[2024-01-24 11:59:51,989] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:51,991] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:51,991] [INFO] DQC Reference Directory: /var/lib/cwl/stg20ae73a4-9f6f-46b9-8b92-04e31c6c4a82/dqc_reference
[2024-01-24 11:59:55,382] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:55,383] [INFO] Task started: Prodigal
[2024-01-24 11:59:55,383] [INFO] Running command: gunzip -c /var/lib/cwl/stg55a28f14-a4e4-401b-820d-822a8c98471e/GCF_025994355.1_ASM2599435v1_genomic.fna.gz | prodigal -d GCF_025994355.1_ASM2599435v1_genomic.fna/cds.fna -a GCF_025994355.1_ASM2599435v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:00:06,806] [INFO] Task succeeded: Prodigal
[2024-01-24 12:00:06,806] [INFO] Task started: HMMsearch
[2024-01-24 12:00:06,806] [INFO] Running command: hmmsearch --tblout GCF_025994355.1_ASM2599435v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg20ae73a4-9f6f-46b9-8b92-04e31c6c4a82/dqc_reference/reference_markers.hmm GCF_025994355.1_ASM2599435v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:00:07,078] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:00:07,079] [INFO] Found 6/6 markers.
[2024-01-24 12:00:07,116] [INFO] Query marker FASTA was written to GCF_025994355.1_ASM2599435v1_genomic.fna/markers.fasta
[2024-01-24 12:00:07,117] [INFO] Task started: Blastn
[2024-01-24 12:00:07,117] [INFO] Running command: blastn -query GCF_025994355.1_ASM2599435v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg20ae73a4-9f6f-46b9-8b92-04e31c6c4a82/dqc_reference/reference_markers.fasta -out GCF_025994355.1_ASM2599435v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:07,928] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:07,932] [INFO] Selected 11 target genomes.
[2024-01-24 12:00:07,933] [INFO] Target genome list was writen to GCF_025994355.1_ASM2599435v1_genomic.fna/target_genomes.txt
[2024-01-24 12:00:07,949] [INFO] Task started: fastANI
[2024-01-24 12:00:07,950] [INFO] Running command: fastANI --query /var/lib/cwl/stg55a28f14-a4e4-401b-820d-822a8c98471e/GCF_025994355.1_ASM2599435v1_genomic.fna.gz --refList GCF_025994355.1_ASM2599435v1_genomic.fna/target_genomes.txt --output GCF_025994355.1_ASM2599435v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:00:16,617] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:16,618] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg20ae73a4-9f6f-46b9-8b92-04e31c6c4a82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:00:16,618] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg20ae73a4-9f6f-46b9-8b92-04e31c6c4a82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:00:16,628] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:00:16,628] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:00:16,629] [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	84.1346	726	1254	95	below_threshold
Gluconacetobacter diazotrophicus	strain=PAl 5; ATCC 49037	GCA_000021325.1	33996	33996	type	True	84.1076	741	1254	95	below_threshold
Gluconacetobacter diazotrophicus	strain=PAl 5	GCA_000067045.1	33996	33996	type	True	84.0716	751	1254	95	below_threshold
Gluconacetobacter dulcium	strain=LMG 1728	GCA_014174165.1	2729096	2729096	type	True	81.9099	639	1254	95	below_threshold
Gluconacetobacter liquefaciens	strain=LMG 1382	GCA_014174285.1	89584	89584	type	True	81.9062	629	1254	95	below_threshold
Gluconacetobacter liquefaciens	strain=NBRC 12388	GCA_006539085.1	89584	89584	type	True	81.8942	619	1254	95	below_threshold
Acetobacter garciniae	strain=TBRC 12339	GCA_017377735.1	2817435	2817435	type	True	78.1218	318	1254	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	77.216	291	1254	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	76.9374	235	1254	95	below_threshold
Roseococcus microcysteis	strain=NIBR12	GCA_014764365.1	2771361	2771361	type	True	76.5872	201	1254	95	below_threshold
Roseococcus thiosulfatophilus	strain=RB-3	GCA_017311575.1	35813	35813	type	True	76.5202	188	1254	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:00:16,630] [INFO] DFAST Taxonomy check result was written to GCF_025994355.1_ASM2599435v1_genomic.fna/tc_result.tsv
[2024-01-24 12:00:16,631] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:00:16,631] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:00:16,631] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg20ae73a4-9f6f-46b9-8b92-04e31c6c4a82/dqc_reference/checkm_data
[2024-01-24 12:00:16,632] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:00:16,670] [INFO] Task started: CheckM
[2024-01-24 12:00:16,670] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025994355.1_ASM2599435v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025994355.1_ASM2599435v1_genomic.fna/checkm_input GCF_025994355.1_ASM2599435v1_genomic.fna/checkm_result
[2024-01-24 12:00:53,022] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:53,026] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:53,051] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:53,052] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:53,053] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025994355.1_ASM2599435v1_genomic.fna/markers.fasta)
[2024-01-24 12:00:53,053] [INFO] Task started: Blastn
[2024-01-24 12:00:53,053] [INFO] Running command: blastn -query GCF_025994355.1_ASM2599435v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg20ae73a4-9f6f-46b9-8b92-04e31c6c4a82/dqc_reference/reference_markers_gtdb.fasta -out GCF_025994355.1_ASM2599435v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:54,338] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:54,343] [INFO] Selected 9 target genomes.
[2024-01-24 12:00:54,343] [INFO] Target genome list was writen to GCF_025994355.1_ASM2599435v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:54,352] [INFO] Task started: fastANI
[2024-01-24 12:00:54,352] [INFO] Running command: fastANI --query /var/lib/cwl/stg55a28f14-a4e4-401b-820d-822a8c98471e/GCF_025994355.1_ASM2599435v1_genomic.fna.gz --refList GCF_025994355.1_ASM2599435v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025994355.1_ASM2599435v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:01:02,336] [INFO] Task succeeded: fastANI
[2024-01-24 12:01:02,350] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:01:02,350] [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_014174355.1	s__Gluconacetobacter azotocaptans	99.9968	1251	1254	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	99.32	99.32	0.91	0.91	2	conclusive
GCF_014174305.1	s__Gluconacetobacter johannae	93.1071	967	1254	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014174155.1	s__Gluconacetobacter tumulisoli	89.925	918	1254	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000021325.1	s__Gluconacetobacter diazotrophicus	84.0917	743	1254	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	99.14	98.86	0.90	0.85	4	-
GCF_014174395.1	s__Gluconacetobacter aggeris	82.7813	675	1254	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	82.7537	728	1254	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	82.4969	691	1254	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	82.3708	672	1254	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014174275.1	s__Gluconacetobacter takamatsuzukensis	82.3381	691	1254	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 12:01:02,352] [INFO] GTDB search result was written to GCF_025994355.1_ASM2599435v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:01:02,353] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:01:02,358] [INFO] DFAST_QC result json was written to GCF_025994355.1_ASM2599435v1_genomic.fna/dqc_result.json
[2024-01-24 12:01:02,358] [INFO] DFAST_QC completed!
[2024-01-24 12:01:02,358] [INFO] Total running time: 0h1m10s