[2024-01-24 14:38:46,496] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:38:46,498] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:38:46,499] [INFO] DQC Reference Directory: /var/lib/cwl/stg38fa8d4c-c14f-4cdf-b14b-49374f0e1063/dqc_reference
[2024-01-24 14:38:47,906] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:38:47,907] [INFO] Task started: Prodigal
[2024-01-24 14:38:47,907] [INFO] Running command: gunzip -c /var/lib/cwl/stgb795572f-efda-47b8-8240-40e2197ae1e8/GCF_003024235.1_ASM302423v1_genomic.fna.gz | prodigal -d GCF_003024235.1_ASM302423v1_genomic.fna/cds.fna -a GCF_003024235.1_ASM302423v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:38:56,494] [INFO] Task succeeded: Prodigal
[2024-01-24 14:38:56,495] [INFO] Task started: HMMsearch
[2024-01-24 14:38:56,495] [INFO] Running command: hmmsearch --tblout GCF_003024235.1_ASM302423v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg38fa8d4c-c14f-4cdf-b14b-49374f0e1063/dqc_reference/reference_markers.hmm GCF_003024235.1_ASM302423v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:38:56,744] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:38:56,745] [INFO] Found 6/6 markers.
[2024-01-24 14:38:56,795] [INFO] Query marker FASTA was written to GCF_003024235.1_ASM302423v1_genomic.fna/markers.fasta
[2024-01-24 14:38:56,796] [INFO] Task started: Blastn
[2024-01-24 14:38:56,796] [INFO] Running command: blastn -query GCF_003024235.1_ASM302423v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg38fa8d4c-c14f-4cdf-b14b-49374f0e1063/dqc_reference/reference_markers.fasta -out GCF_003024235.1_ASM302423v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:38:57,883] [INFO] Task succeeded: Blastn
[2024-01-24 14:38:57,887] [INFO] Selected 13 target genomes.
[2024-01-24 14:38:57,888] [INFO] Target genome list was writen to GCF_003024235.1_ASM302423v1_genomic.fna/target_genomes.txt
[2024-01-24 14:38:57,894] [INFO] Task started: fastANI
[2024-01-24 14:38:57,894] [INFO] Running command: fastANI --query /var/lib/cwl/stgb795572f-efda-47b8-8240-40e2197ae1e8/GCF_003024235.1_ASM302423v1_genomic.fna.gz --refList GCF_003024235.1_ASM302423v1_genomic.fna/target_genomes.txt --output GCF_003024235.1_ASM302423v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:07,939] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:07,939] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg38fa8d4c-c14f-4cdf-b14b-49374f0e1063/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:07,940] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg38fa8d4c-c14f-4cdf-b14b-49374f0e1063/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:07,954] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:39:07,954] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:39:07,954] [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 caeni	strain=z29	GCA_003024235.1	2058085	2058085	type	True	100.0	969	969	95	conclusive
Arenimonas malthae	strain=CC-JY-1	GCA_000747075.1	354197	354197	type	True	88.2654	705	969	95	below_threshold
Arenimonas soli	strain=CGMCC 1.15905	GCA_014643775.1	2269504	2269504	type	True	86.8568	739	969	95	below_threshold
Arenimonas metalli	strain=CF5-1	GCA_000747155.1	948077	948077	type	True	86.4988	722	969	95	below_threshold
Arenimonas donghaensis	strain=HO3-R19	GCA_000743535.1	375061	375061	type	True	86.1929	729	969	95	below_threshold
Arenimonas terrae	strain=R29	GCA_006265115.1	2546226	2546226	type	True	85.7013	704	969	95	below_threshold
Arenimonas fontis	strain=3729k	GCA_008386465.1	2608255	2608255	type	True	83.8112	663	969	95	below_threshold
Arenimonas composti	strain=DSM 18010	GCA_000426365.1	370776	370776	type	True	83.3235	665	969	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	81.1059	478	969	95	below_threshold
Lysobacter silvisoli	strain=zong2l5	GCA_003382365.1	2293254	2293254	type	True	80.9387	577	969	95	below_threshold
Luteimonas weifangensis	strain=WF-2	GCA_003416885.1	2303539	2303539	type	True	80.7175	509	969	95	below_threshold
Pseudoxanthomonas jiangsuensis	strain=DSM 22398	GCA_010093185.1	619688	619688	type	True	80.6771	540	969	95	below_threshold
