[2023-06-30 00:02:28,235] [INFO] DFAST_QC pipeline started.
[2023-06-30 00:02:28,244] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 00:02:28,244] [INFO] DQC Reference Directory: /var/lib/cwl/stgb0c61dd6-2f78-46b8-8478-b0cb1337ce45/dqc_reference
[2023-06-30 00:02:30,693] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 00:02:30,695] [INFO] Task started: Prodigal
[2023-06-30 00:02:30,695] [INFO] Running command: gunzip -c /var/lib/cwl/stg2d933ef4-c125-41ee-8634-9cc5fe762f24/GCA_024708805.1_ASM2470880v1_genomic.fna.gz | prodigal -d GCA_024708805.1_ASM2470880v1_genomic.fna/cds.fna -a GCA_024708805.1_ASM2470880v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 00:02:40,445] [INFO] Task succeeded: Prodigal
[2023-06-30 00:02:40,446] [INFO] Task started: HMMsearch
[2023-06-30 00:02:40,446] [INFO] Running command: hmmsearch --tblout GCA_024708805.1_ASM2470880v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb0c61dd6-2f78-46b8-8478-b0cb1337ce45/dqc_reference/reference_markers.hmm GCA_024708805.1_ASM2470880v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 00:02:40,692] [INFO] Task succeeded: HMMsearch
[2023-06-30 00:02:40,694] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2d933ef4-c125-41ee-8634-9cc5fe762f24/GCA_024708805.1_ASM2470880v1_genomic.fna.gz]
[2023-06-30 00:02:40,725] [INFO] Query marker FASTA was written to GCA_024708805.1_ASM2470880v1_genomic.fna/markers.fasta
[2023-06-30 00:02:40,726] [INFO] Task started: Blastn
[2023-06-30 00:02:40,726] [INFO] Running command: blastn -query GCA_024708805.1_ASM2470880v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0c61dd6-2f78-46b8-8478-b0cb1337ce45/dqc_reference/reference_markers.fasta -out GCA_024708805.1_ASM2470880v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 00:02:41,620] [INFO] Task succeeded: Blastn
[2023-06-30 00:02:41,625] [INFO] Selected 26 target genomes.
[2023-06-30 00:02:41,626] [INFO] Target genome list was writen to GCA_024708805.1_ASM2470880v1_genomic.fna/target_genomes.txt
[2023-06-30 00:02:41,627] [INFO] Task started: fastANI
[2023-06-30 00:02:41,628] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d933ef4-c125-41ee-8634-9cc5fe762f24/GCA_024708805.1_ASM2470880v1_genomic.fna.gz --refList GCA_024708805.1_ASM2470880v1_genomic.fna/target_genomes.txt --output GCA_024708805.1_ASM2470880v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 00:03:03,222] [INFO] Task succeeded: fastANI
[2023-06-30 00:03:03,223] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb0c61dd6-2f78-46b8-8478-b0cb1337ce45/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 00:03:03,223] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb0c61dd6-2f78-46b8-8478-b0cb1337ce45/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 00:03:03,244] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 00:03:03,244] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 00:03:03,245] [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
Acidovorax soli	strain=DSM 25157	GCA_900107605.1	592050	592050	type	True	82.8406	564	903	95	below_threshold
Acidovorax kalamii	strain=KNDSW-TSA6	GCA_002245625.1	2004485	2004485	type	True	82.4855	620	903	95	below_threshold
Acidovorax carolinensis	strain=NA3	GCA_002157145.1	553814	553814	type	True	82.2473	585	903	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	82.1285	547	903	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	82.0131	584	903	95	below_threshold
Acidovorax caeni	strain=R-24608	GCA_001298675.1	343013	343013	type	True	81.6639	523	903	95	below_threshold
Acidovorax caeni	strain=R-24608	GCA_900116825.1	343013	343013	type	True	81.6406	515	903	95	below_threshold
Simplicispira metamorpha	strain=DSM 1837	GCA_004341365.1	80881	80881	type	True	81.5721	514	903	95	below_threshold
Simplicispira metamorpha	strain=NBRC 13960	GCA_003568725.1	80881	80881	type	True	81.5303	509	903	95	below_threshold
Acidovorax anthurii	strain=CFPB 3232	GCA_003269065.1	78229	78229	type	True	81.4548	538	903	95	below_threshold
Acidovorax temperans	strain=DSM 7270	GCA_006716905.1	80878	80878	type	True	81.3688	547	903	95	below_threshold
Acidovorax citrulli	strain=DSM 17060	GCA_900100305.1	80869	80869	type	True	81.2941	514	903	95	below_threshold
Simplicispira hankyongi	strain=NY-02	GCA_003570885.1	2315688	2315688	type	True	81.1251	512	903	95	below_threshold
Acidovorax konjaci	strain=DSM 7481	GCA_900112675.1	32040	32040	type	True	80.8876	497	903	95	below_threshold
Melaminivora alkalimesophila	strain=CY1	GCA_000282995.1	1165852	1165852	type	True	80.7715	328	903	95	below_threshold
Melaminivora alkalimesophila	strain=DSM 26006	GCA_003182375.1	1165852	1165852	type	True	80.692	458	903	95	below_threshold
Melaminivora jejuensis	strain=KCTC 32230	GCA_017811175.1	1267217	1267217	type	True	80.6394	482	903	95	below_threshold
Simplicispira suum	strain=SC1-8	GCA_003008595.1	2109915	2109915	type	True	80.5851	513	903	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	80.3498	458	903	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	79.7545	426	903	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	79.5365	375	903	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	79.4374	449	903	95	below_threshold
Diaphorobacter aerolatus	strain=KACC 16536	GCA_014489535.1	1288495	1288495	type	True	79.1643	389	903	95	below_threshold
