[2024-01-24 12:31:51,062] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:51,064] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:51,064] [INFO] DQC Reference Directory: /var/lib/cwl/stgf1b7dc32-817f-436c-ac76-dda90065c34a/dqc_reference
[2024-01-24 12:31:52,305] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:52,306] [INFO] Task started: Prodigal
[2024-01-24 12:31:52,307] [INFO] Running command: gunzip -c /var/lib/cwl/stgb3f0ede8-f65d-401d-9965-61c36df29afc/GCF_000747175.1_ASM74717v1_genomic.fna.gz | prodigal -d GCF_000747175.1_ASM74717v1_genomic.fna/cds.fna -a GCF_000747175.1_ASM74717v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:32:00,338] [INFO] Task succeeded: Prodigal
[2024-01-24 12:32:00,338] [INFO] Task started: HMMsearch
[2024-01-24 12:32:00,338] [INFO] Running command: hmmsearch --tblout GCF_000747175.1_ASM74717v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf1b7dc32-817f-436c-ac76-dda90065c34a/dqc_reference/reference_markers.hmm GCF_000747175.1_ASM74717v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:32:00,609] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:32:00,611] [INFO] Found 6/6 markers.
[2024-01-24 12:32:00,643] [INFO] Query marker FASTA was written to GCF_000747175.1_ASM74717v1_genomic.fna/markers.fasta
[2024-01-24 12:32:00,643] [INFO] Task started: Blastn
[2024-01-24 12:32:00,643] [INFO] Running command: blastn -query GCF_000747175.1_ASM74717v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf1b7dc32-817f-436c-ac76-dda90065c34a/dqc_reference/reference_markers.fasta -out GCF_000747175.1_ASM74717v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:01,767] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:01,770] [INFO] Selected 13 target genomes.
[2024-01-24 12:32:01,771] [INFO] Target genome list was writen to GCF_000747175.1_ASM74717v1_genomic.fna/target_genomes.txt
[2024-01-24 12:32:01,782] [INFO] Task started: fastANI
[2024-01-24 12:32:01,782] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3f0ede8-f65d-401d-9965-61c36df29afc/GCF_000747175.1_ASM74717v1_genomic.fna.gz --refList GCF_000747175.1_ASM74717v1_genomic.fna/target_genomes.txt --output GCF_000747175.1_ASM74717v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:11,332] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:11,333] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf1b7dc32-817f-436c-ac76-dda90065c34a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:11,333] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf1b7dc32-817f-436c-ac76-dda90065c34a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:11,347] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:32:11,347] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:32:11,348] [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
Arenimonas composti	strain=TR7-09	GCA_000747175.1	370776	370776	type	True	100.0	1006	1012	95	conclusive
Arenimonas composti	strain=DSM 18010	GCA_000426365.1	370776	370776	type	True	99.9765	1008	1012	95	conclusive
Arenimonas metalli	strain=CF5-1	GCA_000747155.1	948077	948077	type	True	83.6847	669	1012	95	below_threshold
Arenimonas terrae	strain=R29	GCA_006265115.1	2546226	2546226	type	True	83.5963	717	1012	95	below_threshold
Arenimonas malthae	strain=CC-JY-1	GCA_000747075.1	354197	354197	type	True	83.4362	619	1012	95	below_threshold
Arenimonas caeni	strain=z29	GCA_003024235.1	2058085	2058085	type	True	83.2552	670	1012	95	below_threshold
Lysobacter arseniciresistens	strain=ZS79	GCA_000768335.1	1385522	1385522	type	True	80.6912	496	1012	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	80.5831	485	1012	95	below_threshold
Luteimonas weifangensis	strain=WF-2	GCA_003416885.1	2303539	2303539	type	True	80.3928	514	1012	95	below_threshold
Thermomonas haemolytica	strain=LMG 19653	GCA_006352395.1	141949	141949	type	True	79.9674	439	1012	95	below_threshold
Thermomonas haemolytica	strain=DSM 13605	GCA_004346265.1	141949	141949	type	True	79.9098	453	1012	95	below_threshold
Pseudoxanthomonas kalamensis	strain=DSM 18571	GCA_010211745.1	289483	289483	type	True	79.682	425	1012	95	below_threshold
Luteimonas salinisoli	strain=SJ-92	GCA_013425525.1	2752307	2752307	type	True	79.5272	538	1012	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:32:11,349] [INFO] DFAST Taxonomy check result was written to GCF_000747175.1_ASM74717v1_genomic.fna/tc_result.tsv
[2024-01-24 12:32:11,350] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:11,351] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:11,351] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf1b7dc32-817f-436c-ac76-dda90065c34a/dqc_reference/checkm_data
[2024-01-24 12:32:11,352] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:11,389] [INFO] Task started: CheckM
[2024-01-24 12:32:11,389] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000747175.1_ASM74717v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000747175.1_ASM74717v1_genomic.fna/checkm_input GCF_000747175.1_ASM74717v1_genomic.fna/checkm_result
[2024-01-24 12:32:50,560] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:50,562] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:50,585] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:50,585] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:50,586] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000747175.1_ASM74717v1_genomic.fna/markers.fasta)
[2024-01-24 12:32:50,586] [INFO] Task started: Blastn
[2024-01-24 12:32:50,587] [INFO] Running command: blastn -query GCF_000747175.1_ASM74717v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf1b7dc32-817f-436c-ac76-dda90065c34a/dqc_reference/reference_markers_gtdb.fasta -out GCF_000747175.1_ASM74717v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:52,764] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:52,768] [INFO] Selected 11 target genomes.
[2024-01-24 12:32:52,769] [INFO] Target genome list was writen to GCF_000747175.1_ASM74717v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:52,777] [INFO] Task started: fastANI
[2024-01-24 12:32:52,777] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3f0ede8-f65d-401d-9965-61c36df29afc/GCF_000747175.1_ASM74717v1_genomic.fna.gz --refList GCF_000747175.1_ASM74717v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000747175.1_ASM74717v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:33:01,136] [INFO] Task succeeded: fastANI
[2024-01-24 12:33:01,156] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:33:01,156] [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_000426365.1	s__Arenimonas composti	99.9765	1008	1012	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	99.98	99.98	1.00	1.00	2	conclusive
GCF_000747155.1	s__Arenimonas metalli	83.7122	667	1012	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006265115.1	s__Arenimonas terrae	83.6091	716	1012	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000747075.1	s__Arenimonas malthae	83.4583	618	1012	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003024235.1	s__Arenimonas caeni	83.2829	668	1012	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001724815.1	s__Arenimonas sp001724815	83.2391	663	1012	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007993735.1	s__Arenimonas daejeonensis	83.1753	678	1012	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003241895.1	s__Arenimonas sp003241895	81.776	597	1012	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000768335.1	s__Lysobacter arseniciresistens	80.6665	498	1012	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004346265.1	s__Thermomonas haemolytica	79.9285	451	1012	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	99.99	99.99	0.99	0.99	3	-
GCF_010211765.1	s__Pseudoxanthomonas kaohsiungensis	79.8441	512	1012	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:33:01,158] [INFO] GTDB search result was written to GCF_000747175.1_ASM74717v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:33:01,159] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:33:01,162] [INFO] DFAST_QC result json was written to GCF_000747175.1_ASM74717v1_genomic.fna/dqc_result.json
[2024-01-24 12:33:01,163] [INFO] DFAST_QC completed!
[2024-01-24 12:33:01,163] [INFO] Total running time: 0h1m10s