[2023-06-27 14:07:57,026] [INFO] DFAST_QC pipeline started.
[2023-06-27 14:07:57,031] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 14:07:57,032] [INFO] DQC Reference Directory: /var/lib/cwl/stgacf0adc9-c92d-4156-ad6f-7e7b122d3c43/dqc_reference
[2023-06-27 14:07:58,275] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 14:07:58,276] [INFO] Task started: Prodigal
[2023-06-27 14:07:58,276] [INFO] Running command: gunzip -c /var/lib/cwl/stg4ee60287-2a09-4488-ab24-af41a914a051/GCA_026225565.1_ASM2622556v1_genomic.fna.gz | prodigal -d GCA_026225565.1_ASM2622556v1_genomic.fna/cds.fna -a GCA_026225565.1_ASM2622556v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 14:08:07,514] [INFO] Task succeeded: Prodigal
[2023-06-27 14:08:07,515] [INFO] Task started: HMMsearch
[2023-06-27 14:08:07,515] [INFO] Running command: hmmsearch --tblout GCA_026225565.1_ASM2622556v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgacf0adc9-c92d-4156-ad6f-7e7b122d3c43/dqc_reference/reference_markers.hmm GCA_026225565.1_ASM2622556v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 14:08:07,727] [INFO] Task succeeded: HMMsearch
[2023-06-27 14:08:07,728] [INFO] Found 6/6 markers.
[2023-06-27 14:08:07,761] [INFO] Query marker FASTA was written to GCA_026225565.1_ASM2622556v1_genomic.fna/markers.fasta
[2023-06-27 14:08:07,761] [INFO] Task started: Blastn
[2023-06-27 14:08:07,761] [INFO] Running command: blastn -query GCA_026225565.1_ASM2622556v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgacf0adc9-c92d-4156-ad6f-7e7b122d3c43/dqc_reference/reference_markers.fasta -out GCA_026225565.1_ASM2622556v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 14:08:08,548] [INFO] Task succeeded: Blastn
[2023-06-27 14:08:08,552] [INFO] Selected 26 target genomes.
[2023-06-27 14:08:08,553] [INFO] Target genome list was writen to GCA_026225565.1_ASM2622556v1_genomic.fna/target_genomes.txt
[2023-06-27 14:08:08,554] [INFO] Task started: fastANI
[2023-06-27 14:08:08,554] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ee60287-2a09-4488-ab24-af41a914a051/GCA_026225565.1_ASM2622556v1_genomic.fna.gz --refList GCA_026225565.1_ASM2622556v1_genomic.fna/target_genomes.txt --output GCA_026225565.1_ASM2622556v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 14:08:29,147] [INFO] Task succeeded: fastANI
[2023-06-27 14:08:29,148] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgacf0adc9-c92d-4156-ad6f-7e7b122d3c43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 14:08:29,148] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgacf0adc9-c92d-4156-ad6f-7e7b122d3c43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 14:08:29,167] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 14:08:29,167] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 14:08:29,167] [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
Phenylobacterium hankyongense	strain=HKS-05	GCA_003254505.1	1813876	1813876	type	True	78.0644	360	1108	95	below_threshold
Caulobacter rhizosphaerae	strain=CGMCC 1.15915	GCA_014645055.1	2010972	2010972	type	True	77.8843	372	1108	95	below_threshold
Phenylobacterium glaciei	strain=20VBR1	GCA_016772415.2	2803784	2803784	type	True	77.8825	320	1108	95	below_threshold
Caulobacter rhizosphaerae	strain=KCTC 52515	GCA_010977555.1	2010972	2010972	type	True	77.8764	374	1108	95	below_threshold
Caulobacter mirabilis	strain=FWC 38	GCA_002749615.1	69666	69666	type	True	77.7402	322	1108	95	below_threshold
Caulobacter radicis	strain=695	GCA_003094615.1	2172650	2172650	type	True	77.7383	369	1108	95	below_threshold
Caulobacter hibisci	strain=KACC 18849	GCA_016135805.1	2035993	2035993	type	True	77.7293	378	1108	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	77.7157	374	1108	95	below_threshold
