[2023-06-28 12:03:15,661] [INFO] DFAST_QC pipeline started.
[2023-06-28 12:03:15,663] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 12:03:15,663] [INFO] DQC Reference Directory: /var/lib/cwl/stg7f158603-30db-4642-b331-73339b4954a7/dqc_reference
[2023-06-28 12:03:16,766] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 12:03:16,767] [INFO] Task started: Prodigal
[2023-06-28 12:03:16,767] [INFO] Running command: gunzip -c /var/lib/cwl/stg4b51d6a9-6697-4a2e-9686-268ac408b761/GCA_020253085.1_ASM2025308v1_genomic.fna.gz | prodigal -d GCA_020253085.1_ASM2025308v1_genomic.fna/cds.fna -a GCA_020253085.1_ASM2025308v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 12:03:25,519] [INFO] Task succeeded: Prodigal
[2023-06-28 12:03:25,519] [INFO] Task started: HMMsearch
[2023-06-28 12:03:25,519] [INFO] Running command: hmmsearch --tblout GCA_020253085.1_ASM2025308v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7f158603-30db-4642-b331-73339b4954a7/dqc_reference/reference_markers.hmm GCA_020253085.1_ASM2025308v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 12:03:25,723] [INFO] Task succeeded: HMMsearch
[2023-06-28 12:03:25,724] [INFO] Found 6/6 markers.
[2023-06-28 12:03:25,750] [INFO] Query marker FASTA was written to GCA_020253085.1_ASM2025308v1_genomic.fna/markers.fasta
[2023-06-28 12:03:25,750] [INFO] Task started: Blastn
[2023-06-28 12:03:25,750] [INFO] Running command: blastn -query GCA_020253085.1_ASM2025308v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f158603-30db-4642-b331-73339b4954a7/dqc_reference/reference_markers.fasta -out GCA_020253085.1_ASM2025308v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:03:26,620] [INFO] Task succeeded: Blastn
[2023-06-28 12:03:26,624] [INFO] Selected 31 target genomes.
[2023-06-28 12:03:26,624] [INFO] Target genome list was writen to GCA_020253085.1_ASM2025308v1_genomic.fna/target_genomes.txt
[2023-06-28 12:03:26,629] [INFO] Task started: fastANI
[2023-06-28 12:03:26,629] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b51d6a9-6697-4a2e-9686-268ac408b761/GCA_020253085.1_ASM2025308v1_genomic.fna.gz --refList GCA_020253085.1_ASM2025308v1_genomic.fna/target_genomes.txt --output GCA_020253085.1_ASM2025308v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 12:03:55,472] [INFO] Task succeeded: fastANI
[2023-06-28 12:03:55,473] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7f158603-30db-4642-b331-73339b4954a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 12:03:55,474] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7f158603-30db-4642-b331-73339b4954a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 12:03:55,491] [INFO] Found 31 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 12:03:55,491] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 12:03:55,491] [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
Rhabdaerophilum calidifontis	strain=SYSU G02060	GCA_008641065.1	2604328	2604328	type	True	79.6622	509	1048	95	below_threshold
Bosea robiniae	strain=DSM 26672	GCA_900102525.1	1036780	1036780	type	True	77.7004	336	1048	95	below_threshold
Bosea psychrotolerans	strain=1131	GCA_002917105.1	1871628	1871628	type	True	77.6724	323	1048	95	below_threshold
Chelatococcus caeni	strain=DSM 103737	GCA_014196925.1	1348468	1348468	type	True	77.6225	290	1048	95	below_threshold
Phreatobacter cathodiphilus	strain=S-12	GCA_003008515.1	1868589	1868589	type	True	77.6008	269	1048	95	below_threshold
Microvirga roseola	strain=SM2	GCA_020866965.1	2883126	2883126	type	True	77.5448	234	1048	95	below_threshold
Ancylobacter rudongensis	strain=CGMCC 1.1761	GCA_900100155.1	177413	177413	type	True	77.5036	217	1048	95	below_threshold
Chelatococcus sambhunathii	strain=DSM 18167	GCA_001418005.1	363953	363953	type	True	77.476	252	1048	95	below_threshold
Chelatococcus sambhunathii	strain=DSM 18167	GCA_001517345.1	363953	363953	type	True	77.4633	253	1048	95	below_threshold
Phreatobacter oligotrophus	strain=DSM 25521	GCA_003046185.1	1122261	1122261	type	True	77.4427	311	1048	95	below_threshold
