[2024-01-24 11:06:04,656] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:06:04,658] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:06:04,658] [INFO] DQC Reference Directory: /var/lib/cwl/stgdb4c4ecd-9f13-483e-b793-7bc7f76e3e99/dqc_reference
[2024-01-24 11:06:07,010] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:06:07,011] [INFO] Task started: Prodigal
[2024-01-24 11:06:07,011] [INFO] Running command: gunzip -c /var/lib/cwl/stg87d349ad-fc65-49c9-a7cd-1080d59bf7a8/GCF_014174155.1_ASM1417415v1_genomic.fna.gz | prodigal -d GCF_014174155.1_ASM1417415v1_genomic.fna/cds.fna -a GCF_014174155.1_ASM1417415v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:06:18,453] [INFO] Task succeeded: Prodigal
[2024-01-24 11:06:18,454] [INFO] Task started: HMMsearch
[2024-01-24 11:06:18,454] [INFO] Running command: hmmsearch --tblout GCF_014174155.1_ASM1417415v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdb4c4ecd-9f13-483e-b793-7bc7f76e3e99/dqc_reference/reference_markers.hmm GCF_014174155.1_ASM1417415v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:06:18,697] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:06:18,699] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg87d349ad-fc65-49c9-a7cd-1080d59bf7a8/GCF_014174155.1_ASM1417415v1_genomic.fna.gz]
[2024-01-24 11:06:18,734] [INFO] Query marker FASTA was written to GCF_014174155.1_ASM1417415v1_genomic.fna/markers.fasta
[2024-01-24 11:06:18,735] [INFO] Task started: Blastn
[2024-01-24 11:06:18,735] [INFO] Running command: blastn -query GCF_014174155.1_ASM1417415v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb4c4ecd-9f13-483e-b793-7bc7f76e3e99/dqc_reference/reference_markers.fasta -out GCF_014174155.1_ASM1417415v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:19,620] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:19,624] [INFO] Selected 13 target genomes.
[2024-01-24 11:06:19,625] [INFO] Target genome list was writen to GCF_014174155.1_ASM1417415v1_genomic.fna/target_genomes.txt
[2024-01-24 11:06:19,632] [INFO] Task started: fastANI
[2024-01-24 11:06:19,632] [INFO] Running command: fastANI --query /var/lib/cwl/stg87d349ad-fc65-49c9-a7cd-1080d59bf7a8/GCF_014174155.1_ASM1417415v1_genomic.fna.gz --refList GCF_014174155.1_ASM1417415v1_genomic.fna/target_genomes.txt --output GCF_014174155.1_ASM1417415v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:29,443] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:29,444] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdb4c4ecd-9f13-483e-b793-7bc7f76e3e99/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:29,444] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdb4c4ecd-9f13-483e-b793-7bc7f76e3e99/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:29,462] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:06:29,462] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:06:29,462] [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 diazotrophicus	strain=LMG 7603	GCA_014174315.1	33996	33996	type	True	83.8215	759	1296	95	below_threshold
Gluconacetobacter diazotrophicus	strain=PAl 5	GCA_000067045.1	33996	33996	type	True	83.8117	792	1296	95	below_threshold
Gluconacetobacter diazotrophicus	strain=PAl 5; ATCC 49037	GCA_000021325.1	33996	33996	type	True	83.8068	792	1296	95	below_threshold
Gluconacetobacter dulcium	strain=LMG 1728	GCA_014174165.1	2729096	2729096	type	True	81.7975	682	1296	95	below_threshold
Gluconacetobacter liquefaciens	strain=LMG 1382	GCA_014174285.1	89584	89584	type	True	81.5586	670	1296	95	below_threshold
Gluconacetobacter liquefaciens	strain=NBRC 12388	GCA_006539085.1	89584	89584	type	True	81.5412	675	1296	95	below_threshold
Gluconacetobacter liquefaciens	strain=DSM 5603	GCA_003350405.1	89584	89584	type	True	81.5067	677	1296	95	below_threshold
Novacetimonas pomaceti	strain=T5K1	GCA_003207955.1	2021998	2021998	type	True	79.2313	436	1296	95	below_threshold
