[2024-01-24 14:38:45,729] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:38:45,732] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:38:45,732] [INFO] DQC Reference Directory: /var/lib/cwl/stg934b7e4b-350a-4719-9933-837318744372/dqc_reference
[2024-01-24 14:38:47,073] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:38:47,074] [INFO] Task started: Prodigal
[2024-01-24 14:38:47,075] [INFO] Running command: gunzip -c /var/lib/cwl/stg5124ce51-5a46-431e-ac50-8a7883891c9f/GCF_001592265.1_ASM159226v1_genomic.fna.gz | prodigal -d GCF_001592265.1_ASM159226v1_genomic.fna/cds.fna -a GCF_001592265.1_ASM159226v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:00,115] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:00,115] [INFO] Task started: HMMsearch
[2024-01-24 14:39:00,115] [INFO] Running command: hmmsearch --tblout GCF_001592265.1_ASM159226v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg934b7e4b-350a-4719-9933-837318744372/dqc_reference/reference_markers.hmm GCF_001592265.1_ASM159226v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:00,417] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:00,418] [INFO] Found 6/6 markers.
[2024-01-24 14:39:00,458] [INFO] Query marker FASTA was written to GCF_001592265.1_ASM159226v1_genomic.fna/markers.fasta
[2024-01-24 14:39:00,458] [INFO] Task started: Blastn
[2024-01-24 14:39:00,458] [INFO] Running command: blastn -query GCF_001592265.1_ASM159226v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg934b7e4b-350a-4719-9933-837318744372/dqc_reference/reference_markers.fasta -out GCF_001592265.1_ASM159226v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:01,472] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:01,476] [INFO] Selected 28 target genomes.
[2024-01-24 14:39:01,476] [INFO] Target genome list was writen to GCF_001592265.1_ASM159226v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:01,501] [INFO] Task started: fastANI
[2024-01-24 14:39:01,501] [INFO] Running command: fastANI --query /var/lib/cwl/stg5124ce51-5a46-431e-ac50-8a7883891c9f/GCF_001592265.1_ASM159226v1_genomic.fna.gz --refList GCF_001592265.1_ASM159226v1_genomic.fna/target_genomes.txt --output GCF_001592265.1_ASM159226v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:26,824] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:26,825] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg934b7e4b-350a-4719-9933-837318744372/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:26,825] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg934b7e4b-350a-4719-9933-837318744372/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:26,846] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:39:26,846] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:39:26,847] [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
Ramlibacter tataouinensis	strain=TTB310	GCA_000215705.1	94132	94132	type	True	81.0451	583	1203	95	below_threshold
Ramlibacter aquaticus	strain=LMG 30558	GCA_015159745.1	2780094	2780094	type	True	80.8127	523	1203	95	below_threshold
Acidovorax soli	strain=DSM 25157	GCA_900107605.1	592050	592050	type	True	80.7402	539	1203	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	80.6422	590	1203	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	80.6339	560	1203	95	below_threshold
Hydrogenophaga pseudoflava	strain=NBRC 102511	GCA_001592285.1	47421	47421	type	True	80.5339	569	1203	95	below_threshold
Variovorax beijingensis	strain=502	GCA_003951285.1	2496117	2496117	type	True	80.5182	574	1203	95	below_threshold
Ottowia beijingensis	strain=GCS-AN-3	GCA_013423955.1	1207057	1207057	type	True	80.512	558	1203	95	below_threshold
Pseudorhodoferax aquiterrae	strain=KCTC 23314	GCA_014652235.1	747304	747304	type	True	80.4873	587	1203	95	below_threshold
Curvibacter gracilis	strain=ATCC BAA-807	GCA_000518645.1	230310	230310	type	True	80.4719	589	1203	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	80.3652	536	1203	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	80.3236	562	1203	95	below_threshold
Variovorax paradoxus	strain=NBRC 15149	GCA_001591365.1	34073	34073	suspected-type	True	80.3171	607	1203	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	80.2583	582	1203	95	below_threshold
Ramlibacter rhizophilus	strain=CCTCC AB2015357	GCA_004681965.1	1781167	1781167	type	True	80.2137	515	1203	95	below_threshold
Pseudorhodoferax soli	strain=DSM 21634	GCA_003337555.1	545864	545864	type	True	80.1921	590	1203	95	below_threshold
Acidovorax citrulli	strain=DSM 17060	GCA_900100305.1	80869	80869	type	True	80.0974	512	1203	95	below_threshold
Acidovorax avenae subsp. avenae	strain=ATCC 19860	GCA_000176855.2	80870	80867	suspected-type	True	80.0817	512	1203	95	below_threshold
Xylophilus ampelinus	strain=CECT 7646	GCA_003217575.1	54067	54067	type	True	80.069	449	1203	95	below_threshold
Acidovorax kalamii	strain=KNDSW-TSA6	GCA_002245625.1	2004485	2004485	type	True	80.0499	566	1203	95	below_threshold
Acidovorax cattleyae	strain=DSM 17101	GCA_900104515.1	80868	80868	type	True	80.049	503	1203	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	80.047	452	1203	95	below_threshold
