[2023-06-27 18:42:50,346] [INFO] DFAST_QC pipeline started.
[2023-06-27 18:42:50,348] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 18:42:50,349] [INFO] DQC Reference Directory: /var/lib/cwl/stg6a87a4fd-4c5a-4f15-9274-e4855b13882b/dqc_reference
[2023-06-27 18:42:51,649] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 18:42:51,650] [INFO] Task started: Prodigal
[2023-06-27 18:42:51,650] [INFO] Running command: gunzip -c /var/lib/cwl/stg5228b9cf-de6c-4ce1-a4bf-6b4ac872dd73/GCA_026005175.1_ASM2600517v1_genomic.fna.gz | prodigal -d GCA_026005175.1_ASM2600517v1_genomic.fna/cds.fna -a GCA_026005175.1_ASM2600517v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 18:43:04,469] [INFO] Task succeeded: Prodigal
[2023-06-27 18:43:04,470] [INFO] Task started: HMMsearch
[2023-06-27 18:43:04,470] [INFO] Running command: hmmsearch --tblout GCA_026005175.1_ASM2600517v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6a87a4fd-4c5a-4f15-9274-e4855b13882b/dqc_reference/reference_markers.hmm GCA_026005175.1_ASM2600517v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 18:43:04,731] [INFO] Task succeeded: HMMsearch
[2023-06-27 18:43:04,733] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg5228b9cf-de6c-4ce1-a4bf-6b4ac872dd73/GCA_026005175.1_ASM2600517v1_genomic.fna.gz]
[2023-06-27 18:43:04,769] [INFO] Query marker FASTA was written to GCA_026005175.1_ASM2600517v1_genomic.fna/markers.fasta
[2023-06-27 18:43:04,770] [INFO] Task started: Blastn
[2023-06-27 18:43:04,770] [INFO] Running command: blastn -query GCA_026005175.1_ASM2600517v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a87a4fd-4c5a-4f15-9274-e4855b13882b/dqc_reference/reference_markers.fasta -out GCA_026005175.1_ASM2600517v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 18:43:05,317] [INFO] Task succeeded: Blastn
[2023-06-27 18:43:05,321] [INFO] Selected 20 target genomes.
[2023-06-27 18:43:05,321] [INFO] Target genome list was writen to GCA_026005175.1_ASM2600517v1_genomic.fna/target_genomes.txt
[2023-06-27 18:43:05,324] [INFO] Task started: fastANI
[2023-06-27 18:43:05,324] [INFO] Running command: fastANI --query /var/lib/cwl/stg5228b9cf-de6c-4ce1-a4bf-6b4ac872dd73/GCA_026005175.1_ASM2600517v1_genomic.fna.gz --refList GCA_026005175.1_ASM2600517v1_genomic.fna/target_genomes.txt --output GCA_026005175.1_ASM2600517v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 18:43:16,709] [INFO] Task succeeded: fastANI
[2023-06-27 18:43:16,710] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6a87a4fd-4c5a-4f15-9274-e4855b13882b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 18:43:16,710] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6a87a4fd-4c5a-4f15-9274-e4855b13882b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 18:43:16,720] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 18:43:16,721] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 18:43:16,721] [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
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	75.6084	126	1324	95	below_threshold
Sulfuritortus calidifontis	strain=J1A	GCA_003967275.1	1914471	1914471	type	True	75.3755	50	1324	95	below_threshold
Aquisalimonas asiatica	strain=CGMCC 1.6291	GCA_900110585.1	406100	406100	type	True	75.3288	54	1324	95	below_threshold
Arhodomonas aquaeolei	strain=DSM 8974	GCA_000374645.1	2369	2369	type	True	75.2232	63	1324	95	below_threshold
Metallibacterium scheffleri	strain=DKE6	GCA_002077135.1	993689	993689	type	True	75.1659	56	1324	95	below_threshold
Metallibacterium scheffleri	strain=DSM 24874	GCA_004798955.1	993689	993689	type	True	75.1659	56	1324	95	below_threshold
Rhodanobacter denitrificans	strain=2APBS1	GCA_000230695.3	666685	666685	type	True	75.1042	88	1324	95	below_threshold
Paenibacillus albicereus	strain=UniB2	GCA_012676905.1	2726185	2726185	type	True	74.9877	53	1324	95	below_threshold
Luteimonas padinae	strain=KCTC 52403	GCA_014652935.1	1714359	1714359	type	True	74.9822	76	1324	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	74.8773	127	1324	95	below_threshold
Nonomuraea coxensis	strain=DSM 45129	GCA_019397265.1	404386	404386	type	True	74.7987	131	1324	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 18:43:16,723] [INFO] DFAST Taxonomy check result was written to GCA_026005175.1_ASM2600517v1_genomic.fna/tc_result.tsv
[2023-06-27 18:43:16,724] [INFO] ===== Taxonomy check completed =====