Bosea caraganae	strain=RCAM 04680	GCA_003351345.1	2763117	2763117	type	True	77.4336	336	1048	95	below_threshold
Bosea vaviloviae	strain=Vaf18	GCA_001741865.1	1526658	1526658	type	True	77.4323	352	1048	95	below_threshold
Candidatus Rhodoblastus alkanivorans		GCA_022760755.1	2954117	2954117	type	True	77.2536	142	1048	95	below_threshold
Ancylobacter sonchi	strain=VKM B-3145	GCA_018390695.1	1937790	1937790	type	True	77.1793	245	1048	95	below_threshold
Methylorubrum extorquens	strain=TK 0001	GCA_900234795.1	408	408	type	True	77.1772	226	1048	95	below_threshold
Ancylobacter aquaticus	strain=DSM 101	GCA_004339465.1	100	100	type	True	77.1577	219	1048	95	below_threshold
Chelatococcus composti	strain=DSM 101465	GCA_018398355.1	1743235	1743235	type	True	77.1118	237	1048	95	below_threshold
Chelatococcus composti	strain=CGMCC 1.15283	GCA_014641535.1	1743235	1743235	type	True	77.0695	240	1048	95	below_threshold
Alsobacter metallidurans	strain=CGMCC 1.12214	GCA_014636935.1	340221	340221	type	True	77.0532	247	1048	95	below_threshold
Chelatococcus composti	strain=DSM 101465	GCA_014201415.1	1743235	1743235	type	True	77.0369	239	1048	95	below_threshold
Salinarimonas ramus	strain=CGMCC 1.9161	GCA_014645695.1	690164	690164	type	True	77.0285	277	1048	95	below_threshold
Salinarimonas rosea	strain=DSM 21201	GCA_000429045.1	552063	552063	type	True	76.9492	234	1048	95	below_threshold
Bradyrhizobium altum	strain=Pear77	GCA_020889705.1	1571202	1571202	type	True	76.9463	213	1048	95	below_threshold
Mesorhizobium caraganae	strain=LMG 24397	GCA_016836705.1	483206	483206	type	True	76.9412	175	1048	95	below_threshold
Mesorhizobium neociceri	strain=CCANP35	GCA_013520985.1	1307853	1307853	type	True	76.9269	179	1048	95	below_threshold
Bradyrhizobium centrolobii	strain=BR 10245	GCA_001641635.1	1505087	1505087	type	True	76.9231	215	1048	95	below_threshold
Bradyrhizobium hipponense	strain=aSej3	GCA_008123965.1	2605638	2605638	type	True	76.8849	186	1048	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_023278185.1	29448	29448	type	True	76.8287	235	1048	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	76.6964	214	1048	95	below_threshold
Bradyrhizobium aeschynomenes	strain=83002	GCA_013178945.1	2734909	2734909	type	True	76.6418	228	1048	95	below_threshold
Paracoccus acridae	strain=CGMCC 1.15419	GCA_014642735.1	1795310	1795310	type	True	75.8438	96	1048	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 12:03:55,493] [INFO] DFAST Taxonomy check result was written to GCA_020253085.1_ASM2025308v1_genomic.fna/tc_result.tsv
[2023-06-28 12:03:55,493] [INFO] ===== Taxonomy check completed =====
[2023-06-28 12:03:55,493] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 12:03:55,494] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7f158603-30db-4642-b331-73339b4954a7/dqc_reference/checkm_data
[2023-06-28 12:03:55,494] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 12:03:55,528] [INFO] Task started: CheckM
[2023-06-28 12:03:55,528] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020253085.1_ASM2025308v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020253085.1_ASM2025308v1_genomic.fna/checkm_input GCA_020253085.1_ASM2025308v1_genomic.fna/checkm_result
[2023-06-28 12:04:33,515] [INFO] Task succeeded: CheckM
[2023-06-28 12:04:33,516] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 12:04:33,538] [INFO] ===== Completeness check finished =====
[2023-06-28 12:04:33,538] [INFO] ===== Start GTDB Search =====
[2023-06-28 12:04:33,539] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020253085.1_ASM2025308v1_genomic.fna/markers.fasta)
[2023-06-28 12:04:33,540] [INFO] Task started: Blastn
[2023-06-28 12:04:33,540] [INFO] Running command: blastn -query GCA_020253085.1_ASM2025308v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f158603-30db-4642-b331-73339b4954a7/dqc_reference/reference_markers_gtdb.fasta -out GCA_020253085.1_ASM2025308v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:04:35,229] [INFO] Task succeeded: Blastn
[2023-06-28 12:04:35,232] [INFO] Selected 17 target genomes.
