to GCF_014174395.1_ASM1417439v1_genomic.fna/markers.fasta
[2024-01-25 18:15:33,436] [INFO] Task started: Blastn
[2024-01-25 18:15:33,436] [INFO] Running command: blastn -query GCF_014174395.1_ASM1417439v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg23d069c0-df0d-409b-9b1b-057459fd8535/dqc_reference/reference_markers.fasta -out GCF_014174395.1_ASM1417439v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:15:34,289] [INFO] Task succeeded: Blastn
[2024-01-25 18:15:34,291] [INFO] Selected 12 target genomes.
[2024-01-25 18:15:34,292] [INFO] Target genome list was writen to GCF_014174395.1_ASM1417439v1_genomic.fna/target_genomes.txt
[2024-01-25 18:15:34,296] [INFO] Task started: fastANI
[2024-01-25 18:15:34,296] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b4c98bc-f303-4a27-82ca-21c9b414506e/GCF_014174395.1_ASM1417439v1_genomic.fna.gz --refList GCF_014174395.1_ASM1417439v1_genomic.fna/target_genomes.txt --output GCF_014174395.1_ASM1417439v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:15:44,854] [INFO] Task succeeded: fastANI
[2024-01-25 18:15:44,855] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg23d069c0-df0d-409b-9b1b-057459fd8535/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:15:44,855] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg23d069c0-df0d-409b-9b1b-057459fd8535/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:15:44,863] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:15:44,863] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:15:44,863] [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
Gluconacetobacter dulcium	strain=LMG 1728	GCA_014174165.1	2729096	2729096	type	True	88.6578	1003	1416	95	below_threshold
Gluconacetobacter liquefaciens	strain=NBRC 12388	GCA_006539085.1	89584	89584	type	True	88.2148	939	1416	95	below_threshold
Gluconacetobacter liquefaciens	strain=LMG 1382	GCA_014174285.1	89584	89584	type	True	88.1091	982	1416	95	below_threshold
Gluconacetobacter liquefaciens	strain=DSM 5603	GCA_003350405.1	89584	89584	type	True	88.0771	980	1416	95	below_threshold
Gluconacetobacter diazotrophicus	strain=PAl 5	GCA_000067045.1	33996	33996	type	True	83.8746	767	1416	95	below_threshold
Gluconacetobacter diazotrophicus	strain=PAl 5; ATCC 49037	GCA_000021325.1	33996	33996	type	True	83.8089	757	1416	95	below_threshold
Gluconacetobacter diazotrophicus	strain=LMG 7603	GCA_014174315.1	33996	33996	type	True	83.7583	759	1416	95	below_threshold
Roseococcus microcysteis	strain=NIBR12	GCA_014764365.1	2771361	2771361	type	True	76.6514	219	1416	95	below_threshold
Roseococcus thiosulfatophilus	strain=RB-3	GCA_017311575.1	35813	35813	type	True	76.6513	207	1416	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	76.2216	79	1416	95	below_threshold
Azospirillum cavernae	strain=K2W22B-5	GCA_003590795.1	2320860	2320860	type	True	76.1743	168	1416	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	75.9609	151	1416	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:15:44,865] [INFO] DFAST Taxonomy check result was written to GCF_014174395.1_ASM1417439v1_genomic.fna/tc_result.tsv
[2024-01-25 18:15:44,865] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:15:44,865] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:15:44,866] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg23d069c0-df0d-409b-9b1b-057459fd8535/dqc_reference/checkm_data
[2024-01-25 18:15:44,866] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:15:44,908] [INFO] Task started: CheckM
[2024-01-25 18:15:44,908] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014174395.1_ASM1417439v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014174395.1_ASM1417439v1_genomic.fna/checkm_input GCF_014174395.1_ASM1417439v1_genomic.fna/checkm_result
[2024-01-25 18:16:24,518] [INFO] Task succeeded: CheckM
[2024-01-25 18:16:24,519] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:16:24,539] [INFO] ===== Completeness check finished =====
[2024-01-25 18:16:24,539] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:16:24,540] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014174395.1_ASM1417439v1_genomic.fna/markers.fasta)
[2024-01-25 18:16:24,540] [INFO] Task started: Blastn
[2024-01-25 18:16:24,540] [INFO] Running command: blastn -query GCF_014174395.1_ASM1417439v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg23d069c0-df0d-409b-9b1b-057459fd8535/dqc_reference/reference_markers_gtdb.fasta -out GCF_014174395.1_ASM1417439v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:16:26,104] [INFO] Task succeeded: Blastn
[2024-01-25 18:16:26,106] [INFO] Selected 6 target genomes.
[2024-01-25 18:16:26,106] [INFO] Target genome list was writen to GCF_014174395.1_ASM1417439v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:16:26,109] [INFO] Task started: fastANI
[2024-01-25 18:16:26,109] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b4c98bc-f303-4a27-82ca-21c9b414506e/GCF_014174395.1_ASM1417439v1_genomic.fna.gz --refList GCF_014174395.1_ASM1417439v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014174395.1_ASM1417439v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:16:32,972] [INFO] Task succeeded: fastANI
[2024-01-25 18:16:32,977] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:16:32,977] [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_014174395.1	s__Gluconacetobacter aggeris	100.0	1415	1416	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	96.2181	N/A	N/A	N/A	N/A	1	conclusive
GCF_014174215.1	s__Gluconacetobacter tumulicola	96.2181	1160	1416	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	96.2181	N/A	N/A	N/A	N/A	1	conclusive
GCF_014174375.1	s__Gluconacetobacter asukensis	95.2301	1135	1416	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	96.0437	N/A	N/A	N/A	N/A	1	-
GCF_014174275.1	s__Gluconacetobacter takamatsuzukensis	89.3665	966	1416	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014174165.1	s__Gluconacetobacter dulcium	88.6587	1002	1416	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	98.93	97.86	0.94	0.88	3	-
GCF_003350405.1	s__Gluconacetobacter liquefaciens	88.0806	980	1416	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	100.00	100.00	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2024-01-25 18:16:32,979] [INFO] GTDB search result was written to GCF_014174395.1_ASM1417439v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:16:32,979] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:16:32,982] [INFO] DFAST_QC result json was written to GCF_014174395.1_ASM1417439v1_genomic.fna/dqc_result.json
[2024-01-25 18:16:32,982] [INFO] DFAST_QC completed!
[2024-01-25 18:16:32,982] [INFO] Total running time: 0h1m12s