Acetobacter garciniae	strain=TBRC 12339	GCA_017377735.1	2817435	2817435	type	True	77.8433	309	1296	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	77.2993	288	1296	95	below_threshold
Asaia lannensis	strain=NBRC 102526	GCA_024054035.1	415421	415421	type	True	77.2962	152	1296	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	76.9689	236	1296	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	76.7338	222	1296	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:29,464] [INFO] DFAST Taxonomy check result was written to GCF_014174155.1_ASM1417415v1_genomic.fna/tc_result.tsv
[2024-01-24 11:06:29,464] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:29,465] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:29,465] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdb4c4ecd-9f13-483e-b793-7bc7f76e3e99/dqc_reference/checkm_data
[2024-01-24 11:06:29,466] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:29,509] [INFO] Task started: CheckM
[2024-01-24 11:06:29,509] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014174155.1_ASM1417415v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014174155.1_ASM1417415v1_genomic.fna/checkm_input GCF_014174155.1_ASM1417415v1_genomic.fna/checkm_result
[2024-01-24 11:07:07,199] [INFO] Task succeeded: CheckM
[2024-01-24 11:07:07,201] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:07:07,218] [INFO] ===== Completeness check finished =====
[2024-01-24 11:07:07,218] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:07:07,219] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014174155.1_ASM1417415v1_genomic.fna/markers.fasta)
[2024-01-24 11:07:07,219] [INFO] Task started: Blastn
[2024-01-24 11:07:07,219] [INFO] Running command: blastn -query GCF_014174155.1_ASM1417415v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb4c4ecd-9f13-483e-b793-7bc7f76e3e99/dqc_reference/reference_markers_gtdb.fasta -out GCF_014174155.1_ASM1417415v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:07:08,711] [INFO] Task succeeded: Blastn
[2024-01-24 11:07:08,714] [INFO] Selected 8 target genomes.
[2024-01-24 11:07:08,715] [INFO] Target genome list was writen to GCF_014174155.1_ASM1417415v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:07:08,721] [INFO] Task started: fastANI
[2024-01-24 11:07:08,721] [INFO] Running command: fastANI --query /var/lib/cwl/stg87d349ad-fc65-49c9-a7cd-1080d59bf7a8/GCF_014174155.1_ASM1417415v1_genomic.fna.gz --refList GCF_014174155.1_ASM1417415v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014174155.1_ASM1417415v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:07:16,028] [INFO] Task succeeded: fastANI
[2024-01-24 11:07:16,041] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:07:16,042] [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_014174155.1	s__Gluconacetobacter tumulisoli	100.0	1293	1296	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014174305.1	s__Gluconacetobacter johannae	90.2926	916	1296	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014174355.1	s__Gluconacetobacter azotocaptans	89.9394	983	1296	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	99.32	99.32	0.91	0.91	2	-
GCF_000021325.1	s__Gluconacetobacter diazotrophicus	83.8182	791	1296	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	99.14	98.86	0.90	0.85	4	-
GCF_014174275.1	s__Gluconacetobacter takamatsuzukensis	82.3708	739	1296	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	82.2051	748	1296	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	82.0819	734	1296	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	82.0327	738	1296	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 11:07:16,043] [INFO] GTDB search result was written to GCF_014174155.1_ASM1417415v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:07:16,044] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:07:16,047] [INFO] DFAST_QC result json was written to GCF_014174155.1_ASM1417415v1_genomic.fna/dqc_result.json
[2024-01-24 11:07:16,047] [INFO] DFAST_QC completed!
[2024-01-24 11:07:16,047] [INFO] Total running time: 0h1m11s