[2024-01-24 14:22:02,019] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:02,021] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:02,021] [INFO] DQC Reference Directory: /var/lib/cwl/stg6e44f0a6-ad1e-4573-8158-d89ca9b2230c/dqc_reference
[2024-01-24 14:22:03,182] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:03,183] [INFO] Task started: Prodigal
[2024-01-24 14:22:03,183] [INFO] Running command: gunzip -c /var/lib/cwl/stgf8ffa689-25f3-4052-807e-6737ad9ded1e/GCF_001270065.2_ASM127006v2_genomic.fna.gz | prodigal -d GCF_001270065.2_ASM127006v2_genomic.fna/cds.fna -a GCF_001270065.2_ASM127006v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:30,497] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:30,498] [INFO] Task started: HMMsearch
[2024-01-24 14:22:30,498] [INFO] Running command: hmmsearch --tblout GCF_001270065.2_ASM127006v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6e44f0a6-ad1e-4573-8158-d89ca9b2230c/dqc_reference/reference_markers.hmm GCF_001270065.2_ASM127006v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:30,795] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:30,796] [INFO] Found 6/6 markers.
[2024-01-24 14:22:30,843] [INFO] Query marker FASTA was written to GCF_001270065.2_ASM127006v2_genomic.fna/markers.fasta
[2024-01-24 14:22:30,843] [INFO] Task started: Blastn
[2024-01-24 14:22:30,843] [INFO] Running command: blastn -query GCF_001270065.2_ASM127006v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e44f0a6-ad1e-4573-8158-d89ca9b2230c/dqc_reference/reference_markers.fasta -out GCF_001270065.2_ASM127006v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:31,702] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:31,707] [INFO] Selected 20 target genomes.
[2024-01-24 14:22:31,707] [INFO] Target genome list was writen to GCF_001270065.2_ASM127006v2_genomic.fna/target_genomes.txt
[2024-01-24 14:22:31,714] [INFO] Task started: fastANI
[2024-01-24 14:22:31,715] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8ffa689-25f3-4052-807e-6737ad9ded1e/GCF_001270065.2_ASM127006v2_genomic.fna.gz --refList GCF_001270065.2_ASM127006v2_genomic.fna/target_genomes.txt --output GCF_001270065.2_ASM127006v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:49,226] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:49,226] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6e44f0a6-ad1e-4573-8158-d89ca9b2230c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:49,226] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6e44f0a6-ad1e-4573-8158-d89ca9b2230c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:49,241] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:22:49,242] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:22:49,242] [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
Limnohabitans planktonicus	strain=II-D5	GCA_001270065.2	540060	540060	type	True	100.0	1560	1562	95	conclusive
Limnohabitans parvus	strain=II-B4	GCA_003063455.1	540061	540061	type	True	84.6166	714	1562	95	below_threshold
Limnohabitans radicicola	strain=JUR4	GCA_014837235.1	2771427	2771427	type	True	83.2209	675	1562	95	below_threshold
Limnohabitans curvus	strain=MWH-C5	GCA_003063475.1	323423	323423	type	True	79.3133	354	1562	95	below_threshold
Acidovorax temperans	strain=DSM 7270	GCA_006716905.1	80878	80878	type	True	78.9686	446	1562	95	below_threshold
Acidovorax carolinensis	strain=NA3	GCA_002157145.1	553814	553814	type	True	78.8862	451	1562	95	below_threshold
Rhodoferax lacus	strain=IMCC26218	GCA_003415675.1	2184758	2184758	type	True	78.8005	413	1562	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	78.6593	427	1562	95	below_threshold
Comamonas phosphati	strain=CGMCC 1.12294	GCA_014637085.1	1211803	1211803	type	True	78.5777	374	1562	95	below_threshold
Comamonas terrigena	strain=NCTC1937	GCA_900461435.1	32013	32013	type	True	78.5221	370	1562	95	below_threshold
Hydrogenophaga borbori	strain=LA-38	GCA_003417535.1	2294117	2294117	type	True	78.5067	394	1562	95	below_threshold
Comamonas koreensis	strain=KCTC 12005	GCA_021026195.1	160825	160825	type	True	78.0801	345	1562	95	below_threshold
Melaminivora jejuensis	strain=KCTC 32230	GCA_017811175.1	1267217	1267217	type	True	78.0312	348	1562	95	below_threshold
Simplicispira psychrophila	strain=DSM 11588	GCA_000688255.1	80882	80882	type	True	77.9874	321	1562	95	below_threshold
Diaphorobacter caeni	strain=NR2-3-3-1	GCA_015354245.1	2784387	2784387	type	True	77.8877	356	1562	95	below_threshold
Brachymonas chironomi	strain=DSM 19884	GCA_000374625.1	491919	491919	type	True	77.8757	230	1562	95	below_threshold
Rhodoferax aquaticus	strain=Gr-4	GCA_006974105.1	2527691	2527691	type	True	77.8482	254	1562	95	below_threshold
Extensimonas perlucida	strain=HX2-24	GCA_007655255.1	2590786	2590786	type	True	77.7966	324	1562	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	77.7561	304	1562	95	below_threshold
