[2024-01-25 17:43:50,338] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:43:50,339] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:43:50,339] [INFO] DQC Reference Directory: /var/lib/cwl/stg783dff5e-067d-470d-a142-773f26b12034/dqc_reference
[2024-01-25 17:43:51,519] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:43:51,520] [INFO] Task started: Prodigal
[2024-01-25 17:43:51,520] [INFO] Running command: gunzip -c /var/lib/cwl/stg0dc659c5-57b0-4872-87f9-1443484abaf7/GCF_000264375.1_Rh18863_genomic.fna.gz | prodigal -d GCF_000264375.1_Rh18863_genomic.fna/cds.fna -a GCF_000264375.1_Rh18863_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:44:02,677] [INFO] Task succeeded: Prodigal
[2024-01-25 17:44:02,677] [INFO] Task started: HMMsearch
[2024-01-25 17:44:02,677] [INFO] Running command: hmmsearch --tblout GCF_000264375.1_Rh18863_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg783dff5e-067d-470d-a142-773f26b12034/dqc_reference/reference_markers.hmm GCF_000264375.1_Rh18863_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:44:02,886] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:44:02,887] [INFO] Found 6/6 markers.
[2024-01-25 17:44:02,918] [INFO] Query marker FASTA was written to GCF_000264375.1_Rh18863_genomic.fna/markers.fasta
[2024-01-25 17:44:02,919] [INFO] Task started: Blastn
[2024-01-25 17:44:02,919] [INFO] Running command: blastn -query GCF_000264375.1_Rh18863_genomic.fna/markers.fasta -db /var/lib/cwl/stg783dff5e-067d-470d-a142-773f26b12034/dqc_reference/reference_markers.fasta -out GCF_000264375.1_Rh18863_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:44:03,927] [INFO] Task succeeded: Blastn
[2024-01-25 17:44:03,929] [INFO] Selected 13 target genomes.
[2024-01-25 17:44:03,929] [INFO] Target genome list was writen to GCF_000264375.1_Rh18863_genomic.fna/target_genomes.txt
[2024-01-25 17:44:03,941] [INFO] Task started: fastANI
[2024-01-25 17:44:03,941] [INFO] Running command: fastANI --query /var/lib/cwl/stg0dc659c5-57b0-4872-87f9-1443484abaf7/GCF_000264375.1_Rh18863_genomic.fna.gz --refList GCF_000264375.1_Rh18863_genomic.fna/target_genomes.txt --output GCF_000264375.1_Rh18863_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:44:16,687] [INFO] Task succeeded: fastANI
[2024-01-25 17:44:16,687] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg783dff5e-067d-470d-a142-773f26b12034/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:44:16,687] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg783dff5e-067d-470d-a142-773f26b12034/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:44:16,696] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:44:16,696] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:44:16,696] [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
Rhodanobacter thiooxydans	strain=LCS2	GCA_000264375.1	416169	416169	type	True	100.0	1287	1297	95	conclusive
Rhodanobacter denitrificans	strain=2APBS1	GCA_000230695.3	666685	666685	type	True	90.6224	1036	1297	95	below_threshold
Rhodanobacter spathiphylli	strain=B39	GCA_000264295.1	347483	347483	type	True	86.2386	831	1297	95	below_threshold
Rhodanobacter panaciterrae	strain=KCTC 22232	GCA_014651895.1	490572	490572	type	True	84.5781	799	1297	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	84.4428	792	1297	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	84.3926	740	1297	95	below_threshold
Rhodanobacter fulvus	strain=Jip2	GCA_000264315.1	219571	219571	type	True	83.7108	765	1297	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	82.6531	708	1297	95	below_threshold
Frateuria terrea	strain=CGMCC 1.7053	GCA_900115705.1	529704	529704	type	True	82.5691	729	1297	95	below_threshold
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	81.0283	671	1297	95	below_threshold
Dyella acidiphila	strain=7MK23	GCA_014863405.1	2775866	2775866	type	True	80.7113	636	1297	95	below_threshold
Dyella japonica	strain=DSM 16301	GCA_001010355.1	231455	231455	type	True	80.5767	607	1297	95	below_threshold