Acidovorax oryzae	strain=ATCC 19882	GCA_000687165.1	862720	862720	type	True	80.0343	500	1203	95	below_threshold
Acidovorax valerianellae	strain=DSM 16619	GCA_900102625.1	187868	187868	type	True	79.9696	515	1203	95	below_threshold
Delftia acidovorans	strain=FDAARGOS_997	GCA_016127415.1	80866	80866	type	True	79.8739	564	1203	95	below_threshold
Delftia acidovorans	strain=NBRC 14950	GCA_001598795.1	80866	80866	type	True	79.8609	550	1203	95	below_threshold
Rhodoferax lacus	strain=IMCC26218	GCA_003415675.1	2184758	2184758	type	True	79.8223	497	1203	95	below_threshold
Brachymonas denitrificans	strain=DSM 15123	GCA_900110225.1	28220	28220	type	True	79.638	378	1203	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:26,848] [INFO] DFAST Taxonomy check result was written to GCF_001592265.1_ASM159226v1_genomic.fna/tc_result.tsv
[2024-01-24 14:39:26,849] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:26,849] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:26,849] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg934b7e4b-350a-4719-9933-837318744372/dqc_reference/checkm_data
[2024-01-24 14:39:26,851] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:26,890] [INFO] Task started: CheckM
[2024-01-24 14:39:26,891] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001592265.1_ASM159226v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001592265.1_ASM159226v1_genomic.fna/checkm_input GCF_001592265.1_ASM159226v1_genomic.fna/checkm_result
[2024-01-24 14:40:14,331] [INFO] Task succeeded: CheckM
[2024-01-24 14:40:14,332] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:40:14,360] [INFO] ===== Completeness check finished =====
[2024-01-24 14:40:14,361] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:40:14,361] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001592265.1_ASM159226v1_genomic.fna/markers.fasta)
[2024-01-24 14:40:14,362] [INFO] Task started: Blastn
[2024-01-24 14:40:14,362] [INFO] Running command: blastn -query GCF_001592265.1_ASM159226v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg934b7e4b-350a-4719-9933-837318744372/dqc_reference/reference_markers_gtdb.fasta -out GCF_001592265.1_ASM159226v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:16,543] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:16,546] [INFO] Selected 10 target genomes.
[2024-01-24 14:40:16,547] [INFO] Target genome list was writen to GCF_001592265.1_ASM159226v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:40:16,556] [INFO] Task started: fastANI
[2024-01-24 14:40:16,556] [INFO] Running command: fastANI --query /var/lib/cwl/stg5124ce51-5a46-431e-ac50-8a7883891c9f/GCF_001592265.1_ASM159226v1_genomic.fna.gz --refList GCF_001592265.1_ASM159226v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001592265.1_ASM159226v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:40:26,573] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:26,585] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:40:26,585] [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_001592265.1	s__Hylemonella delicata	100.0	1201	1203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hylemonella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002633085.1	s__Hylemonella sp002633085	91.0104	935	1203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hylemonella	95.0	96.79	96.79	0.90	0.90	2	-
GCA_001797315.1	s__Hylemonella sp001797315	88.3299	851	1203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hylemonella	95.0	99.98	99.98	0.98	0.98	2	-
GCF_001432305.1	s__Hylemonella sp001432305	83.6404	745	1203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hylemonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013334205.1	s__Hylemonella sp013334205	83.5126	754	1203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hylemonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016185015.1	s__Hylemonella sp016185015	83.3243	751	1203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hylemonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005503335.1	s__SCMQ01 sp005503335	81.7659	605	1203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCMQ01	95.0	99.99	99.99	1.00	1.00	3	-
GCA_016721925.1	s__JAABQG01 sp016721925	80.5598	535	1203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JAABQG01	95.0	98.62	98.32	0.93	0.90	9	-
GCF_004217005.1	s__Variovorax sp004217005	80.4676	562	1203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	99.70	99.70	0.95	0.95	2	-
GCF_900110225.1	s__Brachymonas denitrificans	79.638	378	1203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Brachymonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:40:26,587] [INFO] GTDB search result was written to GCF_001592265.1_ASM159226v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:40:26,587] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:40:26,592] [INFO] DFAST_QC result json was written to GCF_001592265.1_ASM159226v1_genomic.fna/dqc_result.json
[2024-01-24 14:40:26,592] [INFO] DFAST_QC completed!
[2024-01-24 14:40:26,592] [INFO] Total running time: 0h1m41s