[2023-06-28 21:14:08,111] [INFO] DFAST_QC pipeline started.
[2023-06-28 21:14:08,114] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 21:14:08,114] [INFO] DQC Reference Directory: /var/lib/cwl/stg0ae76faf-ab6a-4792-8413-065b44b4d38b/dqc_reference
[2023-06-28 21:14:09,584] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 21:14:09,585] [INFO] Task started: Prodigal
[2023-06-28 21:14:09,585] [INFO] Running command: gunzip -c /var/lib/cwl/stg5061cc6e-e28f-4b25-985e-de6538a50eff/GCA_017304475.1_ASM1730447v1_genomic.fna.gz | prodigal -d GCA_017304475.1_ASM1730447v1_genomic.fna/cds.fna -a GCA_017304475.1_ASM1730447v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 21:14:33,363] [INFO] Task succeeded: Prodigal
[2023-06-28 21:14:33,363] [INFO] Task started: HMMsearch
[2023-06-28 21:14:33,363] [INFO] Running command: hmmsearch --tblout GCA_017304475.1_ASM1730447v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0ae76faf-ab6a-4792-8413-065b44b4d38b/dqc_reference/reference_markers.hmm GCA_017304475.1_ASM1730447v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 21:14:33,719] [INFO] Task succeeded: HMMsearch
[2023-06-28 21:14:33,720] [INFO] Found 6/6 markers.
[2023-06-28 21:14:33,786] [INFO] Query marker FASTA was written to GCA_017304475.1_ASM1730447v1_genomic.fna/markers.fasta
[2023-06-28 21:14:33,787] [INFO] Task started: Blastn
[2023-06-28 21:14:33,787] [INFO] Running command: blastn -query GCA_017304475.1_ASM1730447v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ae76faf-ab6a-4792-8413-065b44b4d38b/dqc_reference/reference_markers.fasta -out GCA_017304475.1_ASM1730447v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 21:14:34,883] [INFO] Task succeeded: Blastn
[2023-06-28 21:14:34,888] [INFO] Selected 20 target genomes.
[2023-06-28 21:14:34,888] [INFO] Target genome list was writen to GCA_017304475.1_ASM1730447v1_genomic.fna/target_genomes.txt
[2023-06-28 21:14:34,893] [INFO] Task started: fastANI
[2023-06-28 21:14:34,893] [INFO] Running command: fastANI --query /var/lib/cwl/stg5061cc6e-e28f-4b25-985e-de6538a50eff/GCA_017304475.1_ASM1730447v1_genomic.fna.gz --refList GCA_017304475.1_ASM1730447v1_genomic.fna/target_genomes.txt --output GCA_017304475.1_ASM1730447v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 21:14:58,715] [INFO] Task succeeded: fastANI
[2023-06-28 21:14:58,716] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0ae76faf-ab6a-4792-8413-065b44b4d38b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 21:14:58,716] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0ae76faf-ab6a-4792-8413-065b44b4d38b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 21:14:58,736] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 21:14:58,737] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 21:14:58,737] [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
Phreatobacter stygius	strain=KCTC 52518	GCA_005144885.1	1940610	1940610	type	True	87.4894	1978	2753	95	below_threshold
Phreatobacter oligotrophus	strain=DSM 25521	GCA_003046185.1	1122261	1122261	type	True	81.2274	1004	2753	95	below_threshold
Phreatobacter cathodiphilus	strain=S-12	GCA_003008515.1	1868589	1868589	type	True	81.1203	1036	2753	95	below_threshold
Ancylobacter dichloromethanicus	strain=VKM B-2484	GCA_018390645.1	518825	518825	type	True	77.5866	551	2753	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	77.5619	573	2753	95	below_threshold
Ancylobacter rudongensis	strain=CGMCC 1.1761	GCA_900100155.1	177413	177413	type	True	77.4803	521	2753	95	below_threshold
Chelatococcus caeni	strain=DSM 103737	GCA_014196925.1	1348468	1348468	type	True	77.3597	617	2753	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	77.3593	664	2753	95	below_threshold
Chelatococcus composti	strain=DSM 101465	GCA_018398355.1	1743235	1743235	type	True	77.2762	412	2753	95	below_threshold
Microvirga ossetica	strain=V5/3M	GCA_002741015.1	1882682	1882682	type	True	77.2537	470	2753	95	below_threshold
Bradyrhizobium quebecense	strain=66S1MB, /ecotype=symbiovar septentrionalis	GCA_013373795.3	2748629	2748629	type	True	77.2387	659	2753	95	below_threshold
Microvirga arabica	strain=SV2184P	GCA_016811235.1	1128671	1128671	type	True	77.2005	376	2753	95	below_threshold
Methylobacterium frigidaeris	strain=JCM 32048	GCA_022179185.1	2038277	2038277	type	True	77.1983	671	2753	95	below_threshold
Methylobrevis pamukkalensis	strain=PK2	GCA_001720135.1	1439726	1439726	type	True	77.0332	462	2753	95	below_threshold