Phenylobacterium soli	strain=LX32	GCA_003254475.1	2170551	2170551	type	True	77.6868	309	1108	95	below_threshold
Phenylobacterium zucineum	strain=HLK1	GCA_000017265.1	284016	284016	type	True	77.6644	316	1108	95	below_threshold
Caulobacter flavus	strain=RHGG3	GCA_003722335.1	1679497	1679497	type	True	77.6327	362	1108	95	below_threshold
Caulobacter zeae	strain=410	GCA_002858925.1	2055137	2055137	type	True	77.5688	364	1108	95	below_threshold
Caulobacter flavus	strain=CGMCC1 15093	GCA_002858845.1	1679497	1679497	type	True	77.5624	367	1108	95	below_threshold
Caulobacter vibrioides	strain=DSM 9893	GCA_002858865.1	155892	155892	type	True	77.5276	316	1108	95	below_threshold
Phenylobacterium kunshanense	strain=BUT-10	GCA_003254525.1	1445034	1445034	type	True	77.5096	277	1108	95	below_threshold
Caulobacter segnis	strain=ATCC 21756	GCA_000092285.1	88688	88688	type	True	77.4996	317	1108	95	below_threshold
Caulobacter segnis	strain=TK0059	GCA_003015125.1	88688	88688	type	True	77.4901	318	1108	95	below_threshold
Phenylobacterium haematophilum	strain=DSM 21793	GCA_014196295.1	98513	98513	type	True	77.361	287	1108	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	77.3189	267	1108	95	below_threshold
Phenylobacterium deserti	strain=YIM 73061	GCA_003254705.1	1914756	1914756	type	True	77.2685	268	1108	95	below_threshold
Brevundimonas vitisensis	strain=GR-TSA-9	GCA_016656965.1	2800818	2800818	type	True	76.8527	177	1108	95	below_threshold
Microvirga lenta	strain=SM9	GCA_020532555.1	2881337	2881337	type	True	76.1208	95	1108	95	below_threshold
Roseomonas coralli	strain=M0104	GCA_009829925.1	2545983	2545983	type	True	75.8176	138	1108	95	below_threshold
Chelatococcus asaccharovorans	strain=DSM 6462	GCA_003201475.1	28210	28210	type	True	75.8015	94	1108	95	below_threshold
Rhodobacter flagellatus	strain=SYSU G03088	GCA_008271465.1	2593021	2593021	type	True	75.7094	76	1108	95	below_threshold
Albimonas pacifica	strain=CGMCC 1.11030	GCA_900113695.1	1114924	1114924	type	True	75.6087	185	1108	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 14:08:29,169] [INFO] DFAST Taxonomy check result was written to GCA_026225565.1_ASM2622556v1_genomic.fna/tc_result.tsv
[2023-06-27 14:08:29,170] [INFO] ===== Taxonomy check completed =====
[2023-06-27 14:08:29,170] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 14:08:29,170] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgacf0adc9-c92d-4156-ad6f-7e7b122d3c43/dqc_reference/checkm_data
[2023-06-27 14:08:29,172] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 14:08:29,210] [INFO] Task started: CheckM
[2023-06-27 14:08:29,210] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026225565.1_ASM2622556v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026225565.1_ASM2622556v1_genomic.fna/checkm_input GCA_026225565.1_ASM2622556v1_genomic.fna/checkm_result
[2023-06-27 14:08:58,812] [INFO] Task succeeded: CheckM
[2023-06-27 14:08:58,813] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 96.46%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 14:08:58,834] [INFO] ===== Completeness check finished =====
[2023-06-27 14:08:58,834] [INFO] ===== Start GTDB Search =====
[2023-06-27 14:08:58,835] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026225565.1_ASM2622556v1_genomic.fna/markers.fasta)
[2023-06-27 14:08:58,835] [INFO] Task started: Blastn
[2023-06-27 14:08:58,835] [INFO] Running command: blastn -query GCA_026225565.1_ASM2622556v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgacf0adc9-c92d-4156-ad6f-7e7b122d3c43/dqc_reference/reference_markers_gtdb.fasta -out GCA_026225565.1_ASM2622556v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 14:09:00,283] [INFO] Task succeeded: Blastn
[2023-06-27 14:09:00,288] [INFO] Selected 28 target genomes.