Tahibacter caeni	strain=BUT-6	GCA_024609805.1	1453545	1453545	type	True	78.5649	429	1297	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:44:16,700] [INFO] DFAST Taxonomy check result was written to GCF_000264375.1_Rh18863_genomic.fna/tc_result.tsv
[2024-01-25 17:44:16,701] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:44:16,701] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:44:16,702] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg783dff5e-067d-470d-a142-773f26b12034/dqc_reference/checkm_data
[2024-01-25 17:44:16,703] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:44:16,757] [INFO] Task started: CheckM
[2024-01-25 17:44:16,757] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000264375.1_Rh18863_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000264375.1_Rh18863_genomic.fna/checkm_input GCF_000264375.1_Rh18863_genomic.fna/checkm_result
[2024-01-25 17:44:57,877] [INFO] Task succeeded: CheckM
[2024-01-25 17:44:57,878] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:44:57,893] [INFO] ===== Completeness check finished =====
[2024-01-25 17:44:57,893] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:44:57,894] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000264375.1_Rh18863_genomic.fna/markers.fasta)
[2024-01-25 17:44:57,894] [INFO] Task started: Blastn
[2024-01-25 17:44:57,894] [INFO] Running command: blastn -query GCF_000264375.1_Rh18863_genomic.fna/markers.fasta -db /var/lib/cwl/stg783dff5e-067d-470d-a142-773f26b12034/dqc_reference/reference_markers_gtdb.fasta -out GCF_000264375.1_Rh18863_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:44:59,978] [INFO] Task succeeded: Blastn
[2024-01-25 17:44:59,980] [INFO] Selected 9 target genomes.
[2024-01-25 17:44:59,981] [INFO] Target genome list was writen to GCF_000264375.1_Rh18863_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:44:59,997] [INFO] Task started: fastANI
[2024-01-25 17:44:59,997] [INFO] Running command: fastANI --query /var/lib/cwl/stg0dc659c5-57b0-4872-87f9-1443484abaf7/GCF_000264375.1_Rh18863_genomic.fna.gz --refList GCF_000264375.1_Rh18863_genomic.fna/target_genomes_gtdb.txt --output GCF_000264375.1_Rh18863_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:45:09,374] [INFO] Task succeeded: fastANI
[2024-01-25 17:45:09,382] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:45:09,382] [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_000264375.1	s__Rhodanobacter thiooxydans	100.0	1287	1297	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	99.24	99.24	0.91	0.91	2	conclusive
GCF_000427505.1	s__Rhodanobacter sp000427505	93.9361	1008	1297	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	99.93	99.93	0.96	0.96	2	-
GCF_000230695.2	s__Rhodanobacter denitrificans	90.6224	1036	1297	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	98.49	98.47	0.91	0.89	4	-
GCF_003069545.1	s__Rhodanobacter thiooxydans_A	90.2494	949	1297	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	98.26	98.26	0.94	0.94	2	-
GCF_003335105.1	s__Rhodanobacter denitrificans_A	89.5213	962	1297	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001617365.1	s__Rhodanobacter sp001617365	89.3607	916	1297	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	99.98	99.98	0.98	0.97	3	-
GCF_018599185.1	s__Rhodanobacter sp018599185	89.2111	966	1297	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001428385.1	s__Rhodanobacter sp001428385	88.996	943	1297	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000264295.1	s__Rhodanobacter spathiphylli	86.2028	835	1297	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.107	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:45:09,386] [INFO] GTDB search result was written to GCF_000264375.1_Rh18863_genomic.fna/result_gtdb.tsv
[2024-01-25 17:45:09,386] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:45:09,390] [INFO] DFAST_QC result json was written to GCF_000264375.1_Rh18863_genomic.fna/dqc_result.json
[2024-01-25 17:45:09,390] [INFO] DFAST_QC completed!
[2024-01-25 17:45:09,390] [INFO] Total running time: 0h1m19s