Methylobacterium dankookense	strain=DSM 22415	GCA_022179165.1	560405	560405	type	True	76.9384	518	2753	95	below_threshold
Microvirga pudoricolor	strain=BT291	GCA_016892705.1	2778729	2778729	type	True	76.9379	325	2753	95	below_threshold
Methylobacterium bullatum	strain=DSM 21893	GCA_022179105.1	570505	570505	type	True	76.8886	386	2753	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	76.7413	649	2753	95	below_threshold
Methylobacterium adhaesivum	strain=DSM 17169	GCA_022179065.1	333297	333297	type	True	76.6326	356	2753	95	below_threshold
Methylobacterium goesingense	strain=DSM 21331	GCA_022179225.1	243690	243690	type	True	76.6232	392	2753	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 21:14:58,739] [INFO] DFAST Taxonomy check result was written to GCA_017304475.1_ASM1730447v1_genomic.fna/tc_result.tsv
[2023-06-28 21:14:58,739] [INFO] ===== Taxonomy check completed =====
[2023-06-28 21:14:58,739] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 21:14:58,739] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0ae76faf-ab6a-4792-8413-065b44b4d38b/dqc_reference/checkm_data
[2023-06-28 21:14:58,740] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 21:14:58,820] [INFO] Task started: CheckM
[2023-06-28 21:14:58,820] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017304475.1_ASM1730447v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017304475.1_ASM1730447v1_genomic.fna/checkm_input GCA_017304475.1_ASM1730447v1_genomic.fna/checkm_result
[2023-06-28 21:16:18,814] [INFO] Task succeeded: CheckM
[2023-06-28 21:16:18,816] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 21:16:18,839] [INFO] ===== Completeness check finished =====
[2023-06-28 21:16:18,839] [INFO] ===== Start GTDB Search =====
[2023-06-28 21:16:18,840] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017304475.1_ASM1730447v1_genomic.fna/markers.fasta)
[2023-06-28 21:16:18,840] [INFO] Task started: Blastn
[2023-06-28 21:16:18,840] [INFO] Running command: blastn -query GCA_017304475.1_ASM1730447v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ae76faf-ab6a-4792-8413-065b44b4d38b/dqc_reference/reference_markers_gtdb.fasta -out GCA_017304475.1_ASM1730447v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 21:16:20,981] [INFO] Task succeeded: Blastn
[2023-06-28 21:16:20,986] [INFO] Selected 8 target genomes.
[2023-06-28 21:16:20,987] [INFO] Target genome list was writen to GCA_017304475.1_ASM1730447v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 21:16:20,993] [INFO] Task started: fastANI
[2023-06-28 21:16:20,993] [INFO] Running command: fastANI --query /var/lib/cwl/stg5061cc6e-e28f-4b25-985e-de6538a50eff/GCA_017304475.1_ASM1730447v1_genomic.fna.gz --refList GCA_017304475.1_ASM1730447v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017304475.1_ASM1730447v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 21:16:35,086] [INFO] Task succeeded: fastANI
[2023-06-28 21:16:35,094] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 21:16:35,095] [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_017304475.1	s__Phreatobacter sp017304475	100.0	2749	2753	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_005144885.1	s__Phreatobacter stygius	87.4932	1977	2753	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000751295.2	s__Phreatobacter sp000751295	83.9117	1645	2753	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005160265.1	s__Phreatobacter sp005160265	81.6153	1116	2753	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793595.1	s__Phreatobacter sp016793595	81.2603	1095	2753	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003046185.1	s__Phreatobacter oligotrophus	81.1696	1011	2753	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003008515.1	s__Phreatobacter cathodiphilus	81.0971	1040	2753	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464235.1	s__Phreatobacter sp001464235	81.0106	847	2753	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 21:16:35,097] [INFO] GTDB search result was written to GCA_017304475.1_ASM1730447v1_genomic.fna/result_gtdb.tsv
[2023-06-28 21:16:35,097] [INFO] ===== GTDB Search completed =====
[2023-06-28 21:16:35,102] [INFO] DFAST_QC result json was written to GCA_017304475.1_ASM1730447v1_genomic.fna/dqc_result.json
[2023-06-28 21:16:35,102] [INFO] DFAST_QC completed!
[2023-06-28 21:16:35,102] [INFO] Total running time: 0h2m27s