[2023-07-01 02:28:31,210] [INFO] DFAST_QC pipeline started.
[2023-07-01 02:28:31,213] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 02:28:31,213] [INFO] DQC Reference Directory: /var/lib/cwl/stgbc8ab9c2-d696-456d-9bc3-a05f7d57e223/dqc_reference
[2023-07-01 02:28:32,475] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 02:28:32,476] [INFO] Task started: Prodigal
[2023-07-01 02:28:32,476] [INFO] Running command: gunzip -c /var/lib/cwl/stg10612212-ef55-45c8-a141-c1c9f25da4a6/GCA_025359665.1_ASM2535966v1_genomic.fna.gz | prodigal -d GCA_025359665.1_ASM2535966v1_genomic.fna/cds.fna -a GCA_025359665.1_ASM2535966v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 02:28:43,318] [INFO] Task succeeded: Prodigal
[2023-07-01 02:28:43,318] [INFO] Task started: HMMsearch
[2023-07-01 02:28:43,318] [INFO] Running command: hmmsearch --tblout GCA_025359665.1_ASM2535966v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbc8ab9c2-d696-456d-9bc3-a05f7d57e223/dqc_reference/reference_markers.hmm GCA_025359665.1_ASM2535966v1_genomic.fna/protein.faa > /dev/null
[2023-07-01 02:28:43,646] [INFO] Task succeeded: HMMsearch
[2023-07-01 02:28:43,647] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg10612212-ef55-45c8-a141-c1c9f25da4a6/GCA_025359665.1_ASM2535966v1_genomic.fna.gz]
[2023-07-01 02:28:43,694] [INFO] Query marker FASTA was written to GCA_025359665.1_ASM2535966v1_genomic.fna/markers.fasta
[2023-07-01 02:28:43,695] [INFO] Task started: Blastn
[2023-07-01 02:28:43,695] [INFO] Running command: blastn -query GCA_025359665.1_ASM2535966v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc8ab9c2-d696-456d-9bc3-a05f7d57e223/dqc_reference/reference_markers.fasta -out GCA_025359665.1_ASM2535966v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 02:28:44,516] [INFO] Task succeeded: Blastn
[2023-07-01 02:28:44,560] [INFO] Selected 22 target genomes.
[2023-07-01 02:28:44,561] [INFO] Target genome list was writen to GCA_025359665.1_ASM2535966v1_genomic.fna/target_genomes.txt
[2023-07-01 02:28:44,564] [INFO] Task started: fastANI
[2023-07-01 02:28:44,564] [INFO] Running command: fastANI --query /var/lib/cwl/stg10612212-ef55-45c8-a141-c1c9f25da4a6/GCA_025359665.1_ASM2535966v1_genomic.fna.gz --refList GCA_025359665.1_ASM2535966v1_genomic.fna/target_genomes.txt --output GCA_025359665.1_ASM2535966v1_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 02:29:00,783] [INFO] Task succeeded: fastANI
[2023-07-01 02:29:00,784] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbc8ab9c2-d696-456d-9bc3-a05f7d57e223/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 02:29:00,784] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbc8ab9c2-d696-456d-9bc3-a05f7d57e223/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 02:29:00,802] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 02:29:00,803] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-07-01 02:29:00,803] [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	77.7067	287	1151	95	below_threshold
Phenylobacterium glaciei	strain=20VBR1	GCA_016772415.2	2803784	2803784	type	True	77.6033	255	1151	95	below_threshold
Phenylobacterium soli	strain=LX32	GCA_003254475.1	2170551	2170551	type	True	77.2894	272	1151	95	below_threshold
Caulobacter flavus	strain=RHGG3	GCA_003722335.1	1679497	1679497	type	True	77.2829	261	1151	95	below_threshold
Phenylobacterium deserti	strain=YIM 73061	GCA_003254705.1	1914756	1914756	type	True	77.2699	180	1151	95	below_threshold
Caulobacter flavus	strain=CGMCC1 15093	GCA_002858845.1	1679497	1679497	type	True	77.2356	261	1151	95	below_threshold
