[2023-06-18 12:49:16,812] [INFO] DFAST_QC pipeline started.
[2023-06-18 12:49:16,814] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 12:49:16,814] [INFO] DQC Reference Directory: /var/lib/cwl/stg55ff9eb6-16c8-49ee-a81c-2c23dea433e8/dqc_reference
[2023-06-18 12:49:18,597] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 12:49:18,598] [INFO] Task started: Prodigal
[2023-06-18 12:49:18,598] [INFO] Running command: gunzip -c /var/lib/cwl/stgd3eca06a-a83e-45c9-bf28-a9888ec5fd55/GCA_018780225.1_ASM1878022v1_genomic.fna.gz | prodigal -d GCA_018780225.1_ASM1878022v1_genomic.fna/cds.fna -a GCA_018780225.1_ASM1878022v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 12:49:31,373] [INFO] Task succeeded: Prodigal
[2023-06-18 12:49:31,374] [INFO] Task started: HMMsearch
[2023-06-18 12:49:31,374] [INFO] Running command: hmmsearch --tblout GCA_018780225.1_ASM1878022v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg55ff9eb6-16c8-49ee-a81c-2c23dea433e8/dqc_reference/reference_markers.hmm GCA_018780225.1_ASM1878022v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 12:49:31,703] [INFO] Task succeeded: HMMsearch
[2023-06-18 12:49:31,704] [INFO] Found 6/6 markers.
[2023-06-18 12:49:31,749] [INFO] Query marker FASTA was written to GCA_018780225.1_ASM1878022v1_genomic.fna/markers.fasta
[2023-06-18 12:49:31,750] [INFO] Task started: Blastn
[2023-06-18 12:49:31,750] [INFO] Running command: blastn -query GCA_018780225.1_ASM1878022v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg55ff9eb6-16c8-49ee-a81c-2c23dea433e8/dqc_reference/reference_markers.fasta -out GCA_018780225.1_ASM1878022v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 12:49:32,903] [INFO] Task succeeded: Blastn
[2023-06-18 12:49:32,908] [INFO] Selected 16 target genomes.
[2023-06-18 12:49:32,908] [INFO] Target genome list was writen to GCA_018780225.1_ASM1878022v1_genomic.fna/target_genomes.txt
[2023-06-18 12:49:32,916] [INFO] Task started: fastANI
[2023-06-18 12:49:32,916] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3eca06a-a83e-45c9-bf28-a9888ec5fd55/GCA_018780225.1_ASM1878022v1_genomic.fna.gz --refList GCA_018780225.1_ASM1878022v1_genomic.fna/target_genomes.txt --output GCA_018780225.1_ASM1878022v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 12:49:49,735] [INFO] Task succeeded: fastANI
[2023-06-18 12:49:49,736] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg55ff9eb6-16c8-49ee-a81c-2c23dea433e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 12:49:49,736] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg55ff9eb6-16c8-49ee-a81c-2c23dea433e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 12:49:49,749] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 12:49:49,749] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 12:49:49,750] [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 haematophilum	strain=DSM 21793	GCA_014196295.1	98513	98513	type	True	84.0662	990	1597	95	below_threshold
Phenylobacterium glaciei	strain=20VBR1	GCA_016772415.2	2803784	2803784	type	True	82.123	770	1597	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	81.7379	833	1597	95	below_threshold
Phenylobacterium hankyongense	strain=HKS-05	GCA_003254505.1	1813876	1813876	type	True	81.5473	692	1597	95	below_threshold
Phenylobacterium soli	strain=LX32	GCA_003254475.1	2170551	2170551	type	True	80.5166	674	1597	95	below_threshold
Phenylobacterium zucineum	strain=HLK1	GCA_000017265.1	284016	284016	type	True	80.2866	702	1597	95	below_threshold
Phenylobacterium kunshanense	strain=BUT-10	GCA_003254525.1	1445034	1445034	type	True	79.7809	631	1597	95	below_threshold
Caulobacter zeae	strain=410	GCA_002858925.1	2055137	2055137	type	True	79.7083	681	1597	95	below_threshold
Caulobacter flavus	strain=CGMCC1 15093	GCA_002858845.1	1679497	1679497	type	True	79.5784	701	1597	95	below_threshold
Caulobacter soli	strain=Ji-3-8	GCA_011045195.1	2708539	2708539	type	True	79.5447	675	1597	95	below_threshold
Caulobacter rhizosphaerae	strain=CGMCC 1.15915	GCA_014645055.1	2010972	2010972	type	True	79.4344	679	1597	95	below_threshold
Caulobacter mirabilis	strain=FWC 38	GCA_002749615.1	69666	69666	type	True	79.4218	679	1597	95	below_threshold
