[2024-01-24 11:05:49,405] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:49,407] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:49,407] [INFO] DQC Reference Directory: /var/lib/cwl/stgbbdd46fe-6610-4b15-b80b-92f3acba40ef/dqc_reference
[2024-01-24 11:05:51,280] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:51,281] [INFO] Task started: Prodigal
[2024-01-24 11:05:51,281] [INFO] Running command: gunzip -c /var/lib/cwl/stg41f44705-208d-41a4-9a38-720e12cd7994/GCF_016654005.1_ASM1665400v1_genomic.fna.gz | prodigal -d GCF_016654005.1_ASM1665400v1_genomic.fna/cds.fna -a GCF_016654005.1_ASM1665400v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:06:01,108] [INFO] Task succeeded: Prodigal
[2024-01-24 11:06:01,108] [INFO] Task started: HMMsearch
[2024-01-24 11:06:01,108] [INFO] Running command: hmmsearch --tblout GCF_016654005.1_ASM1665400v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbbdd46fe-6610-4b15-b80b-92f3acba40ef/dqc_reference/reference_markers.hmm GCF_016654005.1_ASM1665400v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:06:01,315] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:06:01,317] [INFO] Found 6/6 markers.
[2024-01-24 11:06:01,348] [INFO] Query marker FASTA was written to GCF_016654005.1_ASM1665400v1_genomic.fna/markers.fasta
[2024-01-24 11:06:01,348] [INFO] Task started: Blastn
[2024-01-24 11:06:01,348] [INFO] Running command: blastn -query GCF_016654005.1_ASM1665400v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbbdd46fe-6610-4b15-b80b-92f3acba40ef/dqc_reference/reference_markers.fasta -out GCF_016654005.1_ASM1665400v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:02,106] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:02,109] [INFO] Selected 16 target genomes.
[2024-01-24 11:06:02,109] [INFO] Target genome list was writen to GCF_016654005.1_ASM1665400v1_genomic.fna/target_genomes.txt
[2024-01-24 11:06:02,113] [INFO] Task started: fastANI
[2024-01-24 11:06:02,113] [INFO] Running command: fastANI --query /var/lib/cwl/stg41f44705-208d-41a4-9a38-720e12cd7994/GCF_016654005.1_ASM1665400v1_genomic.fna.gz --refList GCF_016654005.1_ASM1665400v1_genomic.fna/target_genomes.txt --output GCF_016654005.1_ASM1665400v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:13,678] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:13,678] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbbdd46fe-6610-4b15-b80b-92f3acba40ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:13,678] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbbdd46fe-6610-4b15-b80b-92f3acba40ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:13,691] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:06:13,691] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:06:13,691] [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 nasdae	strain=JCM 11415	GCA_016654005.1	172043	172043	type	True	100.0	1233	1236	95	conclusive
Brevundimonas huaxiensis	strain=090558	GCA_014218725.1	2725493	2725493	type	True	85.273	742	1236	95	below_threshold
Brevundimonas vesicularis	strain=NBRC 12165	GCA_001592205.1	41276	41276	suspected-type	True	85.1246	747	1236	95	below_threshold
Brevundimonas mediterranea	strain=DSM 14878	GCA_014196125.1	74329	74329	type	True	85.065	769	1236	95	below_threshold
Brevundimonas aurantiaca	strain=DSM 4731	GCA_014199955.1	74316	74316	type	True	84.4802	730	1236	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	84.3512	734	1236	95	below_threshold
Brevundimonas naejangsanensis	strain=DSM 23858	GCA_000421705.1	588932	588932	type	True	82.543	653	1236	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	82.4854	625	1236	95	below_threshold
Brevundimonas vitisensis	strain=GR-TSA-9	GCA_016656965.1	2800818	2800818	type	True	80.3763	522	1236	95	below_threshold
Brevundimonas pishanensis	strain=CHPC 1.3453	GCA_022750635.1	2896315	2896315	type	True	79.4105	411	1236	95	below_threshold
Caulobacter mirabilis	strain=FWC 38	GCA_002749615.1	69666	69666	type	True	78.3917	427	1236	95	below_threshold
Caulobacter rhizosphaerae	strain=CGMCC 1.15915	GCA_014645055.1	2010972	2010972	type	True	78.2104	422	1236	95	below_threshold
Phenylobacterium hankyongense	strain=HKS-05	GCA_003254505.1	1813876	1813876	type	True	77.6226	339	1236	95	below_threshold
Phreatobacter oligotrophus	strain=DSM 25521	GCA_003046185.1	1122261	1122261	type	True	76.3938	145	1236	95	below_threshold
Jannaschia formosa	strain=12N15	GCA_003340555.1	2259592	2259592	type	True	75.6922	122	1236	95	below_threshold
Rubellimicrobium aerolatum	strain=DSM 19297	GCA_017872975.1	490979	490979	type	True	75.3928	116	1236	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:13,693] [INFO] DFAST Taxonomy check result was written to GCF_016654005.1_ASM1665400v1_genomic.fna/tc_result.tsv
