[2024-01-25 20:06:05,754] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:06:05,755] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:06:05,756] [INFO] DQC Reference Directory: /var/lib/cwl/stgb1548527-bdfa-49ce-a488-d267abc0ceef/dqc_reference
[2024-01-25 20:06:06,903] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:06:06,911] [INFO] Task started: Prodigal
[2024-01-25 20:06:06,911] [INFO] Running command: gunzip -c /var/lib/cwl/stg0651a981-0a78-42f9-9439-fb2526814b5d/GCF_014651895.1_ASM1465189v1_genomic.fna.gz | prodigal -d GCF_014651895.1_ASM1465189v1_genomic.fna/cds.fna -a GCF_014651895.1_ASM1465189v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:06:17,253] [INFO] Task succeeded: Prodigal
[2024-01-25 20:06:17,253] [INFO] Task started: HMMsearch
[2024-01-25 20:06:17,253] [INFO] Running command: hmmsearch --tblout GCF_014651895.1_ASM1465189v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb1548527-bdfa-49ce-a488-d267abc0ceef/dqc_reference/reference_markers.hmm GCF_014651895.1_ASM1465189v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:06:17,468] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:06:17,470] [INFO] Found 6/6 markers.
[2024-01-25 20:06:17,498] [INFO] Query marker FASTA was written to GCF_014651895.1_ASM1465189v1_genomic.fna/markers.fasta
[2024-01-25 20:06:17,498] [INFO] Task started: Blastn
[2024-01-25 20:06:17,498] [INFO] Running command: blastn -query GCF_014651895.1_ASM1465189v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb1548527-bdfa-49ce-a488-d267abc0ceef/dqc_reference/reference_markers.fasta -out GCF_014651895.1_ASM1465189v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:06:18,351] [INFO] Task succeeded: Blastn
[2024-01-25 20:06:18,354] [INFO] Selected 13 target genomes.
[2024-01-25 20:06:18,354] [INFO] Target genome list was writen to GCF_014651895.1_ASM1465189v1_genomic.fna/target_genomes.txt
[2024-01-25 20:06:18,370] [INFO] Task started: fastANI
[2024-01-25 20:06:18,370] [INFO] Running command: fastANI --query /var/lib/cwl/stg0651a981-0a78-42f9-9439-fb2526814b5d/GCF_014651895.1_ASM1465189v1_genomic.fna.gz --refList GCF_014651895.1_ASM1465189v1_genomic.fna/target_genomes.txt --output GCF_014651895.1_ASM1465189v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:06:30,016] [INFO] Task succeeded: fastANI
[2024-01-25 20:06:30,017] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb1548527-bdfa-49ce-a488-d267abc0ceef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:06:30,017] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb1548527-bdfa-49ce-a488-d267abc0ceef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:06:30,025] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:06:30,025] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:06:30,026] [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 panaciterrae	strain=KCTC 22232	GCA_014651895.1	490572	490572	type	True	100.0	1148	1148	95	conclusive
Rhodanobacter denitrificans	strain=2APBS1	GCA_000230695.3	666685	666685	type	True	85.1868	864	1148	95	below_threshold
Rhodanobacter thiooxydans	strain=LCS2	GCA_000264375.1	416169	416169	type	True	84.8032	771	1148	95	below_threshold
Rhodanobacter spathiphylli	strain=B39	GCA_000264295.1	347483	347483	type	True	84.5838	842	1148	95	below_threshold
Rhodanobacter fulvus	strain=Jip2	GCA_000264315.1	219571	219571	type	True	82.7429	678	1148	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	81.9916	715	1148	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	81.2333	650	1148	95	below_threshold
Dyella solisilvae	strain=DHG54	GCA_003351225.1	1920168	1920168	type	True	81.0414	630	1148	95	below_threshold
Dyella japonica	strain=DSM 16301	GCA_001010355.1	231455	231455	type	True	80.8072	540	1148	95	below_threshold
Dyella amyloliquefaciens	strain=DHC06	GCA_004296575.1	1770545	1770545	type	True	80.7391	653	1148	95	below_threshold
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	80.5781	671	1148	95	below_threshold
Dyella acidiphila	strain=7MK23	GCA_014863405.1	2775866	2775866	type	True	80.4437	631	1148	95	below_threshold
Tahibacter caeni	strain=BUT-6	GCA_024609805.1	1453545	1453545	type	True	78.4219	331	1148	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:06:30,027] [INFO] DFAST Taxonomy check result was written to GCF_014651895.1_ASM1465189v1_genomic.fna/tc_result.tsv