Caulobacter vibrioides	strain=DSM 9893	GCA_002858865.1	155892	155892	type	True	79.294	570	1597	95	below_threshold
Caulobacter henricii	strain=CB4	GCA_001414055.1	69395	69395	type	True	78.8624	520	1597	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	78.187	355	1597	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	78.1666	407	1597	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 12:49:49,752] [INFO] DFAST Taxonomy check result was written to GCA_018780225.1_ASM1878022v1_genomic.fna/tc_result.tsv
[2023-06-18 12:49:49,753] [INFO] ===== Taxonomy check completed =====
[2023-06-18 12:49:49,753] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 12:49:49,753] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg55ff9eb6-16c8-49ee-a81c-2c23dea433e8/dqc_reference/checkm_data
[2023-06-18 12:49:49,754] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 12:49:49,808] [INFO] Task started: CheckM
[2023-06-18 12:49:49,808] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018780225.1_ASM1878022v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018780225.1_ASM1878022v1_genomic.fna/checkm_input GCA_018780225.1_ASM1878022v1_genomic.fna/checkm_result
[2023-06-18 12:50:30,274] [INFO] Task succeeded: CheckM
[2023-06-18 12:50:30,276] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 12:50:30,307] [INFO] ===== Completeness check finished =====
[2023-06-18 12:50:30,307] [INFO] ===== Start GTDB Search =====
[2023-06-18 12:50:30,308] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018780225.1_ASM1878022v1_genomic.fna/markers.fasta)
[2023-06-18 12:50:30,308] [INFO] Task started: Blastn
[2023-06-18 12:50:30,308] [INFO] Running command: blastn -query GCA_018780225.1_ASM1878022v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg55ff9eb6-16c8-49ee-a81c-2c23dea433e8/dqc_reference/reference_markers_gtdb.fasta -out GCA_018780225.1_ASM1878022v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 12:50:32,136] [INFO] Task succeeded: Blastn
[2023-06-18 12:50:32,142] [INFO] Selected 8 target genomes.
[2023-06-18 12:50:32,142] [INFO] Target genome list was writen to GCA_018780225.1_ASM1878022v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 12:50:32,170] [INFO] Task started: fastANI
[2023-06-18 12:50:32,171] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3eca06a-a83e-45c9-bf28-a9888ec5fd55/GCA_018780225.1_ASM1878022v1_genomic.fna.gz --refList GCA_018780225.1_ASM1878022v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018780225.1_ASM1878022v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 12:50:40,891] [INFO] Task succeeded: fastANI
[2023-06-18 12:50:40,901] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 12:50:40,901] [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_001429025.1	s__Phenylobacterium sp001429025	99.0236	1416	1597	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.02	99.02	0.94	0.94	2	conclusive
GCA_018240795.1	s__Phenylobacterium sp018240795	84.5888	858	1597	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425305.1	s__Phenylobacterium sp001425305	84.4769	979	1597	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.99	99.99	1.00	1.00	3	-
GCA_017991675.1	s__Phenylobacterium sp017991675	84.4181	694	1597	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013822795.1	s__Phenylobacterium sp013822795	84.3202	985	1597	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196295.1	s__Phenylobacterium haematophilum	84.04	994	1597	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016772415.1	s__Phenylobacterium sp016772415	82.0671	776	1597	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	79.707	710	1597	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 12:50:40,905] [INFO] GTDB search result was written to GCA_018780225.1_ASM1878022v1_genomic.fna/result_gtdb.tsv
[2023-06-18 12:50:40,906] [INFO] ===== GTDB Search completed =====
[2023-06-18 12:50:40,913] [INFO] DFAST_QC result json was written to GCA_018780225.1_ASM1878022v1_genomic.fna/dqc_result.json
[2023-06-18 12:50:40,913] [INFO] DFAST_QC completed!
[2023-06-18 12:50:40,913] [INFO] Total running time: 0h1m24s