[2024-01-24 11:06:13,694] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:13,694] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:13,694] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbbdd46fe-6610-4b15-b80b-92f3acba40ef/dqc_reference/checkm_data
[2024-01-24 11:06:13,695] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:13,730] [INFO] Task started: CheckM
[2024-01-24 11:06:13,730] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016654005.1_ASM1665400v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016654005.1_ASM1665400v1_genomic.fna/checkm_input GCF_016654005.1_ASM1665400v1_genomic.fna/checkm_result
[2024-01-24 11:06:45,186] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:45,187] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:45,204] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:45,205] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:45,205] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016654005.1_ASM1665400v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:45,205] [INFO] Task started: Blastn
[2024-01-24 11:06:45,205] [INFO] Running command: blastn -query GCF_016654005.1_ASM1665400v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbbdd46fe-6610-4b15-b80b-92f3acba40ef/dqc_reference/reference_markers_gtdb.fasta -out GCF_016654005.1_ASM1665400v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:46,529] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:46,533] [INFO] Selected 17 target genomes.
[2024-01-24 11:06:46,533] [INFO] Target genome list was writen to GCF_016654005.1_ASM1665400v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:46,543] [INFO] Task started: fastANI
[2024-01-24 11:06:46,543] [INFO] Running command: fastANI --query /var/lib/cwl/stg41f44705-208d-41a4-9a38-720e12cd7994/GCF_016654005.1_ASM1665400v1_genomic.fna.gz --refList GCF_016654005.1_ASM1665400v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016654005.1_ASM1665400v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:59,192] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:59,205] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:06:59,206] [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_016654005.1	s__Brevundimonas nasdae	100.0	1233	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018608325.1	s__Brevundimonas sp018608325	91.6393	890	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002157625.1	s__Brevundimonas sp002157625	85.9542	768	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002434505.1	s__Brevundimonas sp002434505	85.9412	780	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.71	99.71	0.98	0.98	2	-
GCF_004614235.1	s__Brevundimonas intermedia	85.6772	760	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002484265.1	s__Brevundimonas sp002484265	85.6043	780	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.51	99.05	0.94	0.88	3	-
GCA_003248965.1	s__Brevundimonas sp003248965	85.5204	742	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	95.48	95.48	0.80	0.80	2	-
GCF_005484585.1	s__Brevundimonas sp005484585	85.5062	726	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	95.32	95.32	0.86	0.86	2	-
GCF_902506205.1	s__Brevundimonas sp902506205	85.4906	775	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000813765.1	s__Brevundimonas nasdae_A	85.234	733	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	95.42	95.42	0.82	0.82	2	-
GCF_014204545.1	s__Brevundimonas vesicularis_B	85.2207	742	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011064825.1	s__Brevundimonas mediterranea_A	85.2181	774	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0657	98.11	97.23	0.89	0.83	17	-
GCA_013912065.1	s__Brevundimonas sp013912065	84.6837	737	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001796045.1	s__Brevundimonas sp001796045	83.889	570	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013823285.1	s__Brevundimonas sp013823285	80.1427	458	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002749615.1	s__Caulobacter mirabilis	78.3691	430	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241335.1	s__Palsa-881 sp018241335	77.7006	307	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Palsa-881	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:06:59,207] [INFO] GTDB search result was written to GCF_016654005.1_ASM1665400v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:59,208] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:59,211] [INFO] DFAST_QC result json was written to GCF_016654005.1_ASM1665400v1_genomic.fna/dqc_result.json
[2024-01-24 11:06:59,211] [INFO] DFAST_QC completed!
[2024-01-24 11:06:59,211] [INFO] Total running time: 0h1m10s