[2024-01-25 20:06:30,027] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:06:30,027] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:06:30,028] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb1548527-bdfa-49ce-a488-d267abc0ceef/dqc_reference/checkm_data
[2024-01-25 20:06:30,028] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:06:30,062] [INFO] Task started: CheckM
[2024-01-25 20:06:30,062] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014651895.1_ASM1465189v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014651895.1_ASM1465189v1_genomic.fna/checkm_input GCF_014651895.1_ASM1465189v1_genomic.fna/checkm_result
[2024-01-25 20:07:09,386] [INFO] Task succeeded: CheckM
[2024-01-25 20:07:09,388] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:07:09,405] [INFO] ===== Completeness check finished =====
[2024-01-25 20:07:09,405] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:07:09,406] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014651895.1_ASM1465189v1_genomic.fna/markers.fasta)
[2024-01-25 20:07:09,406] [INFO] Task started: Blastn
[2024-01-25 20:07:09,406] [INFO] Running command: blastn -query GCF_014651895.1_ASM1465189v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb1548527-bdfa-49ce-a488-d267abc0ceef/dqc_reference/reference_markers_gtdb.fasta -out GCF_014651895.1_ASM1465189v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:07:11,027] [INFO] Task succeeded: Blastn
[2024-01-25 20:07:11,030] [INFO] Selected 14 target genomes.
[2024-01-25 20:07:11,030] [INFO] Target genome list was writen to GCF_014651895.1_ASM1465189v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:07:11,059] [INFO] Task started: fastANI
[2024-01-25 20:07:11,059] [INFO] Running command: fastANI --query /var/lib/cwl/stg0651a981-0a78-42f9-9439-fb2526814b5d/GCF_014651895.1_ASM1465189v1_genomic.fna.gz --refList GCF_014651895.1_ASM1465189v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014651895.1_ASM1465189v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:07:24,076] [INFO] Task succeeded: fastANI
[2024-01-25 20:07:24,085] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:07:24,085] [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_014651895.1	s__Rhodanobacter panaciterrae	100.0	1148	1148	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900142825.1	s__Rhodanobacter sp900142825	87.7688	923	1148	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002001175.1	s__Rhodanobacter sp002001175	87.1367	903	1148	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006438785.1	s__Rhodanobacter glycinis_A	86.8105	928	1148	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	99.18	99.18	0.94	0.94	2	-
GCF_002001125.1	s__Rhodanobacter sp002001125	86.3745	883	1148	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002001165.1	s__Rhodanobacter sp002001165	86.1759	896	1148	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018599185.1	s__Rhodanobacter sp018599185	86.1302	872	1148	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	86.1094	859	1148	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002001045.1	s__Rhodanobacter sp002001045	85.842	862	1148	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009766065.1	s__Rhodanobacter sp009766065	85.8293	856	1148	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003069545.1	s__Rhodanobacter thiooxydans_A	85.644	819	1148	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	98.26	98.26	0.94	0.94	2	-
GCA_002413455.1	s__Rhodanobacter sp002413455	85.6153	773	1148	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000264375.1	s__Rhodanobacter thiooxydans	84.8155	772	1148	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	99.24	99.24	0.91	0.91	2	-
GCF_002001085.1	s__Rhodanobacter sp002001085	84.4071	818	1148	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:07:24,089] [INFO] GTDB search result was written to GCF_014651895.1_ASM1465189v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:07:24,091] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:07:24,099] [INFO] DFAST_QC result json was written to GCF_014651895.1_ASM1465189v1_genomic.fna/dqc_result.json
[2024-01-25 20:07:24,100] [INFO] DFAST_QC completed!
[2024-01-25 20:07:24,100] [INFO] Total running time: 0h1m18s