[2023-06-28 12:04:35,232] [INFO] Target genome list was writen to GCA_020253085.1_ASM2025308v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 12:04:35,241] [INFO] Task started: fastANI
[2023-06-28 12:04:35,241] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b51d6a9-6697-4a2e-9686-268ac408b761/GCA_020253085.1_ASM2025308v1_genomic.fna.gz --refList GCA_020253085.1_ASM2025308v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020253085.1_ASM2025308v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 12:04:49,354] [INFO] Task succeeded: fastANI
[2023-06-28 12:04:49,364] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 12:04:49,364] [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_002928875.1	s__Rhabdaerophilum sp002928875	85.7995	741	1048	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Rhabdaerophilum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302635.1	s__Rhabdaerophilum sp017302635	80.5264	599	1048	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Rhabdaerophilum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008641065.1	s__Rhabdaerophilum calidifontis	79.6669	509	1048	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Rhabdaerophilum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009773635.1	s__Rhabdaerophilum sp009773635	78.8626	464	1048	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Rhabdaerophilum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009846685.1	s__Rhabdaerophilum sp009846685	78.7291	441	1048	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Rhabdaerophilum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002256205.1	s__Rhabdaerophilum sp002256205	78.6013	452	1048	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Rhabdaerophilum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196925.1	s__Chelatococcus_A caeni	77.6333	289	1048	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Chelatococcus_A	95.0	98.75	98.72	0.96	0.95	3	-
GCF_018390695.1	s__Ancylobacter_B sonchi	77.1775	245	1048	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900234795.1	s__Methylobacterium extorquens	77.1756	226	1048	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	97.03	96.19	0.88	0.73	17	-
GCF_014636935.1	s__Alsobacter metallidurans	77.0423	248	1048	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Alsobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201415.1	s__Chelatococcus_A composti	77.0281	240	1048	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Chelatococcus_A	95.0	99.84	99.53	0.99	0.98	4	-
GCF_018130615.1	s__Bradyrhizobium manausense_A	76.9767	186	1048	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.96	98.89	0.93	0.91	3	-
GCF_014198245.1	s__Bradyrhizobium sp014198245	76.9688	218	1048	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003201865.1	s__Methylobacterium sp003201865	76.9662	221	1048	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000282615.1	s__Bradyrhizobium sp000282615	76.8954	214	1048	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002531575.1	s__Bradyrhizobium sp002531575	76.7503	228	1048	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000740785.1	s__Paenirhodobacter enshiensis	76.4168	94	1048	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paenirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 12:04:49,366] [INFO] GTDB search result was written to GCA_020253085.1_ASM2025308v1_genomic.fna/result_gtdb.tsv
[2023-06-28 12:04:49,367] [INFO] ===== GTDB Search completed =====
[2023-06-28 12:04:49,371] [INFO] DFAST_QC result json was written to GCA_020253085.1_ASM2025308v1_genomic.fna/dqc_result.json
[2023-06-28 12:04:49,371] [INFO] DFAST_QC completed!
[2023-06-28 12:04:49,371] [INFO] Total running time: 0h1m34s