[2024-01-24 11:12:26,283] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:26,285] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:26,285] [INFO] DQC Reference Directory: /var/lib/cwl/stg12112d7f-26a8-48ab-8e4f-364ffebda2c9/dqc_reference
[2024-01-24 11:12:27,672] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:27,673] [INFO] Task started: Prodigal
[2024-01-24 11:12:27,673] [INFO] Running command: gunzip -c /var/lib/cwl/stge87afac8-2c5c-412c-a2e2-3b6cfd016ca8/GCF_002837145.1_ASM283714v1_genomic.fna.gz | prodigal -d GCF_002837145.1_ASM283714v1_genomic.fna/cds.fna -a GCF_002837145.1_ASM283714v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:37,992] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:37,993] [INFO] Task started: HMMsearch
[2024-01-24 11:12:37,993] [INFO] Running command: hmmsearch --tblout GCF_002837145.1_ASM283714v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg12112d7f-26a8-48ab-8e4f-364ffebda2c9/dqc_reference/reference_markers.hmm GCF_002837145.1_ASM283714v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:38,287] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:38,288] [INFO] Found 6/6 markers.
[2024-01-24 11:12:38,337] [INFO] Query marker FASTA was written to GCF_002837145.1_ASM283714v1_genomic.fna/markers.fasta
[2024-01-24 11:12:38,338] [INFO] Task started: Blastn
[2024-01-24 11:12:38,338] [INFO] Running command: blastn -query GCF_002837145.1_ASM283714v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg12112d7f-26a8-48ab-8e4f-364ffebda2c9/dqc_reference/reference_markers.fasta -out GCF_002837145.1_ASM283714v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:39,408] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:39,412] [INFO] Selected 20 target genomes.
[2024-01-24 11:12:39,412] [INFO] Target genome list was writen to GCF_002837145.1_ASM283714v1_genomic.fna/target_genomes.txt
[2024-01-24 11:12:39,419] [INFO] Task started: fastANI
[2024-01-24 11:12:39,419] [INFO] Running command: fastANI --query /var/lib/cwl/stge87afac8-2c5c-412c-a2e2-3b6cfd016ca8/GCF_002837145.1_ASM283714v1_genomic.fna.gz --refList GCF_002837145.1_ASM283714v1_genomic.fna/target_genomes.txt --output GCF_002837145.1_ASM283714v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:12:55,850] [INFO] Task succeeded: fastANI
[2024-01-24 11:12:55,850] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg12112d7f-26a8-48ab-8e4f-364ffebda2c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:12:55,851] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg12112d7f-26a8-48ab-8e4f-364ffebda2c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:12:55,867] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:12:55,867] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:12:55,867] [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
Tepidicella baoligensis	strain=B18-50	GCA_013432195.1	2707016	2707016	type	True	82.4996	547	934	95	below_threshold
Malikia granosa	strain=P1	GCA_002980595.1	263067	263067	type	True	82.1951	533	934	95	below_threshold
Hydrogenophaga palleronii	strain=NBRC 102513	GCA_001571225.1	65655	65655	type	True	82.083	549	934	95	below_threshold
Hydrogenophaga pseudoflava	strain=NBRC 102511	GCA_001592285.1	47421	47421	type	True	82.0691	585	934	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	82.0663	579	934	95	below_threshold
Hydrogenophaga flava	strain=NBRC 102514	GCA_001571145.1	65657	65657	type	True	82.0397	583	934	95	below_threshold
Malikia spinosa	strain=83	GCA_002980625.1	86180	86180	type	True	82.0297	506	934	95	below_threshold
Hydrogenophaga borbori	strain=LA-38	GCA_003417535.1	2294117	2294117	type	True	81.7711	581	934	95	below_threshold
Tepidimonas fonticaldi	strain=AT-A2	GCA_007556755.1	1101373	1101373	type	True	81.4201	526	934	95	below_threshold
Ramlibacter aquaticus	strain=LMG 30558	GCA_015159745.1	2780094	2780094	type	True	81.1111	485	934	95	below_threshold
Serpentinimonas maccroryi	strain=B1	GCA_000828915.1	1458426	1458426	type	True	80.6598	438	934	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	80.6536	476	934	95	below_threshold
Pseudorhodoferax aquiterrae	strain=KCTC 23314	GCA_014652235.1	747304	747304	type	True	80.4837	536	934	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	80.3549	491	934	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	80.2034	424	934	95	below_threshold
Xylophilus ampelinus	strain=CECT 7646	GCA_003217575.1	54067	54067	type	True	80.1843	421	934	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_002933415.1	215580	215580	type	True	80.0419	456	934	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	79.9942	455	934	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	79.8547	472	934	95	below_threshold
