[2023-06-30 15:57:48,594] [INFO] DFAST_QC pipeline started.
[2023-06-30 15:57:48,596] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 15:57:48,597] [INFO] DQC Reference Directory: /var/lib/cwl/stg7084925a-bd69-43fa-9230-5f2419279e98/dqc_reference
[2023-06-30 15:57:49,780] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 15:57:49,780] [INFO] Task started: Prodigal
[2023-06-30 15:57:49,781] [INFO] Running command: gunzip -c /var/lib/cwl/stg82570655-77bf-46e0-9e0c-2e49ff3211ad/GCA_025936155.1_ASM2593615v1_genomic.fna.gz | prodigal -d GCA_025936155.1_ASM2593615v1_genomic.fna/cds.fna -a GCA_025936155.1_ASM2593615v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 15:57:58,219] [INFO] Task succeeded: Prodigal
[2023-06-30 15:57:58,220] [INFO] Task started: HMMsearch
[2023-06-30 15:57:58,220] [INFO] Running command: hmmsearch --tblout GCA_025936155.1_ASM2593615v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7084925a-bd69-43fa-9230-5f2419279e98/dqc_reference/reference_markers.hmm GCA_025936155.1_ASM2593615v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 15:57:58,408] [INFO] Task succeeded: HMMsearch
[2023-06-30 15:57:58,409] [INFO] Found 6/6 markers.
[2023-06-30 15:57:58,438] [INFO] Query marker FASTA was written to GCA_025936155.1_ASM2593615v1_genomic.fna/markers.fasta
[2023-06-30 15:57:58,438] [INFO] Task started: Blastn
[2023-06-30 15:57:58,438] [INFO] Running command: blastn -query GCA_025936155.1_ASM2593615v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7084925a-bd69-43fa-9230-5f2419279e98/dqc_reference/reference_markers.fasta -out GCA_025936155.1_ASM2593615v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 15:57:59,365] [INFO] Task succeeded: Blastn
[2023-06-30 15:57:59,369] [INFO] Selected 21 target genomes.
[2023-06-30 15:57:59,369] [INFO] Target genome list was writen to GCA_025936155.1_ASM2593615v1_genomic.fna/target_genomes.txt
[2023-06-30 15:57:59,370] [INFO] Task started: fastANI
[2023-06-30 15:57:59,370] [INFO] Running command: fastANI --query /var/lib/cwl/stg82570655-77bf-46e0-9e0c-2e49ff3211ad/GCA_025936155.1_ASM2593615v1_genomic.fna.gz --refList GCA_025936155.1_ASM2593615v1_genomic.fna/target_genomes.txt --output GCA_025936155.1_ASM2593615v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 15:58:13,015] [INFO] Task succeeded: fastANI
[2023-06-30 15:58:13,016] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7084925a-bd69-43fa-9230-5f2419279e98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 15:58:13,016] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7084925a-bd69-43fa-9230-5f2419279e98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 15:58:13,032] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 15:58:13,033] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 15:58:13,033] [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
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	78.0232	277	760	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	78.0064	289	760	95	below_threshold
Rhodanobacter denitrificans	strain=2APBS1	GCA_000230695.3	666685	666685	type	True	77.9819	288	760	95	below_threshold
Oleiagrimonas soli	strain=DSM 107085	GCA_014201555.1	1543381	1543381	type	True	77.8701	250	760	95	below_threshold
Frateuria terrea	strain=CGMCC 1.7053	GCA_900115705.1	529704	529704	type	True	77.8603	243	760	95	below_threshold
Frateuria terrea	strain=DSM 26515	GCA_900109025.1	529704	529704	type	True	77.8474	245	760	95	below_threshold
Oleiagrimonas citrea	strain=MEBiC09124	GCA_012395255.1	1665687	1665687	type	True	77.841	216	760	95	below_threshold
Rhodanobacter thiooxydans	strain=LCS2	GCA_000264375.1	416169	416169	type	True	77.8209	292	760	95	below_threshold
Dyella acidiphila	strain=7MK23	GCA_014863405.1	2775866	2775866	type	True	77.7883	222	760	95	below_threshold
Oleiagrimonas soli	strain=3.5X	GCA_000761445.1	1543381	1543381	type	True	77.7836	258	760	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	77.7038	243	760	95	below_threshold
Rhodanobacter panaciterrae	strain=KCTC 22232	GCA_014651895.1	490572	490572	type	True	77.6507	223	760	95	below_threshold
Dyella solisilvae	strain=DHG54	GCA_003351225.1	1920168	1920168	type	True	77.5993	238	760	95	below_threshold
Thermomonas aquatica	strain=SY21	GCA_006337105.1	2202149	2202149	type	True	77.5487	185	760	95	below_threshold
Dokdonella fugitiva	strain=A3	GCA_004342425.1	328517	328517	type	True	77.5003	217	760	95	below_threshold
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	77.4701	220	760	95	below_threshold
Luteimonas gilva	strain=H23	GCA_005239095.1	2572684	2572684	type	True	77.4507	183	760	95	below_threshold
Dyella japonica	strain=DSM 16301	GCA_001010355.1	231455	231455	type	True	77.3754	195	760	95	below_threshold
Tahibacter caeni	strain=BUT-6	GCA_024609805.1	1453545	1453545	type	True	77.3348	191	760	95	below_threshold
Dokdonella koreensis	strain=DS-123	GCA_001632775.1	323415	323415	type	True	77.068	197	760	95	below_threshold
