[2023-06-13 00:45:23,060] [INFO] DFAST_QC pipeline started.
[2023-06-13 00:45:23,062] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 00:45:23,062] [INFO] DQC Reference Directory: /var/lib/cwl/stgb1d2ca0f-fb8f-4599-8574-62e2db71df32/dqc_reference
[2023-06-13 00:45:24,331] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 00:45:24,332] [INFO] Task started: Prodigal
[2023-06-13 00:45:24,332] [INFO] Running command: gunzip -c /var/lib/cwl/stgd8426978-b6aa-4129-b4a4-a5dd0bb7403e/GCA_022735975.1_ASM2273597v1_genomic.fna.gz | prodigal -d GCA_022735975.1_ASM2273597v1_genomic.fna/cds.fna -a GCA_022735975.1_ASM2273597v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 00:45:34,688] [INFO] Task succeeded: Prodigal
[2023-06-13 00:45:34,689] [INFO] Task started: HMMsearch
[2023-06-13 00:45:34,689] [INFO] Running command: hmmsearch --tblout GCA_022735975.1_ASM2273597v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb1d2ca0f-fb8f-4599-8574-62e2db71df32/dqc_reference/reference_markers.hmm GCA_022735975.1_ASM2273597v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 00:45:35,049] [INFO] Task succeeded: HMMsearch
[2023-06-13 00:45:35,050] [INFO] Found 6/6 markers.
[2023-06-13 00:45:35,096] [INFO] Query marker FASTA was written to GCA_022735975.1_ASM2273597v1_genomic.fna/markers.fasta
[2023-06-13 00:45:35,096] [INFO] Task started: Blastn
[2023-06-13 00:45:35,096] [INFO] Running command: blastn -query GCA_022735975.1_ASM2273597v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb1d2ca0f-fb8f-4599-8574-62e2db71df32/dqc_reference/reference_markers.fasta -out GCA_022735975.1_ASM2273597v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 00:45:36,184] [INFO] Task succeeded: Blastn
[2023-06-13 00:45:36,188] [INFO] Selected 14 target genomes.
[2023-06-13 00:45:36,189] [INFO] Target genome list was writen to GCA_022735975.1_ASM2273597v1_genomic.fna/target_genomes.txt
[2023-06-13 00:45:36,193] [INFO] Task started: fastANI
[2023-06-13 00:45:36,194] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8426978-b6aa-4129-b4a4-a5dd0bb7403e/GCA_022735975.1_ASM2273597v1_genomic.fna.gz --refList GCA_022735975.1_ASM2273597v1_genomic.fna/target_genomes.txt --output GCA_022735975.1_ASM2273597v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 00:45:51,803] [INFO] Task succeeded: fastANI
[2023-06-13 00:45:51,804] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb1d2ca0f-fb8f-4599-8574-62e2db71df32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 00:45:51,804] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb1d2ca0f-fb8f-4599-8574-62e2db71df32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 00:45:51,817] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 00:45:51,817] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 00:45:51,818] [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
Caulobacter segnis	strain=TK0059	GCA_003015125.1	88688	88688	type	True	85.8939	971	1347	95	below_threshold
Caulobacter segnis	strain=ATCC 21756	GCA_000092285.1	88688	88688	type	True	85.8673	975	1347	95	below_threshold
Caulobacter vibrioides	strain=DSM 9893	GCA_002858865.1	155892	155892	type	True	85.4298	887	1347	95	below_threshold
Caulobacter zeae	strain=410	GCA_002858925.1	2055137	2055137	type	True	83.644	855	1347	95	below_threshold
Caulobacter radicis	strain=695	GCA_003094615.1	2172650	2172650	type	True	83.5896	868	1347	95	below_threshold
Caulobacter flavus	strain=RHGG3	GCA_003722335.1	1679497	1679497	type	True	83.564	884	1347	95	below_threshold
Caulobacter flavus	strain=CGMCC1 15093	GCA_002858845.1	1679497	1679497	type	True	83.466	901	1347	95	below_threshold
Caulobacter endophyticus	strain=774	GCA_003116815.1	2172652	2172652	type	True	83.4314	835	1347	95	below_threshold
Caulobacter rhizosphaerae	strain=KCTC 52515	GCA_010977555.1	2010972	2010972	type	True	83.2097	896	1347	95	below_threshold
Caulobacter rhizosphaerae	strain=CGMCC 1.15915	GCA_014645055.1	2010972	2010972	type	True	83.1753	889	1347	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	79.3744	615	1347	95	below_threshold
Phenylobacterium glaciei	strain=20VBR1	GCA_016772415.2	2803784	2803784	type	True	79.043	509	1347	95	below_threshold
Brevundimonas vitisensis	strain=GR-TSA-9	GCA_016656965.1	2800818	2800818	type	True	77.6773	288	1347	95	below_threshold
Starkeya koreensis	strain=Jip08	GCA_023016525.1	266121	266121	type	True	76.2347	209	1347	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 00:45:51,833] [INFO] DFAST Taxonomy check result was written to GCA_022735975.1_ASM2273597v1_genomic.fna/tc_result.tsv
