[2024-01-24 14:21:50,774] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:21:50,776] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:21:50,777] [INFO] DQC Reference Directory: /var/lib/cwl/stgdcb2f3de-527a-44e0-a9a4-80819761de9c/dqc_reference
[2024-01-24 14:21:52,138] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:21:52,139] [INFO] Task started: Prodigal
[2024-01-24 14:21:52,139] [INFO] Running command: gunzip -c /var/lib/cwl/stg62392d97-dfd0-4a7d-835f-616cd364a451/GCF_900141975.1_IMG-taxon_2585427611_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900141975.1_IMG-taxon_2585427611_annotated_assembly_genomic.fna/cds.fna -a GCF_900141975.1_IMG-taxon_2585427611_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:05,565] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:05,565] [INFO] Task started: HMMsearch
[2024-01-24 14:22:05,565] [INFO] Running command: hmmsearch --tblout GCF_900141975.1_IMG-taxon_2585427611_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdcb2f3de-527a-44e0-a9a4-80819761de9c/dqc_reference/reference_markers.hmm GCF_900141975.1_IMG-taxon_2585427611_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:05,867] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:05,868] [INFO] Found 6/6 markers.
[2024-01-24 14:22:05,917] [INFO] Query marker FASTA was written to GCF_900141975.1_IMG-taxon_2585427611_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:22:05,918] [INFO] Task started: Blastn
[2024-01-24 14:22:05,918] [INFO] Running command: blastn -query GCF_900141975.1_IMG-taxon_2585427611_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgdcb2f3de-527a-44e0-a9a4-80819761de9c/dqc_reference/reference_markers.fasta -out GCF_900141975.1_IMG-taxon_2585427611_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:06,998] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:07,001] [INFO] Selected 19 target genomes.
[2024-01-24 14:22:07,002] [INFO] Target genome list was writen to GCF_900141975.1_IMG-taxon_2585427611_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:22:07,010] [INFO] Task started: fastANI
[2024-01-24 14:22:07,010] [INFO] Running command: fastANI --query /var/lib/cwl/stg62392d97-dfd0-4a7d-835f-616cd364a451/GCF_900141975.1_IMG-taxon_2585427611_annotated_assembly_genomic.fna.gz --refList GCF_900141975.1_IMG-taxon_2585427611_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900141975.1_IMG-taxon_2585427611_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:25,029] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:25,030] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdcb2f3de-527a-44e0-a9a4-80819761de9c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:25,030] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdcb2f3de-527a-44e0-a9a4-80819761de9c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:25,045] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:22:25,045] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:22:25,045] [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
Aureimonas altamirensis	strain=DSM 21988	GCA_900141975.1	370622	370622	type	True	100.0	1391	1391	95	conclusive
Aureimonas altamirensis	strain=DSM 21988	GCA_001463885.1	370622	370622	type	True	99.9893	1378	1391	95	conclusive
Aureimonas frigidaquae	strain=JCM 14755	GCA_001463905.1	424757	424757	type	True	80.7021	750	1391	95	below_threshold
Aureimonas populi	strain=KCTC 42087	GCA_017815515.1	1701758	1701758	type	True	79.0274	495	1391	95	below_threshold
Aureimonas ureilytica	strain=NBRC 106430	GCA_001463945.1	401562	401562	type	True	78.9559	475	1391	95	below_threshold
Aurantimonas manganoxydans	strain=SI85-9A1	GCA_000153465.1	651183	651183	type	True	78.6731	431	1391	95	below_threshold
Aurantimonas manganoxydans	strain=DSM 21871	GCA_001463865.1	651183	651183	type	True	78.6662	428	1391	95	below_threshold
Aureimonas mangrovi	strain=LMG 31693	GCA_014058705.1	2758041	2758041	type	True	78.6618	469	1391	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	78.4159	428	1391	95	below_threshold
Shinella daejeonensis	strain=JCM 16236	GCA_024281235.1	659017	659017	type	True	78.3891	276	1391	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	78.092	404	1391	95	below_threshold
Aurantimonas marina	strain=SW136	GCA_017183135.1	2780508	2780508	type	True	77.7914	332	1391	95	below_threshold
Consotaella salsifontis	strain=USBA 369	GCA_900167365.1	1365950	1365950	type	True	77.6619	299	1391	95	below_threshold
Aquibium oceanicum	strain=B7	GCA_001889605.1	1670800	1670800	type	True	77.5436	284	1391	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	77.4325	295	1391	95	below_threshold
Rhizobium sophorae	strain=CCBAU 03386	GCA_013087515.1	1535242	1535242	type	True	77.1269	281	1391	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	76.6532	253	1391	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	76.6501	261	1391	95	below_threshold