Luteibacter anthropi	strain=CCUG 25036	GCA_011759365.1	564369	564369	type	True	77.0174	169	760	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 15:58:13,035] [INFO] DFAST Taxonomy check result was written to GCA_025936155.1_ASM2593615v1_genomic.fna/tc_result.tsv
[2023-06-30 15:58:13,036] [INFO] ===== Taxonomy check completed =====
[2023-06-30 15:58:13,036] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 15:58:13,036] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7084925a-bd69-43fa-9230-5f2419279e98/dqc_reference/checkm_data
[2023-06-30 15:58:13,037] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 15:58:13,068] [INFO] Task started: CheckM
[2023-06-30 15:58:13,068] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_025936155.1_ASM2593615v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_025936155.1_ASM2593615v1_genomic.fna/checkm_input GCA_025936155.1_ASM2593615v1_genomic.fna/checkm_result
[2023-06-30 15:58:43,830] [INFO] Task succeeded: CheckM
[2023-06-30 15:58:43,831] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.45%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 15:58:43,849] [INFO] ===== Completeness check finished =====
[2023-06-30 15:58:43,849] [INFO] ===== Start GTDB Search =====
[2023-06-30 15:58:43,849] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_025936155.1_ASM2593615v1_genomic.fna/markers.fasta)
[2023-06-30 15:58:43,850] [INFO] Task started: Blastn
[2023-06-30 15:58:43,850] [INFO] Running command: blastn -query GCA_025936155.1_ASM2593615v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7084925a-bd69-43fa-9230-5f2419279e98/dqc_reference/reference_markers_gtdb.fasta -out GCA_025936155.1_ASM2593615v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 15:58:45,526] [INFO] Task succeeded: Blastn
[2023-06-30 15:58:45,529] [INFO] Selected 13 target genomes.
[2023-06-30 15:58:45,530] [INFO] Target genome list was writen to GCA_025936155.1_ASM2593615v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 15:58:45,535] [INFO] Task started: fastANI
[2023-06-30 15:58:45,535] [INFO] Running command: fastANI --query /var/lib/cwl/stg82570655-77bf-46e0-9e0c-2e49ff3211ad/GCA_025936155.1_ASM2593615v1_genomic.fna.gz --refList GCA_025936155.1_ASM2593615v1_genomic.fna/target_genomes_gtdb.txt --output GCA_025936155.1_ASM2593615v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 15:58:53,630] [INFO] Task succeeded: fastANI
[2023-06-30 15:58:53,641] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 15:58:53,641] [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
GCA_001899805.1	s__66-474 sp001899805	82.939	591	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__66-474	95.0	100.00	100.00	0.98	0.97	3	-
GCA_018971925.1	s__66-474 sp018971925	82.4016	368	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__66-474	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004299705.1	s__66-474 sp004299705	81.9404	539	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__66-474	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241365.1	s__66-474 sp018241365	81.9179	482	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__66-474	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004299555.1	s__66-474 sp004299555	79.4292	369	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__66-474	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241145.1	s__66-474 sp018241145	79.2932	332	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__66-474	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000953855.2	s__Mizugakiibacter sediminis	78.3744	303	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Mizugakiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148905.1	s__Fulvimonas soli	78.0013	289	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Fulvimonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900115705.1	s__Frateuria_A terrea	77.8345	245	760	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_002279065.1	s__Dyella_A sp002279065	77.8175	243	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_A	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000761445.1	s__Oleiagrimonas soli	77.8094	256	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Oleiagrimonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001182895.1	s__Frateuria_B defendens	77.7412	252	760	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_009996615.1	s__Dokdonella_A sp009996615	77.6585	251	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 15:58:53,643] [INFO] GTDB search result was written to GCA_025936155.1_ASM2593615v1_genomic.fna/result_gtdb.tsv
[2023-06-30 15:58:53,644] [INFO] ===== GTDB Search completed =====
[2023-06-30 15:58:53,648] [INFO] DFAST_QC result json was written to GCA_025936155.1_ASM2593615v1_genomic.fna/dqc_result.json
[2023-06-30 15:58:53,648] [INFO] DFAST_QC completed!
[2023-06-30 15:58:53,648] [INFO] Total running time: 0h1m5s