[2023-06-27 06:05:39,685] [INFO] DFAST_QC pipeline started.
[2023-06-27 06:05:39,702] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 06:05:39,702] [INFO] DQC Reference Directory: /var/lib/cwl/stg54132f9d-e131-458d-9d4e-00d3298d1105/dqc_reference
[2023-06-27 06:05:42,363] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 06:05:42,364] [INFO] Task started: Prodigal
[2023-06-27 06:05:42,365] [INFO] Running command: gunzip -c /var/lib/cwl/stga64f991a-272a-4832-98a7-59e38cc5a210/GCA_027402845.1_ASM2740284v1_genomic.fna.gz | prodigal -d GCA_027402845.1_ASM2740284v1_genomic.fna/cds.fna -a GCA_027402845.1_ASM2740284v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 06:05:52,849] [INFO] Task succeeded: Prodigal
[2023-06-27 06:05:52,850] [INFO] Task started: HMMsearch
[2023-06-27 06:05:52,850] [INFO] Running command: hmmsearch --tblout GCA_027402845.1_ASM2740284v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg54132f9d-e131-458d-9d4e-00d3298d1105/dqc_reference/reference_markers.hmm GCA_027402845.1_ASM2740284v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 06:05:53,112] [INFO] Task succeeded: HMMsearch
[2023-06-27 06:05:53,113] [INFO] Found 6/6 markers.
[2023-06-27 06:05:53,158] [INFO] Query marker FASTA was written to GCA_027402845.1_ASM2740284v1_genomic.fna/markers.fasta
[2023-06-27 06:05:53,158] [INFO] Task started: Blastn
[2023-06-27 06:05:53,158] [INFO] Running command: blastn -query GCA_027402845.1_ASM2740284v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg54132f9d-e131-458d-9d4e-00d3298d1105/dqc_reference/reference_markers.fasta -out GCA_027402845.1_ASM2740284v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 06:05:53,845] [INFO] Task succeeded: Blastn
[2023-06-27 06:05:53,850] [INFO] Selected 25 target genomes.
[2023-06-27 06:05:53,851] [INFO] Target genome list was writen to GCA_027402845.1_ASM2740284v1_genomic.fna/target_genomes.txt
[2023-06-27 06:05:53,883] [INFO] Task started: fastANI
[2023-06-27 06:05:53,883] [INFO] Running command: fastANI --query /var/lib/cwl/stga64f991a-272a-4832-98a7-59e38cc5a210/GCA_027402845.1_ASM2740284v1_genomic.fna.gz --refList GCA_027402845.1_ASM2740284v1_genomic.fna/target_genomes.txt --output GCA_027402845.1_ASM2740284v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 06:06:13,687] [INFO] Task succeeded: fastANI
[2023-06-27 06:06:13,688] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg54132f9d-e131-458d-9d4e-00d3298d1105/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 06:06:13,688] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg54132f9d-e131-458d-9d4e-00d3298d1105/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 06:06:13,702] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 06:06:13,703] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 06:06:13,703] [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
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	75.187	64	1264	95	below_threshold
Bradyrhizobium mercantei	strain=SEMIA 6399	GCA_001982635.1	1904807	1904807	type	True	75.1381	62	1264	95	below_threshold
Bradyrhizobium septentrionale	strain=1S1	GCA_011516645.4	1404411	1404411	type	True	75.0375	66	1264	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	75.0324	66	1264	95	below_threshold
Luteimonas salinisoli	strain=SJ-92	GCA_013425525.1	2752307	2752307	type	True	75.0287	60	1264	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	74.9597	63	1264	95	below_threshold
Bradyrhizobium macuxiense	strain=BR 10303	GCA_001542415.1	1755647	1755647	type	True	74.955	62	1264	95	below_threshold
Bradyrhizobium tropiciagri	strain=SEMIA 6148	GCA_001189845.1	312253	312253	type	True	74.9222	63	1264	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_016653355.1	29408	29408	type	True	74.9199	68	1264	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	74.9196	66	1264	95	below_threshold
Methylobrevis albus	strain=L22	GCA_015904235.1	2793297	2793297	type	True	74.8969	62	1264	95	below_threshold
Geodermatophilus siccatus	strain=DSM 45419	GCA_900103785.1	1137991	1137991	type	True	74.861	53	1264	95	below_threshold
Luteimonas saliphila	strain=SJ-9	GCA_016774335.1	2804919	2804919	type	True	74.8397	59	1264	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 06:06:13,705] [INFO] DFAST Taxonomy check result was written to GCA_027402845.1_ASM2740284v1_genomic.fna/tc_result.tsv
[2023-06-27 06:06:13,706] [INFO] ===== Taxonomy check completed =====