Comamonas koreensis	strain=KCTC 12005	GCA_021026195.1	160825	160825	type	True	78.8741	387	903	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	78.6136	360	903	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	78.347	338	903	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 00:03:03,247] [INFO] DFAST Taxonomy check result was written to GCA_024708805.1_ASM2470880v1_genomic.fna/tc_result.tsv
[2023-06-30 00:03:03,248] [INFO] ===== Taxonomy check completed =====
[2023-06-30 00:03:03,248] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 00:03:03,248] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb0c61dd6-2f78-46b8-8478-b0cb1337ce45/dqc_reference/checkm_data
[2023-06-30 00:03:03,249] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 00:03:03,283] [INFO] Task started: CheckM
[2023-06-30 00:03:03,283] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024708805.1_ASM2470880v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024708805.1_ASM2470880v1_genomic.fna/checkm_input GCA_024708805.1_ASM2470880v1_genomic.fna/checkm_result
[2023-06-30 00:03:37,642] [INFO] Task succeeded: CheckM
[2023-06-30 00:03:37,644] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.31%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 00:03:37,665] [INFO] ===== Completeness check finished =====
[2023-06-30 00:03:37,666] [INFO] ===== Start GTDB Search =====
[2023-06-30 00:03:37,666] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024708805.1_ASM2470880v1_genomic.fna/markers.fasta)
[2023-06-30 00:03:37,666] [INFO] Task started: Blastn
[2023-06-30 00:03:37,667] [INFO] Running command: blastn -query GCA_024708805.1_ASM2470880v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0c61dd6-2f78-46b8-8478-b0cb1337ce45/dqc_reference/reference_markers_gtdb.fasta -out GCA_024708805.1_ASM2470880v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 00:03:39,307] [INFO] Task succeeded: Blastn
[2023-06-30 00:03:39,313] [INFO] Selected 19 target genomes.
[2023-06-30 00:03:39,313] [INFO] Target genome list was writen to GCA_024708805.1_ASM2470880v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 00:03:39,318] [INFO] Task started: fastANI
[2023-06-30 00:03:39,319] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d933ef4-c125-41ee-8634-9cc5fe762f24/GCA_024708805.1_ASM2470880v1_genomic.fna.gz --refList GCA_024708805.1_ASM2470880v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024708805.1_ASM2470880v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 00:03:56,334] [INFO] Task succeeded: fastANI
[2023-06-30 00:03:56,355] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 00:03:56,355] [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_001770955.1	s__Giesbergeria sp001770955	88.822	712	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	97.11	95.02	0.83	0.80	5	-
GCF_003604195.1	s__Giesbergeria lacusdiani	88.8081	740	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010020825.1	s__Giesbergeria sp010020825	85.3938	651	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	98.40	98.40	0.98	0.98	2	-
GCA_016192425.1	s__Giesbergeria sp016192425	84.6594	599	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000739995.1	s__Giesbergeria granuli	84.6221	620	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	95.66	95.66	0.85	0.85	2	-
GCF_003852545.1	s__Acidovorax sp003852545	82.9872	597	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003096555.1	s__Giesbergeria sp003096555	82.9672	648	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	99.19	98.39	0.95	0.90	3	-
GCF_014489595.1	s__Acidovorax_F monticola	82.709	598	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_F	95.0	97.51	97.51	0.93	0.93	2	-
GCF_012932145.1	s__Giesbergeria sp012932145	82.579	556	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	98.72	98.72	0.89	0.89	2	-
GCF_014207955.1	s__Acidovorax soli_A	82.5242	632	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001725235.1	s__Acidovorax_C sp001725235	82.3509	581	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_C	95.0	98.36	96.90	0.87	0.83	3	-
GCF_000400995.2	s__MR-S7 sp000400995	82.2611	546	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__MR-S7	95.0	97.31	97.31	0.83	0.83	2	-
GCF_001714725.1	s__Acidovorax sp001714725	82.1371	560	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007993815.1	s__Acidovorax delafieldii	82.1032	599	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	97.08	96.33	0.92	0.90	8	-
GCA_018780365.1	s__Acidovorax sp018780365	82.0495	527	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001724785.1	s__Giesbergeria sp001724785	81.82	437	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001298675.1	s__Acidovorax_C caeni	81.6681	522	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_C	95.0	99.98	99.98	0.98	0.98	2	-
GCF_004341365.1	s__Giesbergeria metamorpha	81.5648	515	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	99.27	98.54	0.92	0.85	3	-
GCF_016428875.1	s__Xylophilus sp016428875	80.7173	432	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Xylophilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 00:03:56,357] [INFO] GTDB search result was written to GCA_024708805.1_ASM2470880v1_genomic.fna/result_gtdb.tsv
[2023-06-30 00:03:56,358] [INFO] ===== GTDB Search completed =====
[2023-06-30 00:03:56,362] [INFO] DFAST_QC result json was written to GCA_024708805.1_ASM2470880v1_genomic.fna/dqc_result.json
[2023-06-30 00:03:56,363] [INFO] DFAST_QC completed!
[2023-06-30 00:03:56,363] [INFO] Total running time: 0h1m28s