Caulobacter henricii	strain=CB4	GCA_001414055.1	69395	69395	type	True	77.2122	206	1151	95	below_threshold
Phenylobacterium zucineum	strain=HLK1	GCA_000017265.1	284016	284016	type	True	77.1929	266	1151	95	below_threshold
Caulobacter rhizosphaerae	strain=KCTC 52515	GCA_010977555.1	2010972	2010972	type	True	77.1815	274	1151	95	below_threshold
Caulobacter endophyticus	strain=774	GCA_003116815.1	2172652	2172652	type	True	77.1766	265	1151	95	below_threshold
Caulobacter rhizosphaerae	strain=CGMCC 1.15915	GCA_014645055.1	2010972	2010972	type	True	77.1599	272	1151	95	below_threshold
Phenylobacterium kunshanense	strain=BUT-10	GCA_003254525.1	1445034	1445034	type	True	77.1579	240	1151	95	below_threshold
Brevundimonas basaltis	strain=DSM 25335	GCA_014202075.1	472166	472166	type	True	77.1012	147	1151	95	below_threshold
Phenylobacterium haematophilum	strain=DSM 21793	GCA_014196295.1	98513	98513	type	True	77.0	260	1151	95	below_threshold
Brevundimonas fluminis	strain=LA-55	GCA_003934285.1	2487274	2487274	type	True	76.728	145	1151	95	below_threshold
Paracoccus binzhouensis	strain=wg1	GCA_016446475.1	2796149	2796149	type	True	76.0085	105	1151	95	below_threshold
Methylorubrum rhodesianum	strain=DSM 5687	GCA_014199985.1	29427	29427	type	True	75.9403	108	1151	95	below_threshold
Sphingomonas gilva	strain=ZDH117	GCA_003515075.1	2305907	2305907	type	True	75.7111	91	1151	95	below_threshold
Rhizorhabdus histidinilytica	strain=UM2	GCA_900167915.1	439228	439228	type	True	75.5532	117	1151	95	below_threshold
Methylosinus sporium	strain=DSM 17706	GCA_009811675.1	428	428	type	True	75.4669	67	1151	95	below_threshold
Jannaschia formosa	strain=12N15	GCA_003340555.1	2259592	2259592	type	True	75.4555	77	1151	95	below_threshold
Methylosinus sporium	strain=DSM 17706	GCA_003113265.1	428	428	type	True	75.3333	61	1151	95	below_threshold
--------------------------------------------------------------------------------
[2023-07-01 02:29:00,805] [INFO] DFAST Taxonomy check result was written to GCA_025359665.1_ASM2535966v1_genomic.fna/tc_result.tsv
[2023-07-01 02:29:00,806] [INFO] ===== Taxonomy check completed =====
[2023-07-01 02:29:00,806] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 02:29:00,806] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbc8ab9c2-d696-456d-9bc3-a05f7d57e223/dqc_reference/checkm_data
[2023-07-01 02:29:00,807] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 02:29:00,855] [INFO] Task started: CheckM
[2023-07-01 02:29:00,855] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_025359665.1_ASM2535966v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_025359665.1_ASM2535966v1_genomic.fna/checkm_input GCA_025359665.1_ASM2535966v1_genomic.fna/checkm_result
[2023-07-01 02:29:36,743] [INFO] Task succeeded: CheckM
[2023-07-01 02:29:36,744] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.61%
Contamintation: 6.25%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-07-01 02:29:36,770] [INFO] ===== Completeness check finished =====
[2023-07-01 02:29:36,770] [INFO] ===== Start GTDB Search =====
[2023-07-01 02:29:36,771] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_025359665.1_ASM2535966v1_genomic.fna/markers.fasta)
[2023-07-01 02:29:36,771] [INFO] Task started: Blastn
[2023-07-01 02:29:36,771] [INFO] Running command: blastn -query GCA_025359665.1_ASM2535966v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc8ab9c2-d696-456d-9bc3-a05f7d57e223/dqc_reference/reference_markers_gtdb.fasta -out GCA_025359665.1_ASM2535966v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 02:29:38,138] [INFO] Task succeeded: Blastn
[2023-07-01 02:29:38,143] [INFO] Selected 19 target genomes.