[2023-06-27 06:06:13,706] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 06:06:13,706] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg54132f9d-e131-458d-9d4e-00d3298d1105/dqc_reference/checkm_data
[2023-06-27 06:06:13,707] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 06:06:13,843] [INFO] Task started: CheckM
[2023-06-27 06:06:13,843] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027402845.1_ASM2740284v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027402845.1_ASM2740284v1_genomic.fna/checkm_input GCA_027402845.1_ASM2740284v1_genomic.fna/checkm_result
[2023-06-27 06:06:47,903] [INFO] Task succeeded: CheckM
[2023-06-27 06:06:47,905] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 06:06:47,957] [INFO] ===== Completeness check finished =====
[2023-06-27 06:06:47,958] [INFO] ===== Start GTDB Search =====
[2023-06-27 06:06:47,958] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027402845.1_ASM2740284v1_genomic.fna/markers.fasta)
[2023-06-27 06:06:47,959] [INFO] Task started: Blastn
[2023-06-27 06:06:47,959] [INFO] Running command: blastn -query GCA_027402845.1_ASM2740284v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg54132f9d-e131-458d-9d4e-00d3298d1105/dqc_reference/reference_markers_gtdb.fasta -out GCA_027402845.1_ASM2740284v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 06:06:48,980] [INFO] Task succeeded: Blastn
[2023-06-27 06:06:48,990] [INFO] Selected 21 target genomes.
[2023-06-27 06:06:48,990] [INFO] Target genome list was writen to GCA_027402845.1_ASM2740284v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 06:06:49,031] [INFO] Task started: fastANI
[2023-06-27 06:06:49,031] [INFO] Running command: fastANI --query /var/lib/cwl/stga64f991a-272a-4832-98a7-59e38cc5a210/GCA_027402845.1_ASM2740284v1_genomic.fna.gz --refList GCA_027402845.1_ASM2740284v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027402845.1_ASM2740284v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 06:07:02,906] [INFO] Task succeeded: fastANI
[2023-06-27 06:07:03,045] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 06:07:03,046] [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_003135135.1	s__Binatus sp003135135	76.5984	108	1264	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__Binatales;f__Binataceae;g__Binatus	95.0	99.92	99.78	0.98	0.97	5	-
GCA_002479255.1	s__Binatus soli	76.5423	105	1264	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__Binatales;f__Binataceae;g__Binatus	95.0	100.00	100.00	0.99	0.99	2	-
GCA_015478645.1	s__JADMIL01 sp015478645	76.4126	138	1264	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__Binatales;f__Binataceae;g__JADMIL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011334465.1	s__DTIX01 sp011334465	76.2463	117	1264	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__Binatales;f__Binataceae;g__DTIX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019237115.1	s__JAFAHS01 sp019237115	75.9818	79	1264	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__Binatales;f__Binataceae;g__JAFAHS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003135855.1	s__Binatus sp003135855	75.8633	77	1264	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__Binatales;f__Binataceae;g__Binatus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016189835.1	s__JACPRU01 sp016189835	75.3577	62	1264	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__JACPRU01;f__JACPRU01;g__JACPRU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016874715.1	s__VGTK01 sp016874715	75.1112	102	1264	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__UBA12015;f__UBA12015;g__VGTK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017853315.1	s__REEB422 sp017853315	75.093	59	1264	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__UBA12015;f__UBA12015;g__REEB422	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013425525.1	s__Luteimonas sp013425525	75.0287	60	1264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 06:07:03,051] [INFO] GTDB search result was written to GCA_027402845.1_ASM2740284v1_genomic.fna/result_gtdb.tsv
[2023-06-27 06:07:03,051] [INFO] ===== GTDB Search completed =====
[2023-06-27 06:07:03,059] [INFO] DFAST_QC result json was written to GCA_027402845.1_ASM2740284v1_genomic.fna/dqc_result.json
[2023-06-27 06:07:03,060] [INFO] DFAST_QC completed!
[2023-06-27 06:07:03,060] [INFO] Total running time: 0h1m23s