[2024-01-24 14:47:08,540] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:47:08,542] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:47:08,542] [INFO] DQC Reference Directory: /var/lib/cwl/stga1a67474-5c0b-4d82-81cd-5d2feac235ef/dqc_reference
[2024-01-24 14:47:09,969] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:47:09,970] [INFO] Task started: Prodigal
[2024-01-24 14:47:09,970] [INFO] Running command: gunzip -c /var/lib/cwl/stgdbfdf085-c9e0-4cdb-b7f8-f483c151c075/GCF_014174285.1_ASM1417428v1_genomic.fna.gz | prodigal -d GCF_014174285.1_ASM1417428v1_genomic.fna/cds.fna -a GCF_014174285.1_ASM1417428v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:22,936] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:22,937] [INFO] Task started: HMMsearch
[2024-01-24 14:47:22,937] [INFO] Running command: hmmsearch --tblout GCF_014174285.1_ASM1417428v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga1a67474-5c0b-4d82-81cd-5d2feac235ef/dqc_reference/reference_markers.hmm GCF_014174285.1_ASM1417428v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:23,295] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:23,296] [INFO] Found 6/6 markers.
[2024-01-24 14:47:23,332] [INFO] Query marker FASTA was written to GCF_014174285.1_ASM1417428v1_genomic.fna/markers.fasta
[2024-01-24 14:47:23,332] [INFO] Task started: Blastn
[2024-01-24 14:47:23,333] [INFO] Running command: blastn -query GCF_014174285.1_ASM1417428v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga1a67474-5c0b-4d82-81cd-5d2feac235ef/dqc_reference/reference_markers.fasta -out GCF_014174285.1_ASM1417428v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:24,297] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:24,301] [INFO] Selected 12 target genomes.
[2024-01-24 14:47:24,301] [INFO] Target genome list was writen to GCF_014174285.1_ASM1417428v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:24,310] [INFO] Task started: fastANI
[2024-01-24 14:47:24,310] [INFO] Running command: fastANI --query /var/lib/cwl/stgdbfdf085-c9e0-4cdb-b7f8-f483c151c075/GCF_014174285.1_ASM1417428v1_genomic.fna.gz --refList GCF_014174285.1_ASM1417428v1_genomic.fna/target_genomes.txt --output GCF_014174285.1_ASM1417428v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:33,943] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:33,943] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga1a67474-5c0b-4d82-81cd-5d2feac235ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:33,944] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga1a67474-5c0b-4d82-81cd-5d2feac235ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:33,954] [INFO] Found 11 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:47:33,954] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:33,955] [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 liquefaciens	strain=LMG 1382	GCA_014174285.1	89584	89584	type	True	100.0	1378	1379	95	conclusive
Gluconacetobacter liquefaciens	strain=DSM 5603	GCA_003350405.1	89584	89584	type	True	99.9952	1368	1379	95	conclusive
Gluconacetobacter liquefaciens	strain=NBRC 12388	GCA_006539085.1	89584	89584	type	True	99.9662	1343	1379	95	conclusive
Gluconacetobacter dulcium	strain=LMG 1728	GCA_014174165.1	2729096	2729096	type	True	94.9969	1105	1379	95	below_threshold
Gluconacetobacter diazotrophicus	strain=PAl 5	GCA_000067045.1	33996	33996	type	True	83.0464	728	1379	95	below_threshold
Gluconacetobacter diazotrophicus	strain=LMG 7603	GCA_014174315.1	33996	33996	type	True	83.0407	712	1379	95	below_threshold
Gluconacetobacter diazotrophicus	strain=PAl 5; ATCC 49037	GCA_000021325.1	33996	33996	type	True	82.9739	736	1379	95	below_threshold
Asaia lannensis	strain=NBRC 102526	GCA_024054035.1	415421	415421	type	True	77.806	168	1379	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	76.8602	185	1379	95	below_threshold
Roseococcus microcysteis	strain=NIBR12	GCA_014764365.1	2771361	2771361	type	True	76.7339	185	1379	95	below_threshold
Roseococcus thiosulfatophilus	strain=RB-3	GCA_017311575.1	35813	35813	type	True	76.3989	194	1379	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:33,956] [INFO] DFAST Taxonomy check result was written to GCF_014174285.1_ASM1417428v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:33,957] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:33,957] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:33,958] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga1a67474-5c0b-4d82-81cd-5d2feac235ef/dqc_reference/checkm_data
[2024-01-24 14:47:33,959] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:34,018] [INFO] Task started: CheckM
[2024-01-24 14:47:34,019] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014174285.1_ASM1417428v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014174285.1_ASM1417428v1_genomic.fna/checkm_input GCF_014174285.1_ASM1417428v1_genomic.fna/checkm_result
[2024-01-24 14:48:16,374] [INFO] Task succeeded: CheckM
[2024-01-24 14:48:16,375] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:48:16,401] [INFO] ===== Completeness check finished =====
[2024-01-24 14:48:16,402] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:48:16,402] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014174285.1_ASM1417428v1_genomic.fna/markers.fasta)
[2024-01-24 14:48:16,403] [INFO] Task started: Blastn
[2024-01-24 14:48:16,403] [INFO] Running command: blastn -query GCF_014174285.1_ASM1417428v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga1a67474-5c0b-4d82-81cd-5d2feac235ef/dqc_reference/reference_markers_gtdb.fasta -out GCF_014174285.1_ASM1417428v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:18,158] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:18,162] [INFO] Selected 7 target genomes.
[2024-01-24 14:48:18,162] [INFO] Target genome list was writen to GCF_014174285.1_ASM1417428v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:48:18,167] [INFO] Task started: fastANI
[2024-01-24 14:48:18,168] [INFO] Running command: fastANI --query /var/lib/cwl/stgdbfdf085-c9e0-4cdb-b7f8-f483c151c075/GCF_014174285.1_ASM1417428v1_genomic.fna.gz --refList GCF_014174285.1_ASM1417428v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014174285.1_ASM1417428v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:48:25,696] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:25,703] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:48:25,703] [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_003350405.1	s__Gluconacetobacter liquefaciens	99.9952	1368	1379	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	100.00	100.00	1.00	1.00	3	conclusive
GCF_014174165.1	s__Gluconacetobacter dulcium	94.9969	1105	1379	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	98.93	97.86	0.94	0.88	3	-
GCF_014174275.1	s__Gluconacetobacter takamatsuzukensis	88.4192	966	1379	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014174375.1	s__Gluconacetobacter asukensis	88.3234	999	1379	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	96.0437	N/A	N/A	N/A	N/A	1	-
GCF_014174215.1	s__Gluconacetobacter tumulicola	88.2442	983	1379	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	96.2181	N/A	N/A	N/A	N/A	1	-
GCF_014174395.1	s__Gluconacetobacter aggeris	88.0373	975	1379	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	96.2181	N/A	N/A	N/A	N/A	1	-
GCF_014174255.1	s__Gluconacetobacter sacchari	86.6796	938	1379	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:48:25,705] [INFO] GTDB search result was written to GCF_014174285.1_ASM1417428v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:48:25,705] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:48:25,709] [INFO] DFAST_QC result json was written to GCF_014174285.1_ASM1417428v1_genomic.fna/dqc_result.json
[2024-01-24 14:48:25,709] [INFO] DFAST_QC completed!
[2024-01-24 14:48:25,709] [INFO] Total running time: 0h1m17s