Rhodoferax ferrireducens	strain=DSM 15236	GCA_000013605.1	192843	192843	type	True	77.6672	323	1562	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:49,244] [INFO] DFAST Taxonomy check result was written to GCF_001270065.2_ASM127006v2_genomic.fna/tc_result.tsv
[2024-01-24 14:22:49,244] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:49,244] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:49,245] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6e44f0a6-ad1e-4573-8158-d89ca9b2230c/dqc_reference/checkm_data
[2024-01-24 14:22:49,246] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:49,291] [INFO] Task started: CheckM
[2024-01-24 14:22:49,292] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001270065.2_ASM127006v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001270065.2_ASM127006v2_genomic.fna/checkm_input GCF_001270065.2_ASM127006v2_genomic.fna/checkm_result
[2024-01-24 14:24:19,748] [INFO] Task succeeded: CheckM
[2024-01-24 14:24:19,749] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:24:19,764] [INFO] ===== Completeness check finished =====
[2024-01-24 14:24:19,764] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:24:19,765] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001270065.2_ASM127006v2_genomic.fna/markers.fasta)
[2024-01-24 14:24:19,765] [INFO] Task started: Blastn
[2024-01-24 14:24:19,765] [INFO] Running command: blastn -query GCF_001270065.2_ASM127006v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e44f0a6-ad1e-4573-8158-d89ca9b2230c/dqc_reference/reference_markers_gtdb.fasta -out GCF_001270065.2_ASM127006v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:24:21,314] [INFO] Task succeeded: Blastn
[2024-01-24 14:24:21,318] [INFO] Selected 17 target genomes.
[2024-01-24 14:24:21,318] [INFO] Target genome list was writen to GCF_001270065.2_ASM127006v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:24:21,340] [INFO] Task started: fastANI
[2024-01-24 14:24:21,341] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8ffa689-25f3-4052-807e-6737ad9ded1e/GCF_001270065.2_ASM127006v2_genomic.fna.gz --refList GCF_001270065.2_ASM127006v2_genomic.fna/target_genomes_gtdb.txt --output GCF_001270065.2_ASM127006v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:24:38,967] [INFO] Task succeeded: fastANI
[2024-01-24 14:24:38,980] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:24:38,980] [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_001270065.2	s__Limnohabitans_A planktonicus	100.0	1560	1562	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001269385.1	s__Limnohabitans_A sp001269385	91.0494	1191	1562	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017848645.1	s__Limnohabitans_A sp017848645	86.4789	816	1562	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	97.74	96.96	0.88	0.84	5	-
GCF_003063315.1	s__Limnohabitans_A sp003063315	86.4451	981	1562	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903894995.1	s__Limnohabitans_A sp903894995	85.5046	637	1562	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	99.22	99.21	0.83	0.82	3	-
GCF_003063665.1	s__Limnohabitans_A sp003063665	85.1813	725	1562	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	96.02	95.55	0.82	0.79	4	-
GCF_003063435.1	s__Limnohabitans_A sp003063435	84.8448	789	1562	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003063575.1	s__Limnohabitans_A sp003063575	84.8445	764	1562	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003063355.1	s__Limnohabitans_A sp003063355	84.8322	745	1562	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001269345.1	s__Limnohabitans_A sp001269345	84.8163	736	1562	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003063455.1	s__Limnohabitans_A parvus	84.6511	711	1562	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003063335.1	s__Limnohabitans_A sp003063335	84.4728	731	1562	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	99.88	99.88	0.96	0.96	2	-
GCF_003063505.1	s__Limnohabitans_A sp003063505	84.3138	779	1562	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002778285.1	s__Limnohabitans_A sp002778285	84.2766	735	1562	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017986605.1	s__Limnohabitans_A sp017986605	84.1158	513	1562	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002255935.1	s__Limnohabitans_A sp002255935	83.8107	672	1562	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014837235.1	s__Limnohabitans_A sp014837235	83.214	676	1562	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:24:38,981] [INFO] GTDB search result was written to GCF_001270065.2_ASM127006v2_genomic.fna/result_gtdb.tsv
[2024-01-24 14:24:38,982] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:24:38,986] [INFO] DFAST_QC result json was written to GCF_001270065.2_ASM127006v2_genomic.fna/dqc_result.json
[2024-01-24 14:24:38,986] [INFO] DFAST_QC completed!
[2024-01-24 14:24:38,986] [INFO] Total running time: 0h2m37s