[2024-01-24 13:58:25,665] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:25,667] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:25,667] [INFO] DQC Reference Directory: /var/lib/cwl/stgce11847f-479f-4d43-bc9a-c4143fe2e407/dqc_reference
[2024-01-24 13:58:27,049] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:27,050] [INFO] Task started: Prodigal
[2024-01-24 13:58:27,050] [INFO] Running command: gunzip -c /var/lib/cwl/stg53d78817-5452-4902-ba6d-e1a44acc83be/GCF_021117385.1_ASM2111738v1_genomic.fna.gz | prodigal -d GCF_021117385.1_ASM2111738v1_genomic.fna/cds.fna -a GCF_021117385.1_ASM2111738v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:38,384] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:38,384] [INFO] Task started: HMMsearch
[2024-01-24 13:58:38,384] [INFO] Running command: hmmsearch --tblout GCF_021117385.1_ASM2111738v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgce11847f-479f-4d43-bc9a-c4143fe2e407/dqc_reference/reference_markers.hmm GCF_021117385.1_ASM2111738v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:38,641] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:38,643] [INFO] Found 6/6 markers.
[2024-01-24 13:58:38,683] [INFO] Query marker FASTA was written to GCF_021117385.1_ASM2111738v1_genomic.fna/markers.fasta
[2024-01-24 13:58:38,684] [INFO] Task started: Blastn
[2024-01-24 13:58:38,684] [INFO] Running command: blastn -query GCF_021117385.1_ASM2111738v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgce11847f-479f-4d43-bc9a-c4143fe2e407/dqc_reference/reference_markers.fasta -out GCF_021117385.1_ASM2111738v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:39,779] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:39,783] [INFO] Selected 11 target genomes.
[2024-01-24 13:58:39,783] [INFO] Target genome list was writen to GCF_021117385.1_ASM2111738v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:39,793] [INFO] Task started: fastANI
[2024-01-24 13:58:39,793] [INFO] Running command: fastANI --query /var/lib/cwl/stg53d78817-5452-4902-ba6d-e1a44acc83be/GCF_021117385.1_ASM2111738v1_genomic.fna.gz --refList GCF_021117385.1_ASM2111738v1_genomic.fna/target_genomes.txt --output GCF_021117385.1_ASM2111738v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:50,612] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:50,612] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgce11847f-479f-4d43-bc9a-c4143fe2e407/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:50,613] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgce11847f-479f-4d43-bc9a-c4143fe2e407/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:50,628] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:58:50,629] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:58:50,629] [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
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	89.3288	1000	1162	95	below_threshold
Frateuria terrea	strain=DSM 26515	GCA_900109025.1	529704	529704	type	True	87.2782	934	1162	95	below_threshold
Frateuria terrea	strain=CGMCC 1.7053	GCA_900115705.1	529704	529704	type	True	87.2196	943	1162	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	84.4389	782	1162	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	84.3675	723	1162	95	below_threshold
Rhodanobacter thiooxydans	strain=LCS2	GCA_000264375.1	416169	416169	type	True	82.8884	717	1162	95	below_threshold
Dyella kyungheensis	strain=THG-B117	GCA_016905005.1	1242174	1242174	type	True	81.0734	664	1162	95	below_threshold
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	81.0061	647	1162	95	below_threshold
Dyella japonica	strain=DSM 16301	GCA_001010355.1	231455	231455	type	True	81.0037	538	1162	95	below_threshold
Dyella acidiphila	strain=7MK23	GCA_014863405.1	2775866	2775866	type	True	80.5159	592	1162	95	below_threshold
Tahibacter caeni	strain=BUT-6	GCA_024609805.1	1453545	1453545	type	True	78.6533	410	1162	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:50,630] [INFO] DFAST Taxonomy check result was written to GCF_021117385.1_ASM2111738v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:50,631] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:50,631] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:50,631] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgce11847f-479f-4d43-bc9a-c4143fe2e407/dqc_reference/checkm_data
[2024-01-24 13:58:50,632] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:50,674] [INFO] Task started: CheckM
[2024-01-24 13:58:50,675] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021117385.1_ASM2111738v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021117385.1_ASM2111738v1_genomic.fna/checkm_input GCF_021117385.1_ASM2111738v1_genomic.fna/checkm_result
[2024-01-24 13:59:33,653] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:33,654] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:33,674] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:33,675] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:33,675] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021117385.1_ASM2111738v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:33,676] [INFO] Task started: Blastn
[2024-01-24 13:59:33,676] [INFO] Running command: blastn -query GCF_021117385.1_ASM2111738v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgce11847f-479f-4d43-bc9a-c4143fe2e407/dqc_reference/reference_markers_gtdb.fasta -out GCF_021117385.1_ASM2111738v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:35,972] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:35,975] [INFO] Selected 12 target genomes.
[2024-01-24 13:59:35,975] [INFO] Target genome list was writen to GCF_021117385.1_ASM2111738v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:35,996] [INFO] Task started: fastANI
[2024-01-24 13:59:35,996] [INFO] Running command: fastANI --query /var/lib/cwl/stg53d78817-5452-4902-ba6d-e1a44acc83be/GCF_021117385.1_ASM2111738v1_genomic.fna.gz --refList GCF_021117385.1_ASM2111738v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021117385.1_ASM2111738v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:47,104] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:47,114] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:59:47,115] [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_017837635.1	s__Frateuria_A sp017837635	89.3237	1000	1162	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Frateuria_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115705.1	s__Frateuria_A terrea	87.225	943	1162	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Frateuria_A	95.0	100.00	100.00	1.00	1.00	2	-
GCA_013362045.1	s__Frateuria_A sp013362045	86.9822	709	1162	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Frateuria_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148905.1	s__Fulvimonas soli	84.4735	779	1162	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Fulvimonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001428405.1	s__Frateuria_A sp001428405	84.1876	794	1162	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Frateuria_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001182895.1	s__Frateuria_B defendens	83.4915	695	1162	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Frateuria_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017848855.1	s__Rhodanobacter denitrificans_B	83.0506	693	1162	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112865.1	s__Dyella marensis	82.7822	735	1162	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000334915.1	s__Dyella_A ginsengisoli	82.7606	737	1162	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018970895.1	s__Dyella_A sp018970895	82.7223	650	1162	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012275375.1	s__Dyella sp012275375	82.7026	723	1162	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	96.64	95.58	0.92	0.90	4	-
GCF_003332825.1	s__Dyella sp003332825	81.8124	672	1162	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:47,116] [INFO] GTDB search result was written to GCF_021117385.1_ASM2111738v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:47,117] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:47,121] [INFO] DFAST_QC result json was written to GCF_021117385.1_ASM2111738v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:47,122] [INFO] DFAST_QC completed!
[2024-01-24 13:59:47,122] [INFO] Total running time: 0h1m21s