[2024-01-24 13:31:35,293] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:35,300] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:35,301] [INFO] DQC Reference Directory: /var/lib/cwl/stg5274bc40-5425-459c-b8e6-c5b57f4e5280/dqc_reference
[2024-01-24 13:31:36,660] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:36,661] [INFO] Task started: Prodigal
[2024-01-24 13:31:36,661] [INFO] Running command: gunzip -c /var/lib/cwl/stgfca53f61-f417-4d99-8a2a-c63224cb110f/GCF_004458765.1_ASM445876v1_genomic.fna.gz | prodigal -d GCF_004458765.1_ASM445876v1_genomic.fna/cds.fna -a GCF_004458765.1_ASM445876v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:53,456] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:53,457] [INFO] Task started: HMMsearch
[2024-01-24 13:31:53,457] [INFO] Running command: hmmsearch --tblout GCF_004458765.1_ASM445876v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5274bc40-5425-459c-b8e6-c5b57f4e5280/dqc_reference/reference_markers.hmm GCF_004458765.1_ASM445876v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:53,862] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:53,864] [INFO] Found 6/6 markers.
[2024-01-24 13:31:53,921] [INFO] Query marker FASTA was written to GCF_004458765.1_ASM445876v1_genomic.fna/markers.fasta
[2024-01-24 13:31:53,922] [INFO] Task started: Blastn
[2024-01-24 13:31:53,922] [INFO] Running command: blastn -query GCF_004458765.1_ASM445876v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5274bc40-5425-459c-b8e6-c5b57f4e5280/dqc_reference/reference_markers.fasta -out GCF_004458765.1_ASM445876v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:54,978] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:54,982] [INFO] Selected 16 target genomes.
[2024-01-24 13:31:54,982] [INFO] Target genome list was writen to GCF_004458765.1_ASM445876v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:55,005] [INFO] Task started: fastANI
[2024-01-24 13:31:55,006] [INFO] Running command: fastANI --query /var/lib/cwl/stgfca53f61-f417-4d99-8a2a-c63224cb110f/GCF_004458765.1_ASM445876v1_genomic.fna.gz --refList GCF_004458765.1_ASM445876v1_genomic.fna/target_genomes.txt --output GCF_004458765.1_ASM445876v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:15,561] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:15,562] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5274bc40-5425-459c-b8e6-c5b57f4e5280/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:15,562] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5274bc40-5425-459c-b8e6-c5b57f4e5280/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:15,575] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:15,576] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:15,576] [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
Microvirga pakistanensis	strain=NCCP-1258	GCA_004458765.1	1682650	1682650	type	True	100.0	1830	1834	95	conclusive
Microvirga makkahensis	strain=KCTC 23863	GCA_009830105.1	1128670	1128670	type	True	86.1413	1120	1834	95	below_threshold
Microvirga vignae	strain=BR3299	GCA_001017175.1	1225564	1225564	type	True	84.0889	1038	1834	95	below_threshold
Microvirga guangxiensis	strain=CGMCC 1.7666	GCA_900102135.1	549386	549386	type	True	83.9443	941	1834	95	below_threshold
Microvirga flocculans	strain=ATCC BAA-817	GCA_000518665.1	217168	217168	type	True	83.2699	804	1834	95	below_threshold
Microvirga splendida	strain=BT325	GCA_016427565.1	2795727	2795727	type	True	83.0205	900	1834	95	below_threshold
Microvirga arabica	strain=SV2184P	GCA_016811235.1	1128671	1128671	type	True	82.9201	979	1834	95	below_threshold
Microvirga mediterraneensis	strain=Marseille-Q2068	GCA_013520865.1	2754695	2754695	type	True	82.8961	888	1834	95	below_threshold
Microvirga lotononidis	strain=WSM3557	GCA_000262405.1	864069	864069	type	True	82.6113	941	1834	95	below_threshold
Microvirga zambiensis	strain=WSM3693	GCA_016735695.1	1402137	1402137	type	True	82.4627	928	1834	95	below_threshold
Microvirga roseola	strain=SM2	GCA_020866965.1	2883126	2883126	type	True	82.3538	841	1834	95	below_threshold
Microvirga subterranea	strain=DSM 14364	GCA_003350535.1	186651	186651	type	True	82.0233	829	1834	95	below_threshold
Microvirga lenta	strain=SM9	GCA_020532555.1	2881337	2881337	type	True	82.0161	814	1834	95	below_threshold
Microvirga rosea	strain=CGMCC1.16488	GCA_020595095.1	2715425	2715425	type	True	79.9364	612	1834	95	below_threshold