Ottowia testudinis	strain=27C	GCA_017498525.1	2816950	2816950	type	True	79.7377	463	934	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:12:55,869] [INFO] DFAST Taxonomy check result was written to GCF_002837145.1_ASM283714v1_genomic.fna/tc_result.tsv
[2024-01-24 11:12:55,869] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:12:55,870] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:12:55,870] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg12112d7f-26a8-48ab-8e4f-364ffebda2c9/dqc_reference/checkm_data
[2024-01-24 11:12:55,871] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:12:55,904] [INFO] Task started: CheckM
[2024-01-24 11:12:55,904] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002837145.1_ASM283714v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002837145.1_ASM283714v1_genomic.fna/checkm_input GCF_002837145.1_ASM283714v1_genomic.fna/checkm_result
[2024-01-24 11:13:42,226] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:42,228] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.71%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2024-01-24 11:13:42,259] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:42,259] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:42,260] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002837145.1_ASM283714v1_genomic.fna/markers.fasta)
[2024-01-24 11:13:42,261] [INFO] Task started: Blastn
[2024-01-24 11:13:42,261] [INFO] Running command: blastn -query GCF_002837145.1_ASM283714v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg12112d7f-26a8-48ab-8e4f-364ffebda2c9/dqc_reference/reference_markers_gtdb.fasta -out GCF_002837145.1_ASM283714v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:44,122] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:44,127] [INFO] Selected 14 target genomes.
[2024-01-24 11:13:44,127] [INFO] Target genome list was writen to GCF_002837145.1_ASM283714v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:44,154] [INFO] Task started: fastANI
[2024-01-24 11:13:44,155] [INFO] Running command: fastANI --query /var/lib/cwl/stge87afac8-2c5c-412c-a2e2-3b6cfd016ca8/GCF_002837145.1_ASM283714v1_genomic.fna.gz --refList GCF_002837145.1_ASM283714v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002837145.1_ASM283714v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:13:54,119] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:54,135] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:13:54,136] [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_002837145.1	s__BK-30 sp002837145	100.0	924	934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__BK-30	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002837135.1	s__Macromonas bipunctata	82.5168	449	934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Macromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013432195.1	s__Tepidicella baoligensis	82.4953	547	934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363315.1	s__Tepidicella xavieri	82.2874	552	934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002980595.1	s__Malikia granosa	82.2339	531	934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Malikia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002127215.1	s__Hydrogenophaga sp002127215	82.1404	550	934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002980625.1	s__Malikia spinosa	82.0603	504	934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Malikia	95.0	97.79	97.60	0.88	0.88	3	-
GCA_003599455.1	s__Hydrogenophaga sp003599455	82.0446	548	934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002291945.1	s__UBA997 sp002291945	81.8354	416	934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA997	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016741995.1	s__Hydrogenophaga sp016741995	81.4804	500	934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007556755.1	s__Tepidimonas fonticaldi	81.3861	531	934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidimonas	95.0	97.94	97.94	0.88	0.88	2	-
GCA_018903185.1	s__Hydrogenophaga sp018903185	81.1398	293	934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	99.34	99.34	0.82	0.82	2	-
GCF_016428875.1	s__Xylophilus sp016428875	80.8733	480	934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Xylophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652235.1	s__Pseudorhodoferax aquiterrae	80.4829	536	934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudorhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:13:54,137] [INFO] GTDB search result was written to GCF_002837145.1_ASM283714v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:13:54,138] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:13:54,142] [INFO] DFAST_QC result json was written to GCF_002837145.1_ASM283714v1_genomic.fna/dqc_result.json
[2024-01-24 11:13:54,142] [INFO] DFAST_QC completed!
[2024-01-24 11:13:54,142] [INFO] Total running time: 0h1m28s