Stenotrophomonas acidaminiphila	strain=DSM 13117	GCA_024221815.1	128780	128780	type	True	80.0648	532	969	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:07,959] [INFO] DFAST Taxonomy check result was written to GCF_003024235.1_ASM302423v1_genomic.fna/tc_result.tsv
[2024-01-24 14:39:07,960] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:07,960] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:07,960] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg38fa8d4c-c14f-4cdf-b14b-49374f0e1063/dqc_reference/checkm_data
[2024-01-24 14:39:07,961] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:07,994] [INFO] Task started: CheckM
[2024-01-24 14:39:07,994] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003024235.1_ASM302423v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003024235.1_ASM302423v1_genomic.fna/checkm_input GCF_003024235.1_ASM302423v1_genomic.fna/checkm_result
[2024-01-24 14:39:39,664] [INFO] Task succeeded: CheckM
[2024-01-24 14:39:39,665] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:39:39,687] [INFO] ===== Completeness check finished =====
[2024-01-24 14:39:39,687] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:39:39,688] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003024235.1_ASM302423v1_genomic.fna/markers.fasta)
[2024-01-24 14:39:39,688] [INFO] Task started: Blastn
[2024-01-24 14:39:39,688] [INFO] Running command: blastn -query GCF_003024235.1_ASM302423v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg38fa8d4c-c14f-4cdf-b14b-49374f0e1063/dqc_reference/reference_markers_gtdb.fasta -out GCF_003024235.1_ASM302423v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:41,905] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:41,909] [INFO] Selected 13 target genomes.
[2024-01-24 14:39:41,909] [INFO] Target genome list was writen to GCF_003024235.1_ASM302423v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:39:41,920] [INFO] Task started: fastANI
[2024-01-24 14:39:41,921] [INFO] Running command: fastANI --query /var/lib/cwl/stgb795572f-efda-47b8-8240-40e2197ae1e8/GCF_003024235.1_ASM302423v1_genomic.fna.gz --refList GCF_003024235.1_ASM302423v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003024235.1_ASM302423v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:39:53,112] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:53,127] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:39:53,127] [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_003024235.1	s__Arenimonas caeni	100.0	969	969	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_001724815.1	s__Arenimonas sp001724815	90.594	802	969	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	88.2776	704	969	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003497545.1	s__Arenimonas sp003497545	87.1541	533	969	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	99.43	99.43	0.81	0.81	2	-
GCF_014643775.1	s__Arenimonas soli	86.8403	740	969	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000747155.1	s__Arenimonas metalli	86.4829	723	969	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000743535.1	s__Arenimonas donghaensis	86.1674	730	969	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	85.7173	703	969	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	85.0517	719	969	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008386465.1	s__Arenimonas fontis	83.7947	664	969	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000513995.1	s__Pseudoxanthomonas sp000513995	81.1831	540	969	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003382365.1	s__Lysobacter silvisoli	80.9194	579	969	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010093185.1	s__Pseudoxanthomonas jiangsuensis	80.6436	543	969	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 14:39:53,131] [INFO] GTDB search result was written to GCF_003024235.1_ASM302423v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:39:53,132] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:39:53,136] [INFO] DFAST_QC result json was written to GCF_003024235.1_ASM302423v1_genomic.fna/dqc_result.json
[2024-01-24 14:39:53,136] [INFO] DFAST_QC completed!
[2024-01-24 14:39:53,136] [INFO] Total running time: 0h1m7s