Methylobacterium isbiliense	strain=DSM 17168	GCA_022179325.1	315478	315478	type	True	76.4802	241	1391	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:25,047] [INFO] DFAST Taxonomy check result was written to GCF_900141975.1_IMG-taxon_2585427611_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:22:25,048] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:25,048] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:25,048] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdcb2f3de-527a-44e0-a9a4-80819761de9c/dqc_reference/checkm_data
[2024-01-24 14:22:25,049] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:25,095] [INFO] Task started: CheckM
[2024-01-24 14:22:25,095] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900141975.1_IMG-taxon_2585427611_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900141975.1_IMG-taxon_2585427611_annotated_assembly_genomic.fna/checkm_input GCF_900141975.1_IMG-taxon_2585427611_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:23:05,089] [INFO] Task succeeded: CheckM
[2024-01-24 14:23:05,091] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:23:05,116] [INFO] ===== Completeness check finished =====
[2024-01-24 14:23:05,116] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:23:05,117] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900141975.1_IMG-taxon_2585427611_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:23:05,117] [INFO] Task started: Blastn
[2024-01-24 14:23:05,117] [INFO] Running command: blastn -query GCF_900141975.1_IMG-taxon_2585427611_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgdcb2f3de-527a-44e0-a9a4-80819761de9c/dqc_reference/reference_markers_gtdb.fasta -out GCF_900141975.1_IMG-taxon_2585427611_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:07,054] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:07,058] [INFO] Selected 15 target genomes.
[2024-01-24 14:23:07,058] [INFO] Target genome list was writen to GCF_900141975.1_IMG-taxon_2585427611_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:23:07,071] [INFO] Task started: fastANI
[2024-01-24 14:23:07,071] [INFO] Running command: fastANI --query /var/lib/cwl/stg62392d97-dfd0-4a7d-835f-616cd364a451/GCF_900141975.1_IMG-taxon_2585427611_annotated_assembly_genomic.fna.gz --refList GCF_900141975.1_IMG-taxon_2585427611_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900141975.1_IMG-taxon_2585427611_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:20,916] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:20,929] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:20,929] [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_001463885.1	s__Aureimonas altamirensis	99.9893	1378	1391	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_014844055.1	s__Aureimonas altamirensis_A	91.8158	1166	1391	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	97.71	97.71	0.89	0.89	2	-
GCF_001463905.1	s__Aureimonas frigidaquae	80.6858	752	1391	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017815515.1	s__Aureimonas populi	79.0278	495	1391	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382705.1	s__Aureimonas ureilytica	78.9536	482	1391	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000153465.1	s__Aurantimonas manganoxydans	78.6837	429	1391	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.4342	99.99	99.99	1.00	1.00	2	-
GCF_014058705.1	s__Aureimonas mangrovi	78.671	469	1391	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001463705.1	s__Aureimonas sp001463705	78.626	494	1391	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000421645.1	s__Aurantimonas coralicida	78.4467	472	1391	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.4342	97.41	96.44	0.92	0.87	5	-
GCF_017353515.1	s__Jiella sp017353515	78.1011	403	1391	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017349315.1	s__Jiella sp017349315	77.6523	323	1391	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001889605.1	s__Mesorhizobium_E oceanicum	77.5769	281	1391	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001262505.1	s__Shinella sp001262505	77.214	324	1391	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	98.95	98.39	0.91	0.87	4	-
GCF_004004555.2	s__Methylobacterium sp004004555	76.6715	254	1391	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001423085.1	s__Methylobacterium sp001423085	76.5061	192	1391	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	97.83	97.83	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:23:20,931] [INFO] GTDB search result was written to GCF_900141975.1_IMG-taxon_2585427611_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:20,931] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:20,936] [INFO] DFAST_QC result json was written to GCF_900141975.1_IMG-taxon_2585427611_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:23:20,937] [INFO] DFAST_QC completed!
[2024-01-24 14:23:20,937] [INFO] Total running time: 0h1m30s