[2023-06-30 21:27:01,590] [INFO] DFAST_QC pipeline started.
[2023-06-30 21:27:01,593] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 21:27:01,593] [INFO] DQC Reference Directory: /var/lib/cwl/stg4de876f2-ea85-4c76-a74d-053825bd119a/dqc_reference
[2023-06-30 21:27:04,459] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 21:27:04,460] [INFO] Task started: Prodigal
[2023-06-30 21:27:04,461] [INFO] Running command: gunzip -c /var/lib/cwl/stg51edbc71-f003-4c4a-975b-10b1db7f6c32/GCA_903945585.1_freshwater_MAG_---_I-3_bin-201_genomic.fna.gz | prodigal -d GCA_903945585.1_freshwater_MAG_---_I-3_bin-201_genomic.fna/cds.fna -a GCA_903945585.1_freshwater_MAG_---_I-3_bin-201_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 21:27:14,795] [INFO] Task succeeded: Prodigal
[2023-06-30 21:27:14,796] [INFO] Task started: HMMsearch
[2023-06-30 21:27:14,796] [INFO] Running command: hmmsearch --tblout GCA_903945585.1_freshwater_MAG_---_I-3_bin-201_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4de876f2-ea85-4c76-a74d-053825bd119a/dqc_reference/reference_markers.hmm GCA_903945585.1_freshwater_MAG_---_I-3_bin-201_genomic.fna/protein.faa > /dev/null
[2023-06-30 21:27:15,030] [INFO] Task succeeded: HMMsearch
[2023-06-30 21:27:15,031] [INFO] Found 6/6 markers.
[2023-06-30 21:27:15,067] [INFO] Query marker FASTA was written to GCA_903945585.1_freshwater_MAG_---_I-3_bin-201_genomic.fna/markers.fasta
[2023-06-30 21:27:15,067] [INFO] Task started: Blastn
[2023-06-30 21:27:15,067] [INFO] Running command: blastn -query GCA_903945585.1_freshwater_MAG_---_I-3_bin-201_genomic.fna/markers.fasta -db /var/lib/cwl/stg4de876f2-ea85-4c76-a74d-053825bd119a/dqc_reference/reference_markers.fasta -out GCA_903945585.1_freshwater_MAG_---_I-3_bin-201_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 21:27:15,785] [INFO] Task succeeded: Blastn
[2023-06-30 21:27:15,790] [INFO] Selected 22 target genomes.
[2023-06-30 21:27:15,790] [INFO] Target genome list was writen to GCA_903945585.1_freshwater_MAG_---_I-3_bin-201_genomic.fna/target_genomes.txt
[2023-06-30 21:27:15,796] [INFO] Task started: fastANI
[2023-06-30 21:27:15,797] [INFO] Running command: fastANI --query /var/lib/cwl/stg51edbc71-f003-4c4a-975b-10b1db7f6c32/GCA_903945585.1_freshwater_MAG_---_I-3_bin-201_genomic.fna.gz --refList GCA_903945585.1_freshwater_MAG_---_I-3_bin-201_genomic.fna/target_genomes.txt --output GCA_903945585.1_freshwater_MAG_---_I-3_bin-201_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 21:27:29,836] [INFO] Task succeeded: fastANI
[2023-06-30 21:27:29,838] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4de876f2-ea85-4c76-a74d-053825bd119a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 21:27:29,839] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4de876f2-ea85-4c76-a74d-053825bd119a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 21:27:29,861] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 21:27:29,861] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 21:27:29,861] [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
Brevundimonas alba	strain=DSM 4736	GCA_011927945.1	74314	74314	type	True	76.4494	82	1130	95	below_threshold
Caulobacter henricii	strain=CB4	GCA_001414055.1	69395	69395	type	True	76.4421	125	1130	95	below_threshold
Caulobacter soli	strain=Ji-3-8	GCA_011045195.1	2708539	2708539	type	True	76.4299	121	1130	95	below_threshold
Brevundimonas bacteroides	strain=DSM 4726	GCA_000701445.1	74311	74311	type	True	76.42	67	1130	95	below_threshold
Caulobacter hibisci	strain=KACC 18849	GCA_016135805.1	2035993	2035993	type	True	76.3967	124	1130	95	below_threshold
Caulobacter vibrioides	strain=DSM 9893	GCA_002858865.1	155892	155892	type	True	76.3696	113	1130	95	below_threshold
Phenylobacterium hankyongense	strain=HKS-05	GCA_003254505.1	1813876	1813876	type	True	76.3486	99	1130	95	below_threshold
Caulobacter mirabilis	strain=FWC 38	GCA_002749615.1	69666	69666	type	True	76.3207	102	1130	95	below_threshold
Caulobacter radicis	strain=695	GCA_003094615.1	2172650	2172650	type	True	76.3128	121	1130	95	below_threshold
Brevundimonas vesicularis	strain=NBRC 12165	GCA_001592205.1	41276	41276	suspected-type	True	76.3026	81	1130	95	below_threshold
Phenylobacterium soli	strain=LX32	GCA_003254475.1	2170551	2170551	type	True	76.2544	106	1130	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	76.2346	80	1130	95	below_threshold
Caulobacter zeae	strain=410	GCA_002858925.1	2055137	2055137	type	True	76.17	116	1130	95	below_threshold
Brevundimonas lenta	strain=DSM 23960	GCA_014196335.1	424796	424796	type	True	76.1514	74	1130	95	below_threshold
Caulobacter endophyticus	strain=774	GCA_003116815.1	2172652	2172652	type	True	76.1357	118	1130	95	below_threshold
Brevundimonas naejangsanensis	strain=DSM 23858	GCA_000421705.1	588932	588932	type	True	76.059	90	1130	95	below_threshold
Caulobacter segnis	strain=TK0059	GCA_003015125.1	88688	88688	type	True	76.0027	125	1130	95	below_threshold
Caulobacter flavus	strain=CGMCC1 15093	GCA_002858845.1	1679497	1679497	type	True	75.9067	128	1130	95	below_threshold
Caulobacter flavus	strain=RHGG3	GCA_003722335.1	1679497	1679497	type	True	75.8932	131	1130	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 21:27:29,863] [INFO] DFAST Taxonomy check result was written to GCA_903945585.1_freshwater_MAG_---_I-3_bin-201_genomic.fna/tc_result.tsv
