[2024-01-24 15:14:52,329] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:14:52,332] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:14:52,332] [INFO] DQC Reference Directory: /var/lib/cwl/stg5b6339fc-ae75-450f-98db-0a5e43e959f0/dqc_reference
[2024-01-24 15:14:53,652] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:14:53,653] [INFO] Task started: Prodigal
[2024-01-24 15:14:53,653] [INFO] Running command: gunzip -c /var/lib/cwl/stg7b88fc5e-dfc7-4857-a445-4b260580c236/GCF_001544075.1_ASM154407v1_genomic.fna.gz | prodigal -d GCF_001544075.1_ASM154407v1_genomic.fna/cds.fna -a GCF_001544075.1_ASM154407v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:15:09,814] [INFO] Task succeeded: Prodigal
[2024-01-24 15:15:09,814] [INFO] Task started: HMMsearch
[2024-01-24 15:15:09,815] [INFO] Running command: hmmsearch --tblout GCF_001544075.1_ASM154407v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5b6339fc-ae75-450f-98db-0a5e43e959f0/dqc_reference/reference_markers.hmm GCF_001544075.1_ASM154407v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:15:10,128] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:15:10,130] [INFO] Found 6/6 markers.
[2024-01-24 15:15:10,172] [INFO] Query marker FASTA was written to GCF_001544075.1_ASM154407v1_genomic.fna/markers.fasta
[2024-01-24 15:15:10,172] [INFO] Task started: Blastn
[2024-01-24 15:15:10,173] [INFO] Running command: blastn -query GCF_001544075.1_ASM154407v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b6339fc-ae75-450f-98db-0a5e43e959f0/dqc_reference/reference_markers.fasta -out GCF_001544075.1_ASM154407v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:15:11,182] [INFO] Task succeeded: Blastn
[2024-01-24 15:15:11,187] [INFO] Selected 22 target genomes.
[2024-01-24 15:15:11,188] [INFO] Target genome list was writen to GCF_001544075.1_ASM154407v1_genomic.fna/target_genomes.txt
[2024-01-24 15:15:11,197] [INFO] Task started: fastANI
[2024-01-24 15:15:11,198] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b88fc5e-dfc7-4857-a445-4b260580c236/GCF_001544075.1_ASM154407v1_genomic.fna.gz --refList GCF_001544075.1_ASM154407v1_genomic.fna/target_genomes.txt --output GCF_001544075.1_ASM154407v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:15:34,360] [INFO] Task succeeded: fastANI
[2024-01-24 15:15:34,360] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5b6339fc-ae75-450f-98db-0a5e43e959f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:15:34,361] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5b6339fc-ae75-450f-98db-0a5e43e959f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:15:34,381] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:15:34,381] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:15:34,381] [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
Comamonas terrae	strain=NBRC 106524	GCA_001544075.1	673548	673548	type	True	100.0	1552	1555	95	conclusive
Comamonas phosphati	strain=CGMCC 1.12294	GCA_014637085.1	1211803	1211803	type	True	90.5013	1036	1555	95	below_threshold
Delftia acidovorans	strain=NBRC 14950	GCA_001598795.1	80866	80866	type	True	84.5766	1084	1555	95	below_threshold
Delftia acidovorans	strain=FDAARGOS_997	GCA_016127415.1	80866	80866	type	True	84.554	1103	1555	95	below_threshold
Comamonas testosteroni	strain=ATCC 11996	GCA_000241525.2	285	285	suspected-type	True	84.1262	1108	1555	95	below_threshold
Comamonas testosteroni	strain=NBRC 14951	GCA_000740035.1	285	285	suspected-type	True	84.1112	1089	1555	95	below_threshold
Comamonas testosteroni	strain=NCTC10698	GCA_900461225.1	285	285	suspected-type	True	84.1079	1117	1555	95	below_threshold
Comamonas thiooxydans	strain=DSM 17888	GCA_000964545.1	363952	363952	type	True	83.9648	1088	1555	95	below_threshold
Comamonas thiooxydans	strain=DSM 17888	GCA_001418295.1	363952	363952	type	True	83.9639	1095	1555	95	below_threshold
Comamonas thiooxydans	strain=DSM 17888	GCA_001517325.1	363952	363952	type	True	83.9453	1098	1555	95	below_threshold
Comamonas aquatica	strain=NBRC 14918	GCA_000739875.1	225991	225991	type	True	82.515	751	1555	95	below_threshold
Comamonas fluminis	strain=CJ34	GCA_019186805.1	2796366	2796366	type	True	82.5077	954	1555	95	below_threshold
Comamonas terrigena	strain=NCTC1937	GCA_900461435.1	32013	32013	type	True	82.3064	874	1555	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	82.0463	820	1555	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	80.3231	640	1555	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	80.0305	632	1555	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	79.788	632	1555	95	below_threshold
Ottowia testudinis	strain=27C	GCA_017498525.1	2816950	2816950	type	True	79.2375	555	1555	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	77.4919	310	1555	95	below_threshold
Noviherbaspirillum pedocola	strain=DKR-6	GCA_016632335.1	2801341	2801341	type	True	77.032	325	1555	95	below_threshold