[2023-06-27 18:43:16,724] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 18:43:16,724] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6a87a4fd-4c5a-4f15-9274-e4855b13882b/dqc_reference/checkm_data
[2023-06-27 18:43:16,726] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 18:43:16,767] [INFO] Task started: CheckM
[2023-06-27 18:43:16,767] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026005175.1_ASM2600517v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026005175.1_ASM2600517v1_genomic.fna/checkm_input GCA_026005175.1_ASM2600517v1_genomic.fna/checkm_result
[2023-06-27 18:43:55,115] [INFO] Task succeeded: CheckM
[2023-06-27 18:43:55,117] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 18:43:55,151] [INFO] ===== Completeness check finished =====
[2023-06-27 18:43:55,152] [INFO] ===== Start GTDB Search =====
[2023-06-27 18:43:55,152] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026005175.1_ASM2600517v1_genomic.fna/markers.fasta)
[2023-06-27 18:43:55,153] [INFO] Task started: Blastn
[2023-06-27 18:43:55,153] [INFO] Running command: blastn -query GCA_026005175.1_ASM2600517v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a87a4fd-4c5a-4f15-9274-e4855b13882b/dqc_reference/reference_markers_gtdb.fasta -out GCA_026005175.1_ASM2600517v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 18:43:55,763] [INFO] Task succeeded: Blastn
[2023-06-27 18:43:55,768] [INFO] Selected 20 target genomes.
[2023-06-27 18:43:55,768] [INFO] Target genome list was writen to GCA_026005175.1_ASM2600517v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 18:43:55,775] [INFO] Task started: fastANI
[2023-06-27 18:43:55,775] [INFO] Running command: fastANI --query /var/lib/cwl/stg5228b9cf-de6c-4ce1-a4bf-6b4ac872dd73/GCA_026005175.1_ASM2600517v1_genomic.fna.gz --refList GCA_026005175.1_ASM2600517v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026005175.1_ASM2600517v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 18:44:08,091] [INFO] Task succeeded: fastANI
[2023-06-27 18:44:08,107] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 18:44:08,107] [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
GCA_000522425.1	s__Entotheonella factor	75.6742	61	1324	d__Bacteria;p__Tectomicrobia;c__Entotheonellia;o__Entotheonellales;f__Entotheonellaceae;g__Entotheonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004634385.1	s__Thermaerobacter sp004634385	75.4071	73	1324	d__Bacteria;p__Firmicutes_E;c__Thermaerobacteria;o__Thermaerobacterales;f__Thermaerobacteraceae;g__Thermaerobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009772925.1	s__PFJX01 sp009772925	75.2996	54	1324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__PFJX01	95.0	99.99	99.98	1.00	0.99	4	-
GCA_005774545.1	s__VAUL01 sp005774545	75.2223	64	1324	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__BM103;g__VAUL01	95.0	99.97	99.97	0.96	0.96	2	-
GCA_016873935.1	s__PFJX01 sp016873935	75.1808	60	1324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__PFJX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016720425.1	s__CAIWHR01 sp016720425	75.0734	79	1324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Casimicrobiaceae;g__CAIWHR01	95.0	98.60	97.38	0.93	0.90	10	-
GCA_016192455.1	s__JACPUC01 sp016192455	74.9728	76	1324	d__Bacteria;p__JACPUC01;c__JACPUC01;o__JACPUC01;f__JACPUC01;g__JACPUC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015494165.1	s__S144-34 sp015494165	74.8868	88	1324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__S144-34;f__S144-34;g__S144-34	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003697015.1	s__J023 sp003697015	74.8738	115	1324	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__J023	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002432195.1	s__UBA5852 sp002432195	74.8071	60	1324	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__UBA5852;g__UBA5852	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 18:44:08,109] [INFO] GTDB search result was written to GCA_026005175.1_ASM2600517v1_genomic.fna/result_gtdb.tsv
[2023-06-27 18:44:08,110] [INFO] ===== GTDB Search completed =====
[2023-06-27 18:44:08,113] [INFO] DFAST_QC result json was written to GCA_026005175.1_ASM2600517v1_genomic.fna/dqc_result.json
[2023-06-27 18:44:08,113] [INFO] DFAST_QC completed!
[2023-06-27 18:44:08,113] [INFO] Total running time: 0h1m18s