[2023-06-30 21:27:29,864] [INFO] ===== Taxonomy check completed =====
[2023-06-30 21:27:29,864] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 21:27:29,864] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4de876f2-ea85-4c76-a74d-053825bd119a/dqc_reference/checkm_data
[2023-06-30 21:27:29,865] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 21:27:29,906] [INFO] Task started: CheckM
[2023-06-30 21:27:29,906] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903945585.1_freshwater_MAG_---_I-3_bin-201_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903945585.1_freshwater_MAG_---_I-3_bin-201_genomic.fna/checkm_input GCA_903945585.1_freshwater_MAG_---_I-3_bin-201_genomic.fna/checkm_result
[2023-06-30 21:28:04,491] [INFO] Task succeeded: CheckM
[2023-06-30 21:28:04,493] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-30 21:28:04,516] [INFO] ===== Completeness check finished =====
[2023-06-30 21:28:04,517] [INFO] ===== Start GTDB Search =====
[2023-06-30 21:28:04,517] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903945585.1_freshwater_MAG_---_I-3_bin-201_genomic.fna/markers.fasta)
[2023-06-30 21:28:04,518] [INFO] Task started: Blastn
[2023-06-30 21:28:04,518] [INFO] Running command: blastn -query GCA_903945585.1_freshwater_MAG_---_I-3_bin-201_genomic.fna/markers.fasta -db /var/lib/cwl/stg4de876f2-ea85-4c76-a74d-053825bd119a/dqc_reference/reference_markers_gtdb.fasta -out GCA_903945585.1_freshwater_MAG_---_I-3_bin-201_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 21:28:05,680] [INFO] Task succeeded: Blastn
[2023-06-30 21:28:05,685] [INFO] Selected 19 target genomes.
[2023-06-30 21:28:05,686] [INFO] Target genome list was writen to GCA_903945585.1_freshwater_MAG_---_I-3_bin-201_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 21:28:05,701] [INFO] Task started: fastANI
[2023-06-30 21:28:05,702] [INFO] Running command: fastANI --query /var/lib/cwl/stg51edbc71-f003-4c4a-975b-10b1db7f6c32/GCA_903945585.1_freshwater_MAG_---_I-3_bin-201_genomic.fna.gz --refList GCA_903945585.1_freshwater_MAG_---_I-3_bin-201_genomic.fna/target_genomes_gtdb.txt --output GCA_903945585.1_freshwater_MAG_---_I-3_bin-201_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 21:28:17,708] [INFO] Task succeeded: fastANI
[2023-06-30 21:28:17,722] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 21:28:17,722] [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_903840435.1	s__CAIMFV01 sp903840435	99.6963	1035	1130	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__CAIMFV01	95.0	99.80	99.59	0.94	0.92	5	conclusive
GCA_903884425.1	s__CAIMFV01 sp903884425	77.409	220	1130	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__CAIMFV01	95.0	99.90	99.80	0.98	0.97	6	-
GCA_903874895.1	s__CAIMFV01 sp903874895	77.1493	166	1130	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__CAIMFV01	95.0	98.54	98.54	0.83	0.83	2	-
GCA_903858685.1	s__CAIMFV01 sp903858685	77.1406	231	1130	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__CAIMFV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903851655.1	s__CAIMFV01 sp903851655	76.941	195	1130	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__CAIMFV01	95.0	99.52	99.51	0.87	0.86	3	-
GCA_903903715.1	s__CAIMFV01 sp903903715	76.7855	109	1130	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__CAIMFV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765965.1	s__CAHJWH01 sp009765965	76.7017	114	1130	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__CAHJWH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903884915.1	s__CAISGS01 sp903884915	76.5097	93	1130	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__CAISGS01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011927945.1	s__Brevundimonas alba	76.4494	82	1130	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013912005.1	s__Brevundimonas sp013912005	76.3829	92	1130	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903858185.1	s__Caulobacter sp903858185	76.2941	107	1130	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	99.71	99.71	0.95	0.95	2	-
GCF_010975005.1	s__17J80-11 sp010975005	76.2549	100	1130	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__17J80-11	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002742645.2	s__Caulobacter sp002742645	76.2115	128	1130	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	99.59	99.58	0.91	0.91	3	-
GCA_018241995.1	s__17J80-11 sp018241995	76.1558	103	1130	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__17J80-11	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003722335.1	s__Caulobacter flavus	75.8963	129	1130	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	99.98	99.98	0.98	0.98	2	-
GCA_018240795.1	s__Phenylobacterium sp018240795	75.87	92	1130	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 21:28:17,724] [INFO] GTDB search result was written to GCA_903945585.1_freshwater_MAG_---_I-3_bin-201_genomic.fna/result_gtdb.tsv
[2023-06-30 21:28:17,725] [INFO] ===== GTDB Search completed =====
[2023-06-30 21:28:17,729] [INFO] DFAST_QC result json was written to GCA_903945585.1_freshwater_MAG_---_I-3_bin-201_genomic.fna/dqc_result.json
[2023-06-30 21:28:17,729] [INFO] DFAST_QC completed!
[2023-06-30 21:28:17,729] [INFO] Total running time: 0h1m16s