Salinarimonas soli	strain=BN140002	GCA_008386575.1	1638099	1638099	type	True	78.9032	537	1834	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	78.0752	462	1834	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:15,577] [INFO] DFAST Taxonomy check result was written to GCF_004458765.1_ASM445876v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:15,578] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:15,578] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:15,578] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5274bc40-5425-459c-b8e6-c5b57f4e5280/dqc_reference/checkm_data
[2024-01-24 13:32:15,579] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:15,634] [INFO] Task started: CheckM
[2024-01-24 13:32:15,635] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004458765.1_ASM445876v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004458765.1_ASM445876v1_genomic.fna/checkm_input GCF_004458765.1_ASM445876v1_genomic.fna/checkm_result
[2024-01-24 13:33:10,042] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:10,071] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:10,098] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:10,098] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:10,099] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004458765.1_ASM445876v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:10,099] [INFO] Task started: Blastn
[2024-01-24 13:33:10,099] [INFO] Running command: blastn -query GCF_004458765.1_ASM445876v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5274bc40-5425-459c-b8e6-c5b57f4e5280/dqc_reference/reference_markers_gtdb.fasta -out GCF_004458765.1_ASM445876v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:12,268] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:12,271] [INFO] Selected 13 target genomes.
[2024-01-24 13:33:12,271] [INFO] Target genome list was writen to GCF_004458765.1_ASM445876v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:12,296] [INFO] Task started: fastANI
[2024-01-24 13:33:12,296] [INFO] Running command: fastANI --query /var/lib/cwl/stgfca53f61-f417-4d99-8a2a-c63224cb110f/GCF_004458765.1_ASM445876v1_genomic.fna.gz --refList GCF_004458765.1_ASM445876v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004458765.1_ASM445876v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:30,887] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:30,904] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:30,904] [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_004458765.1	s__Microvirga pakistanensis	100.0	1830	1834	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009830105.1	s__Microvirga makkahensis	86.1276	1121	1834	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003075415.1	s__Microvirga sp003075415	84.2334	1016	1834	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001017175.1	s__Microvirga vignae	84.0625	1041	1834	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102135.1	s__Microvirga guangxiensis	83.959	940	1834	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000518665.1	s__Microvirga flocculans	83.27	804	1834	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	100.00	100.00	0.99	0.99	2	-
GCF_009910705.1	s__Microvirga sp009910705	83.2276	902	1834	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016811235.1	s__Microvirga arabica	82.9186	979	1834	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013520865.1	s__Microvirga mediterraneensis	82.9174	885	1834	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000262405.1	s__Microvirga lotononidis	82.6153	940	1834	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002741015.1	s__Microvirga ossetica	82.5643	962	1834	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003347665.1	s__Microvirga calopogonii	82.5612	934	1834	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018069605.1	s__Microvirga sp018069605	82.4641	890	1834	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:30,906] [INFO] GTDB search result was written to GCF_004458765.1_ASM445876v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:30,906] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:30,910] [INFO] DFAST_QC result json was written to GCF_004458765.1_ASM445876v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:30,910] [INFO] DFAST_QC completed!
[2024-01-24 13:33:30,910] [INFO] Total running time: 0h1m56s