[2023-06-13 00:45:51,834] [INFO] ===== Taxonomy check completed =====
[2023-06-13 00:45:51,835] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 00:45:51,835] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb1d2ca0f-fb8f-4599-8574-62e2db71df32/dqc_reference/checkm_data
[2023-06-13 00:45:51,837] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 00:45:51,884] [INFO] Task started: CheckM
[2023-06-13 00:45:51,884] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022735975.1_ASM2273597v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022735975.1_ASM2273597v1_genomic.fna/checkm_input GCA_022735975.1_ASM2273597v1_genomic.fna/checkm_result
[2023-06-13 00:46:25,181] [INFO] Task succeeded: CheckM
[2023-06-13 00:46:25,182] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 00:46:25,206] [INFO] ===== Completeness check finished =====
[2023-06-13 00:46:25,206] [INFO] ===== Start GTDB Search =====
[2023-06-13 00:46:25,206] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022735975.1_ASM2273597v1_genomic.fna/markers.fasta)
[2023-06-13 00:46:25,207] [INFO] Task started: Blastn
[2023-06-13 00:46:25,207] [INFO] Running command: blastn -query GCA_022735975.1_ASM2273597v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb1d2ca0f-fb8f-4599-8574-62e2db71df32/dqc_reference/reference_markers_gtdb.fasta -out GCA_022735975.1_ASM2273597v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 00:46:27,041] [INFO] Task succeeded: Blastn
[2023-06-13 00:46:27,046] [INFO] Selected 14 target genomes.
[2023-06-13 00:46:27,046] [INFO] Target genome list was writen to GCA_022735975.1_ASM2273597v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 00:46:27,059] [INFO] Task started: fastANI
[2023-06-13 00:46:27,059] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8426978-b6aa-4129-b4a4-a5dd0bb7403e/GCA_022735975.1_ASM2273597v1_genomic.fna.gz --refList GCA_022735975.1_ASM2273597v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022735975.1_ASM2273597v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 00:46:42,738] [INFO] Task succeeded: fastANI
[2023-06-13 00:46:42,762] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 00:46:42,763] [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_000372645.1	s__Caulobacter vibrioides_E	99.8333	1255	1347	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	98.89	97.90	0.89	0.86	5	conclusive
GCA_903900155.1	s__Caulobacter sp903900155	86.6099	977	1347	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	99.93	99.90	0.95	0.93	3	-
GCA_017744445.1	s__Caulobacter sp017744445	86.5291	992	1347	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000799245.1	s__Caulobacter sp000799245	86.3769	1006	1347	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	96.44	96.44	0.92	0.92	3	-
GCF_002742635.1	s__Caulobacter sp002742635	86.356	998	1347	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003931565.1	s__Caulobacter sp003931565	86.338	1020	1347	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001556515.1	s__Caulobacter sp001556515	86.178	873	1347	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003243465.1	s__Caulobacter segnis_A	86.0915	910	1347	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000092285.1	s__Caulobacter segnis	85.844	977	1347	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014207215.1	s__Caulobacter sp014207215	85.7967	972	1347	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013181195.1	s__Caulobacter sp013181195	85.6374	959	1347	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002858865.1	s__Caulobacter vibrioides	85.42	888	1347	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	98.80	98.06	0.96	0.95	6	-
GCF_002310375.3	s__Caulobacter vibrioides_D	85.3153	905	1347	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002280275.1	s__Caulobacter vibrioides_A	84.6925	663	1347	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 00:46:42,765] [INFO] GTDB search result was written to GCA_022735975.1_ASM2273597v1_genomic.fna/result_gtdb.tsv
[2023-06-13 00:46:42,765] [INFO] ===== GTDB Search completed =====
[2023-06-13 00:46:42,769] [INFO] DFAST_QC result json was written to GCA_022735975.1_ASM2273597v1_genomic.fna/dqc_result.json
[2023-06-13 00:46:42,769] [INFO] DFAST_QC completed!
[2023-06-13 00:46:42,769] [INFO] Total running time: 0h1m20s