[2024-01-24 11:26:28,142] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:28,144] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:28,144] [INFO] DQC Reference Directory: /var/lib/cwl/stge03fb419-818a-41dc-ab50-6bf74d9cbb57/dqc_reference
[2024-01-24 11:26:29,528] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:29,529] [INFO] Task started: Prodigal
[2024-01-24 11:26:29,529] [INFO] Running command: gunzip -c /var/lib/cwl/stg81c6e153-ce66-4f14-afe9-272371c936fe/GCF_014174165.1_ASM1417416v1_genomic.fna.gz | prodigal -d GCF_014174165.1_ASM1417416v1_genomic.fna/cds.fna -a GCF_014174165.1_ASM1417416v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:42,887] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:42,887] [INFO] Task started: HMMsearch
[2024-01-24 11:26:42,887] [INFO] Running command: hmmsearch --tblout GCF_014174165.1_ASM1417416v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge03fb419-818a-41dc-ab50-6bf74d9cbb57/dqc_reference/reference_markers.hmm GCF_014174165.1_ASM1417416v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:43,218] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:43,220] [INFO] Found 6/6 markers.
[2024-01-24 11:26:43,276] [INFO] Query marker FASTA was written to GCF_014174165.1_ASM1417416v1_genomic.fna/markers.fasta
[2024-01-24 11:26:43,277] [INFO] Task started: Blastn
[2024-01-24 11:26:43,277] [INFO] Running command: blastn -query GCF_014174165.1_ASM1417416v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge03fb419-818a-41dc-ab50-6bf74d9cbb57/dqc_reference/reference_markers.fasta -out GCF_014174165.1_ASM1417416v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:44,225] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:44,228] [INFO] Selected 12 target genomes.
[2024-01-24 11:26:44,229] [INFO] Target genome list was writen to GCF_014174165.1_ASM1417416v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:44,233] [INFO] Task started: fastANI
[2024-01-24 11:26:44,233] [INFO] Running command: fastANI --query /var/lib/cwl/stg81c6e153-ce66-4f14-afe9-272371c936fe/GCF_014174165.1_ASM1417416v1_genomic.fna.gz --refList GCF_014174165.1_ASM1417416v1_genomic.fna/target_genomes.txt --output GCF_014174165.1_ASM1417416v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:54,952] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:54,953] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge03fb419-818a-41dc-ab50-6bf74d9cbb57/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:54,953] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge03fb419-818a-41dc-ab50-6bf74d9cbb57/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:54,965] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:26:54,965] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:26:54,966] [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	100.0	1434	1438	95	conclusive
Gluconacetobacter liquefaciens	strain=LMG 1382	GCA_014174285.1	89584	89584	type	True	94.9254	1112	1438	95	below_threshold
Gluconacetobacter liquefaciens	strain=DSM 5603	GCA_003350405.1	89584	89584	type	True	94.8958	1121	1438	95	below_threshold
Gluconacetobacter liquefaciens	strain=NBRC 12388	GCA_006539085.1	89584	89584	type	True	94.8958	1095	1438	95	below_threshold
Gluconacetobacter diazotrophicus	strain=PAl 5; ATCC 49037	GCA_000021325.1	33996	33996	type	True	83.4564	749	1438	95	below_threshold
Gluconacetobacter diazotrophicus	strain=LMG 7603	GCA_014174315.1	33996	33996	type	True	83.4132	764	1438	95	below_threshold
Gluconacetobacter diazotrophicus	strain=PAl 5	GCA_000067045.1	33996	33996	type	True	83.4041	758	1438	95	below_threshold
Acetobacter garciniae	strain=TBRC 12339	GCA_017377735.1	2817435	2817435	type	True	78.4408	340	1438	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	77.1563	228	1438	95	below_threshold
Roseococcus thiosulfatophilus	strain=RB-3	GCA_017311575.1	35813	35813	type	True	76.4917	189	1438	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	75.9616	82	1438	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	75.9435	83	1438	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:54,968] [INFO] DFAST Taxonomy check result was written to GCF_014174165.1_ASM1417416v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:54,968] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:54,969] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:54,969] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge03fb419-818a-41dc-ab50-6bf74d9cbb57/dqc_reference/checkm_data
[2024-01-24 11:26:54,970] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:55,021] [INFO] Task started: CheckM
[2024-01-24 11:26:55,022] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014174165.1_ASM1417416v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014174165.1_ASM1417416v1_genomic.fna/checkm_input GCF_014174165.1_ASM1417416v1_genomic.fna/checkm_result
[2024-01-24 11:27:37,025] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:37,027] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:37,046] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:37,047] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:37,047] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014174165.1_ASM1417416v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:37,047] [INFO] Task started: Blastn
[2024-01-24 11:27:37,048] [INFO] Running command: blastn -query GCF_014174165.1_ASM1417416v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge03fb419-818a-41dc-ab50-6bf74d9cbb57/dqc_reference/reference_markers_gtdb.fasta -out GCF_014174165.1_ASM1417416v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:38,681] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:38,685] [INFO] Selected 6 target genomes.
[2024-01-24 11:27:38,686] [INFO] Target genome list was writen to GCF_014174165.1_ASM1417416v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:38,691] [INFO] Task started: fastANI
[2024-01-24 11:27:38,691] [INFO] Running command: fastANI --query /var/lib/cwl/stg81c6e153-ce66-4f14-afe9-272371c936fe/GCF_014174165.1_ASM1417416v1_genomic.fna.gz --refList GCF_014174165.1_ASM1417416v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014174165.1_ASM1417416v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:45,286] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:45,297] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:45,298] [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_014174165.1	s__Gluconacetobacter dulcium	100.0	1434	1438	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	98.93	97.86	0.94	0.88	3	conclusive
GCF_003350405.1	s__Gluconacetobacter liquefaciens	94.8958	1121	1438	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	100.00	100.00	1.00	1.00	3	-
GCF_014174395.1	s__Gluconacetobacter aggeris	88.5258	1010	1438	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	96.2181	N/A	N/A	N/A	N/A	1	-
GCF_014174375.1	s__Gluconacetobacter asukensis	88.5177	981	1438	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	88.5127	958	1438	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014174215.1	s__Gluconacetobacter tumulicola	88.4749	977	1438	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	96.2181	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:45,300] [INFO] GTDB search result was written to GCF_014174165.1_ASM1417416v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:45,300] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:45,304] [INFO] DFAST_QC result json was written to GCF_014174165.1_ASM1417416v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:45,305] [INFO] DFAST_QC completed!
[2024-01-24 11:27:45,305] [INFO] Total running time: 0h1m17s