[2023-07-01 02:29:38,143] [INFO] Target genome list was writen to GCA_025359665.1_ASM2535966v1_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 02:29:38,151] [INFO] Task started: fastANI
[2023-07-01 02:29:38,151] [INFO] Running command: fastANI --query /var/lib/cwl/stg10612212-ef55-45c8-a141-c1c9f25da4a6/GCA_025359665.1_ASM2535966v1_genomic.fna.gz --refList GCA_025359665.1_ASM2535966v1_genomic.fna/target_genomes_gtdb.txt --output GCA_025359665.1_ASM2535966v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 02:29:51,547] [INFO] Task succeeded: fastANI
[2023-07-01 02:29:51,566] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-07-01 02:29:51,566] [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_903923135.1	s__Palsa-881 sp903923135	79.8792	551	1151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Palsa-881	95.0	99.95	99.94	0.96	0.95	3	-
GCA_903870555.1	s__Palsa-881 sp903870555	79.4836	432	1151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Palsa-881	95.0	99.20	99.20	0.85	0.85	2	-
GCA_903872075.1	s__Palsa-881 sp903872075	79.3895	527	1151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Palsa-881	95.0	99.76	99.48	0.94	0.93	7	-
GCA_018241335.1	s__Palsa-881 sp018241335	78.048	342	1151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Palsa-881	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254505.1	s__Phenylobacterium hankyongense	77.7455	285	1151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017418605.1	s__CAISGS01 sp017418605	77.7398	290	1151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__CAISGS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016125585.1	s__Caulobacter sp016125585	77.6495	268	1151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240795.1	s__Phenylobacterium sp018240795	77.4623	237	1151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001429025.1	s__Phenylobacterium sp001429025	77.4521	278	1151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.02	99.02	0.94	0.94	2	-
GCA_003165275.1	s__BOG-935 sp003165275	77.4347	274	1151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__BOG-935	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004799515.1	s__Phenylobacterium sp004799515	77.3914	284	1151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017991675.1	s__Phenylobacterium sp017991675	77.351	193	1151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000712075.1	s__Caulobacter sp000712075	77.1974	306	1151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000017265.1	s__Phenylobacterium zucineum	77.1925	266	1151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.11	99.11	0.98	0.98	2	-
GCA_018820275.1	s__Brevundimonas sp018820275	76.7155	138	1151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.93	99.85	0.97	0.95	5	-
GCA_018820665.1	s__Brevundimonas sp018820665	76.4507	140	1151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.88	99.88	0.93	0.93	2	-
GCF_016446475.1	s__Paracoccus binzhouensis	76.0243	104	1151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000518925.1	s__Paracoccus sp000518925	75.7823	108	1151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.13	98.71	0.90	0.89	3	-
GCA_011046725.1	s__DSPG01 sp011046725	75.3951	81	1151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__DSPG01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-07-01 02:29:51,569] [INFO] GTDB search result was written to GCA_025359665.1_ASM2535966v1_genomic.fna/result_gtdb.tsv
[2023-07-01 02:29:51,569] [INFO] ===== GTDB Search completed =====
[2023-07-01 02:29:51,578] [INFO] DFAST_QC result json was written to GCA_025359665.1_ASM2535966v1_genomic.fna/dqc_result.json
[2023-07-01 02:29:51,578] [INFO] DFAST_QC completed!
[2023-07-01 02:29:51,578] [INFO] Total running time: 0h1m20s