[2024-01-24 13:57:56,657] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:56,658] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:56,659] [INFO] DQC Reference Directory: /var/lib/cwl/stg27c6886f-2021-4b61-81aa-14520b47377f/dqc_reference
[2024-01-24 13:57:57,980] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:57,981] [INFO] Task started: Prodigal
[2024-01-24 13:57:57,981] [INFO] Running command: gunzip -c /var/lib/cwl/stg0f311a06-fbf7-4b47-9239-b40cfe630219/GCF_025994535.1_ASM2599453v1_genomic.fna.gz | prodigal -d GCF_025994535.1_ASM2599453v1_genomic.fna/cds.fna -a GCF_025994535.1_ASM2599453v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:11,274] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:11,274] [INFO] Task started: HMMsearch
[2024-01-24 13:58:11,275] [INFO] Running command: hmmsearch --tblout GCF_025994535.1_ASM2599453v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg27c6886f-2021-4b61-81aa-14520b47377f/dqc_reference/reference_markers.hmm GCF_025994535.1_ASM2599453v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:11,662] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:11,663] [INFO] Found 6/6 markers.
[2024-01-24 13:58:11,734] [INFO] Query marker FASTA was written to GCF_025994535.1_ASM2599453v1_genomic.fna/markers.fasta
[2024-01-24 13:58:11,735] [INFO] Task started: Blastn
[2024-01-24 13:58:11,735] [INFO] Running command: blastn -query GCF_025994535.1_ASM2599453v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg27c6886f-2021-4b61-81aa-14520b47377f/dqc_reference/reference_markers.fasta -out GCF_025994535.1_ASM2599453v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:12,555] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:12,558] [INFO] Selected 12 target genomes.
[2024-01-24 13:58:12,558] [INFO] Target genome list was writen to GCF_025994535.1_ASM2599453v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:12,618] [INFO] Task started: fastANI
[2024-01-24 13:58:12,619] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f311a06-fbf7-4b47-9239-b40cfe630219/GCF_025994535.1_ASM2599453v1_genomic.fna.gz --refList GCF_025994535.1_ASM2599453v1_genomic.fna/target_genomes.txt --output GCF_025994535.1_ASM2599453v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:22,709] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:22,710] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg27c6886f-2021-4b61-81aa-14520b47377f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:22,710] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg27c6886f-2021-4b61-81aa-14520b47377f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:22,721] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:58:22,721] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:58:22,721] [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	87.1002	898	1421	95	below_threshold
Gluconacetobacter liquefaciens	strain=NBRC 12388	GCA_006539085.1	89584	89584	type	True	86.5727	842	1421	95	below_threshold
Gluconacetobacter liquefaciens	strain=LMG 1382	GCA_014174285.1	89584	89584	type	True	86.571	867	1421	95	below_threshold
Gluconacetobacter liquefaciens	strain=DSM 5603	GCA_003350405.1	89584	89584	type	True	86.5612	869	1421	95	below_threshold
Gluconacetobacter diazotrophicus	strain=PAl 5; ATCC 49037	GCA_000021325.1	33996	33996	type	True	83.9293	700	1421	95	below_threshold
Gluconacetobacter diazotrophicus	strain=PAl 5	GCA_000067045.1	33996	33996	type	True	83.8882	702	1421	95	below_threshold
Gluconacetobacter diazotrophicus	strain=LMG 7603	GCA_014174315.1	33996	33996	type	True	83.7864	712	1421	95	below_threshold
Acetobacter garciniae	strain=TBRC 12339	GCA_017377735.1	2817435	2817435	type	True	78.4878	318	1421	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	77.0612	253	1421	95	below_threshold
Elioraea tepida	strain=MS-P2	GCA_019203965.1	2843330	2843330	type	True	76.357	132	1421	95	below_threshold
Azospirillum cavernae	strain=K2W22B-5	GCA_003590795.1	2320860	2320860	type	True	75.9701	187	1421	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	75.8767	130	1421	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:22,723] [INFO] DFAST Taxonomy check result was written to GCF_025994535.1_ASM2599453v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:22,724] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:22,724] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:22,724] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg27c6886f-2021-4b61-81aa-14520b47377f/dqc_reference/checkm_data
[2024-01-24 13:58:22,726] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:22,780] [INFO] Task started: CheckM
[2024-01-24 13:58:22,780] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025994535.1_ASM2599453v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025994535.1_ASM2599453v1_genomic.fna/checkm_input GCF_025994535.1_ASM2599453v1_genomic.fna/checkm_result
[2024-01-24 13:59:05,309] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:05,310] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:05,333] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:05,334] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:05,334] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025994535.1_ASM2599453v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:05,335] [INFO] Task started: Blastn
[2024-01-24 13:59:05,335] [INFO] Running command: blastn -query GCF_025994535.1_ASM2599453v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg27c6886f-2021-4b61-81aa-14520b47377f/dqc_reference/reference_markers_gtdb.fasta -out GCF_025994535.1_ASM2599453v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:06,540] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:06,543] [INFO] Selected 8 target genomes.
[2024-01-24 13:59:06,543] [INFO] Target genome list was writen to GCF_025994535.1_ASM2599453v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:06,597] [INFO] Task started: fastANI
[2024-01-24 13:59:06,598] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f311a06-fbf7-4b47-9239-b40cfe630219/GCF_025994535.1_ASM2599453v1_genomic.fna.gz --refList GCF_025994535.1_ASM2599453v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025994535.1_ASM2599453v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:13,953] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:13,960] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:13,960] [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_014174255.1	s__Gluconacetobacter sacchari	99.9994	1418	1421	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_014174275.1	s__Gluconacetobacter takamatsuzukensis	88.0574	834	1421	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	88.0373	865	1421	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	87.9256	866	1421	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	87.7668	894	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	96.2181	N/A	N/A	N/A	N/A	1	-
GCF_014174165.1	s__Gluconacetobacter dulcium	87.0708	900	1421	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	86.5782	868	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	100.00	100.00	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:13,962] [INFO] GTDB search result was written to GCF_025994535.1_ASM2599453v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:13,962] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:13,966] [INFO] DFAST_QC result json was written to GCF_025994535.1_ASM2599453v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:13,966] [INFO] DFAST_QC completed!
[2024-01-24 13:59:13,966] [INFO] Total running time: 0h1m17s