[2023-06-27 14:09:00,288] [INFO] Target genome list was writen to GCA_026225565.1_ASM2622556v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 14:09:00,310] [INFO] Task started: fastANI
[2023-06-27 14:09:00,310] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ee60287-2a09-4488-ab24-af41a914a051/GCA_026225565.1_ASM2622556v1_genomic.fna.gz --refList GCA_026225565.1_ASM2622556v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026225565.1_ASM2622556v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 14:09:20,542] [INFO] Task succeeded: fastANI
[2023-06-27 14:09:20,563] [INFO] Found 28 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 14:09:20,564] [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_903837135.1	s__CAIOYC01 sp903837135	78.7489	450	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__CAIOYC01	95.0	99.97	99.97	0.97	0.97	3	-
GCA_903862425.1	s__CAIOYC01 sp903862425	78.5817	407	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__CAIOYC01	95.0	99.98	99.98	0.99	0.99	2	-
GCA_002280485.1	s__NCED01 sp002280485	78.4859	295	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__NCED01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017418605.1	s__CAISGS01 sp017418605	78.304	368	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__CAISGS01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765965.1	s__CAHJWH01 sp009765965	78.2917	393	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__CAHJWH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018135625.1	s__BOG-935 sp018135625	78.1833	400	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__BOG-935	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016467375.1	s__Caulobacter sp016467375	78.1148	268	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254505.1	s__Phenylobacterium hankyongense	78.078	358	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903851655.1	s__CAIMFV01 sp903851655	77.9908	310	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__CAIMFV01	95.0	99.52	99.51	0.87	0.86	3	-
GCA_903884425.1	s__CAIMFV01 sp903884425	77.9502	314	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__CAIMFV01	95.0	99.90	99.80	0.98	0.97	6	-
GCA_003165275.1	s__BOG-935 sp003165275	77.9099	342	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__BOG-935	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016772415.1	s__Phenylobacterium sp016772415	77.9046	318	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_903642205.1	s__CAHJWH01 sp903642205	77.8498	294	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__CAHJWH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010975005.1	s__17J80-11 sp010975005	77.8348	297	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__17J80-11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004799515.1	s__Phenylobacterium sp004799515	77.8257	341	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001449105.1	s__Caulobacter vibrioides_C	77.757	362	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016135805.1	s__Caulobacter hibisci	77.7292	378	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254475.1	s__Phenylobacterium soli	77.7084	307	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002742635.1	s__Caulobacter sp002742635	77.7005	342	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013911965.1	s__Phenylobacterium sp013911965	77.6852	339	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	98.20	98.20	0.93	0.93	2	-
GCF_002749615.1	s__Caulobacter mirabilis	77.6812	328	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017307205.1	s__Caulobacter sp001896875	77.6514	224	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	99.25	99.25	0.75	0.75	2	-
GCA_003136395.1	s__Phenylobacterium sp003136395	77.6447	296	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016234625.1	s__Caulobacter sp016234625	77.6157	275	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004799395.1	s__Phenylobacterium sp004799395	77.5057	275	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002002865.1	s__Brevundimonas sp002002865	77.4212	211	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903822175.1	s__Phenylobacterium sp903822175	77.4026	301	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.88	99.77	0.95	0.93	4	-
GCA_016793225.1	s__Phenylobacterium sp016793225	77.0594	251	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 14:09:20,566] [INFO] GTDB search result was written to GCA_026225565.1_ASM2622556v1_genomic.fna/result_gtdb.tsv
[2023-06-27 14:09:20,567] [INFO] ===== GTDB Search completed =====
[2023-06-27 14:09:20,572] [INFO] DFAST_QC result json was written to GCA_026225565.1_ASM2622556v1_genomic.fna/dqc_result.json
[2023-06-27 14:09:20,573] [INFO] DFAST_QC completed!
[2023-06-27 14:09:20,573] [INFO] Total running time: 0h1m24s