Brevundimonas alba	strain=DSM 4736	GCA_011927945.1	74314	74314	type	True	75.8279	83	1555	95	below_threshold
Marinobacterium arenosum	strain=CAU 1594	GCA_019795155.1	2862496	2862496	type	True	75.3916	102	1555	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:15:34,383] [INFO] DFAST Taxonomy check result was written to GCF_001544075.1_ASM154407v1_genomic.fna/tc_result.tsv
[2024-01-24 15:15:34,383] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:15:34,383] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:15:34,384] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5b6339fc-ae75-450f-98db-0a5e43e959f0/dqc_reference/checkm_data
[2024-01-24 15:15:34,384] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:15:34,428] [INFO] Task started: CheckM
[2024-01-24 15:15:34,428] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001544075.1_ASM154407v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001544075.1_ASM154407v1_genomic.fna/checkm_input GCF_001544075.1_ASM154407v1_genomic.fna/checkm_result
[2024-01-24 15:16:25,281] [INFO] Task succeeded: CheckM
[2024-01-24 15:16:25,282] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:16:25,301] [INFO] ===== Completeness check finished =====
[2024-01-24 15:16:25,301] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:16:25,302] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001544075.1_ASM154407v1_genomic.fna/markers.fasta)
[2024-01-24 15:16:25,302] [INFO] Task started: Blastn
[2024-01-24 15:16:25,302] [INFO] Running command: blastn -query GCF_001544075.1_ASM154407v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b6339fc-ae75-450f-98db-0a5e43e959f0/dqc_reference/reference_markers_gtdb.fasta -out GCF_001544075.1_ASM154407v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:16:27,188] [INFO] Task succeeded: Blastn
[2024-01-24 15:16:27,192] [INFO] Selected 15 target genomes.
[2024-01-24 15:16:27,193] [INFO] Target genome list was writen to GCF_001544075.1_ASM154407v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:16:27,207] [INFO] Task started: fastANI
[2024-01-24 15:16:27,207] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b88fc5e-dfc7-4857-a445-4b260580c236/GCF_001544075.1_ASM154407v1_genomic.fna.gz --refList GCF_001544075.1_ASM154407v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001544075.1_ASM154407v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:16:45,872] [INFO] Task succeeded: fastANI
[2024-01-24 15:16:45,887] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:16:45,888] [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_001544075.1	s__Comamonas terrae	100.0	1552	1555	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014637085.1	s__Comamonas phosphati	90.488	1037	1555	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019236485.1	s__Comamonas sp019236485	86.2617	767	1555	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000739375.1	s__Comamonas testosteroni_B	84.6986	1114	1555	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	97.94	95.50	0.89	0.85	10	-
GCF_001598795.1	s__Comamonas acidovorans	84.609	1080	1555	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.4801	97.72	96.19	0.89	0.80	41	-
GCF_001571325.1	s__Comamonas tsuruhatensis	84.5929	1074	1555	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.4801	98.55	98.21	0.90	0.80	27	-
GCF_014076415.1	s__Comamonas testosteroni_F	84.2716	1135	1555	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000241525.1	s__Comamonas testosteroni	84.1176	1109	1555	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	99.74	98.70	0.99	0.94	6	-
GCF_000964545.1	s__Comamonas thiooxydans	83.9869	1085	1555	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	97.51	95.23	0.90	0.87	29	-
GCA_009360615.1	s__Comamonas sp009360615	83.8311	1018	1555	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900564145.1	s__Comamonas sp900564145	83.2285	1035	1555	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003569915.1	s__Comamonas testosteroni_D	82.967	962	1555	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000739875.1	s__Comamonas aquatica	82.4826	754	1555	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	96.97	96.57	0.89	0.87	7	-
GCF_900461435.1	s__Comamonas terrigena	82.3069	874	1555	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	97.97	95.46	0.95	0.91	7	-
GCF_014207955.1	s__Acidovorax soli_A	81.566	892	1555	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:16:45,890] [INFO] GTDB search result was written to GCF_001544075.1_ASM154407v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:16:45,890] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:16:45,894] [INFO] DFAST_QC result json was written to GCF_001544075.1_ASM154407v1_genomic.fna/dqc_result.json
[2024-01-24 15:16:45,894] [INFO] DFAST_QC completed!
[2024-01-24 15:16:45,894] [INFO] Total running time: 0h1m54s