[2024-01-25 17:52:20,841] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:52:20,843] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:52:20,843] [INFO] DQC Reference Directory: /var/lib/cwl/stg0295a052-f436-4df7-8ce0-b4aad8ac3f16/dqc_reference
[2024-01-25 17:52:21,984] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:52:21,985] [INFO] Task started: Prodigal
[2024-01-25 17:52:21,985] [INFO] Running command: gunzip -c /var/lib/cwl/stg4b864211-81a7-48ca-8cba-36537a256fa4/GCF_000430725.1_ASM43072v1_genomic.fna.gz | prodigal -d GCF_000430725.1_ASM43072v1_genomic.fna/cds.fna -a GCF_000430725.1_ASM43072v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:52:56,790] [INFO] Task succeeded: Prodigal
[2024-01-25 17:52:56,790] [INFO] Task started: HMMsearch
[2024-01-25 17:52:56,791] [INFO] Running command: hmmsearch --tblout GCF_000430725.1_ASM43072v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0295a052-f436-4df7-8ce0-b4aad8ac3f16/dqc_reference/reference_markers.hmm GCF_000430725.1_ASM43072v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:52:57,088] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:52:57,089] [INFO] Found 6/6 markers.
[2024-01-25 17:52:57,151] [INFO] Query marker FASTA was written to GCF_000430725.1_ASM43072v1_genomic.fna/markers.fasta
[2024-01-25 17:52:57,151] [INFO] Task started: Blastn
[2024-01-25 17:52:57,151] [INFO] Running command: blastn -query GCF_000430725.1_ASM43072v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0295a052-f436-4df7-8ce0-b4aad8ac3f16/dqc_reference/reference_markers.fasta -out GCF_000430725.1_ASM43072v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:52:58,189] [INFO] Task succeeded: Blastn
[2024-01-25 17:52:58,191] [INFO] Selected 15 target genomes.
[2024-01-25 17:52:58,191] [INFO] Target genome list was writen to GCF_000430725.1_ASM43072v1_genomic.fna/target_genomes.txt
[2024-01-25 17:52:58,195] [INFO] Task started: fastANI
[2024-01-25 17:52:58,195] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b864211-81a7-48ca-8cba-36537a256fa4/GCF_000430725.1_ASM43072v1_genomic.fna.gz --refList GCF_000430725.1_ASM43072v1_genomic.fna/target_genomes.txt --output GCF_000430725.1_ASM43072v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:53:22,261] [INFO] Task succeeded: fastANI
[2024-01-25 17:53:22,261] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0295a052-f436-4df7-8ce0-b4aad8ac3f16/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:53:22,262] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0295a052-f436-4df7-8ce0-b4aad8ac3f16/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:53:22,271] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:53:22,272] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:53:22,272] [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
Azohydromonas australica	strain=DSM 1124	GCA_000430725.1	364039	364039	type	True	99.999	2837	2851	95	conclusive
Azohydromonas caseinilytica	strain=G-1-1-14	GCA_012927045.1	2728836	2728836	type	True	88.2631	1610	2851	95	below_threshold
Azohydromonas aeria	strain=CFCC 13393	GCA_009760915.1	2590212	2590212	type	True	87.5326	1657	2851	95	below_threshold
Azohydromonas lata	strain=NBRC 102462	GCA_001571085.1	45677	45677	type	True	87.4488	1599	2851	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	80.5864	775	2851	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000190375.2	316997	316997	type	True	80.4038	793	2851	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000420125.1	316997	316997	type	True	80.3771	813	2851	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	80.3537	764	2851	95	below_threshold
Sphaerotilus natans	strain=ATCC 13338	GCA_900156335.1	34103	34103	type	True	80.3519	863	2851	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	80.1077	826	2851	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	80.0499	728	2851	95	below_threshold
Ideonella livida	strain=TBM-1	GCA_010499455.1	2707176	2707176	type	True	79.6112	798	2851	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	79.3912	769	2851	95	below_threshold
Schlegelella brevitalea	strain=DSM 7029	GCA_001017435.1	413882	413882	type	True	78.9396	715	2851	95	below_threshold
Inhella proteolytica	strain=1Y17	GCA_016093275.1	2795029	2795029	type	True	78.6382	771	2851	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:53:22,273] [INFO] DFAST Taxonomy check result was written to GCF_000430725.1_ASM43072v1_genomic.fna/tc_result.tsv
[2024-01-25 17:53:22,274] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:53:22,274] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:53:22,274] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0295a052-f436-4df7-8ce0-b4aad8ac3f16/dqc_reference/checkm_data
[2024-01-25 17:53:22,275] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:53:22,354] [INFO] Task started: CheckM
[2024-01-25 17:53:22,355] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000430725.1_ASM43072v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000430725.1_ASM43072v1_genomic.fna/checkm_input GCF_000430725.1_ASM43072v1_genomic.fna/checkm_result
[2024-01-25 17:55:44,924] [INFO] Task succeeded: CheckM
[2024-01-25 17:55:44,925] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:55:44,944] [INFO] ===== Completeness check finished =====
[2024-01-25 17:55:44,944] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:55:44,951] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000430725.1_ASM43072v1_genomic.fna/markers.fasta)
[2024-01-25 17:55:44,951] [INFO] Task started: Blastn
[2024-01-25 17:55:44,951] [INFO] Running command: blastn -query GCF_000430725.1_ASM43072v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0295a052-f436-4df7-8ce0-b4aad8ac3f16/dqc_reference/reference_markers_gtdb.fasta -out GCF_000430725.1_ASM43072v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:55:47,251] [INFO] Task succeeded: Blastn
[2024-01-25 17:55:47,255] [INFO] Selected 10 target genomes.
[2024-01-25 17:55:47,255] [INFO] Target genome list was writen to GCF_000430725.1_ASM43072v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:55:47,262] [INFO] Task started: fastANI
[2024-01-25 17:55:47,263] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b864211-81a7-48ca-8cba-36537a256fa4/GCF_000430725.1_ASM43072v1_genomic.fna.gz --refList GCF_000430725.1_ASM43072v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000430725.1_ASM43072v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:56:08,896] [INFO] Task succeeded: fastANI
[2024-01-25 17:56:08,903] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:56:08,903] [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_000430725.1	s__Azohydromonas australica	99.999	2837	2851	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Azohydromonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_012927045.1	s__Azohydromonas caseinilytica	88.2019	1619	2851	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Azohydromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009760915.1	s__Azohydromonas aeria	87.5995	1648	2851	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Azohydromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001571085.1	s__Azohydromonas lata	87.4314	1601	2851	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Azohydromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003569765.1	s__Aquabacterium_B tepidiphilum	80.878	964	2851	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014873965.1	s__VBDL01 sp014873965	80.7682	997	2851	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__VBDL01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000969605.1	s__Aquincola tertiaricarbonis	80.4735	1046	2851	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquincola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013294065.1	s__Sphaerotilus sp013294065	80.3537	929	2851	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sphaerotilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016213265.1	s__Ideonella sp016213265	80.1794	770	2851	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005403045.1	s__Aquabacterium_A pictum	79.6442	988	2851	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:56:08,914] [INFO] GTDB search result was written to GCF_000430725.1_ASM43072v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:56:08,915] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:56:08,918] [INFO] DFAST_QC result json was written to GCF_000430725.1_ASM43072v1_genomic.fna/dqc_result.json
[2024-01-25 17:56:08,918] [INFO] DFAST_QC completed!
[2024-01-25 17:56:08,918] [INFO] Total running time: 0h3m48s