[2023-06-17 01:07:53,585] [INFO] DFAST_QC pipeline started.
[2023-06-17 01:07:53,588] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 01:07:53,589] [INFO] DQC Reference Directory: /var/lib/cwl/stg38bc7c2f-fd48-4547-98fa-cd62903581f5/dqc_reference
[2023-06-17 01:07:54,992] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 01:07:54,993] [INFO] Task started: Prodigal
[2023-06-17 01:07:54,993] [INFO] Running command: gunzip -c /var/lib/cwl/stg42a2ee87-67ca-4a03-8ed8-8926857747f9/GCA_013205645.1_ASM1320564v1_genomic.fna.gz | prodigal -d GCA_013205645.1_ASM1320564v1_genomic.fna/cds.fna -a GCA_013205645.1_ASM1320564v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 01:08:02,455] [INFO] Task succeeded: Prodigal
[2023-06-17 01:08:02,455] [INFO] Task started: HMMsearch
[2023-06-17 01:08:02,455] [INFO] Running command: hmmsearch --tblout GCA_013205645.1_ASM1320564v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg38bc7c2f-fd48-4547-98fa-cd62903581f5/dqc_reference/reference_markers.hmm GCA_013205645.1_ASM1320564v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 01:08:02,721] [INFO] Task succeeded: HMMsearch
[2023-06-17 01:08:02,723] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg42a2ee87-67ca-4a03-8ed8-8926857747f9/GCA_013205645.1_ASM1320564v1_genomic.fna.gz]
[2023-06-17 01:08:02,753] [INFO] Query marker FASTA was written to GCA_013205645.1_ASM1320564v1_genomic.fna/markers.fasta
[2023-06-17 01:08:02,754] [INFO] Task started: Blastn
[2023-06-17 01:08:02,754] [INFO] Running command: blastn -query GCA_013205645.1_ASM1320564v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg38bc7c2f-fd48-4547-98fa-cd62903581f5/dqc_reference/reference_markers.fasta -out GCA_013205645.1_ASM1320564v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 01:08:03,543] [INFO] Task succeeded: Blastn
[2023-06-17 01:08:03,547] [INFO] Selected 28 target genomes.
[2023-06-17 01:08:03,548] [INFO] Target genome list was writen to GCA_013205645.1_ASM1320564v1_genomic.fna/target_genomes.txt
[2023-06-17 01:08:03,622] [INFO] Task started: fastANI
[2023-06-17 01:08:03,623] [INFO] Running command: fastANI --query /var/lib/cwl/stg42a2ee87-67ca-4a03-8ed8-8926857747f9/GCA_013205645.1_ASM1320564v1_genomic.fna.gz --refList GCA_013205645.1_ASM1320564v1_genomic.fna/target_genomes.txt --output GCA_013205645.1_ASM1320564v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 01:08:25,508] [INFO] Task succeeded: fastANI
[2023-06-17 01:08:25,508] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg38bc7c2f-fd48-4547-98fa-cd62903581f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 01:08:25,509] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg38bc7c2f-fd48-4547-98fa-cd62903581f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 01:08:25,530] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 01:08:25,531] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 01:08:25,531] [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
Polaromonas naphthalenivorans	strain=CJ2	GCA_000015505.1	216465	216465	type	True	78.4173	242	616	95	below_threshold
Polaromonas jejuensis	strain=NBRC 106434	GCA_001598235.1	457502	457502	type	True	78.1469	250	616	95	below_threshold
Polaromonas eurypsychrophila	strain=CGMCC 1.15322	GCA_014641715.1	1614635	1614635	type	True	78.0577	243	616	95	below_threshold
Polaromonas vacuolata	strain=KCTC 22033	GCA_012584515.1	37448	37448	type	True	77.435	116	616	95	below_threshold
Limnohabitans radicicola	strain=JUR4	GCA_014837235.1	2771427	2771427	type	True	77.2779	139	616	95	below_threshold
Pseudorhodoferax soli	strain=DSM 21634	GCA_003337555.1	545864	545864	type	True	77.1666	157	616	95	below_threshold
Simplicispira metamorpha	strain=NBRC 13960	GCA_003568725.1	80881	80881	type	True	77.1594	132	616	95	below_threshold
Simplicispira metamorpha	strain=DSM 1837	GCA_004341365.1	80881	80881	type	True	77.1444	133	616	95	below_threshold
Curvibacter lanceolatus	strain=ATCC 14669	GCA_000381265.1	86182	86182	type	True	77.12	155	616	95	below_threshold
Hydrogenophaga aromaticivorans	strain=D2P1	GCA_013387465.1	2610898	2610898	type	True	77.0954	161	616	95	below_threshold
Acidovorax kalamii	strain=KNDSW-TSA6	GCA_002245625.1	2004485	2004485	type	True	77.0903	149	616	95	below_threshold
Curvibacter gracilis	strain=ATCC BAA-807	GCA_000518645.1	230310	230310	type	True	77.0272	155	616	95	below_threshold
Limnohabitans parvus	strain=II-B4	GCA_003063455.1	540061	540061	type	True	76.9551	147	616	95	below_threshold
Pseudorhodoferax aquiterrae	strain=KCTC 23314	GCA_014652235.1	747304	747304	type	True	76.951	155	616	95	below_threshold
Hydrogenophaga pseudoflava	strain=NBRC 102511	GCA_001592285.1	47421	47421	type	True	76.9134	144	616	95	below_threshold
Rhodoferax lacus	strain=IMCC26218	GCA_003415675.1	2184758	2184758	type	True	76.8963	132	616	95	below_threshold
Acidovorax temperans	strain=DSM 7270	GCA_006716905.1	80878	80878	type	True	76.8705	147	616	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	76.8549	149	616	95	below_threshold
Ramlibacter algicola	strain=CrO1	GCA_016641735.1	2795217	2795217	type	True	76.8484	124	616	95	below_threshold
Acidovorax valerianellae	strain=DSM 16619	GCA_900102625.1	187868	187868	type	True	76.7757	128	616	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	76.7123	133	616	95	below_threshold
Sphaerotilus montanus	strain=HS	GCA_013426955.1	522889	522889	type	True	76.6167	100	616	95	below_threshold
Sphaerotilus montanus	strain=DSM 21226	GCA_013410775.1	522889	522889	type	True	76.6135	100	616	95	below_threshold
Delftia acidovorans	strain=FDAARGOS_997	GCA_016127415.1	80866	80866	type	True	76.6121	134	616	95	below_threshold
Delftia acidovorans	strain=NBRC 14950	GCA_001598795.1	80866	80866	type	True	76.5848	135	616	95	below_threshold
Ideonella azotifigens	strain=DSM 21438	GCA_006519715.1	513160	513160	type	True	76.4879	85	616	95	below_threshold
Ottowia testudinis	strain=27C	GCA_017498525.1	2816950	2816950	type	True	76.4507	138	616	95	below_threshold
Comamonas koreensis	strain=KCTC 12005	GCA_021026195.1	160825	160825	type	True	76.2502	117	616	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 01:08:25,533] [INFO] DFAST Taxonomy check result was written to GCA_013205645.1_ASM1320564v1_genomic.fna/tc_result.tsv
[2023-06-17 01:08:25,534] [INFO] ===== Taxonomy check completed =====
[2023-06-17 01:08:25,534] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 01:08:25,534] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg38bc7c2f-fd48-4547-98fa-cd62903581f5/dqc_reference/checkm_data
[2023-06-17 01:08:25,536] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 01:08:25,566] [INFO] Task started: CheckM
[2023-06-17 01:08:25,566] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013205645.1_ASM1320564v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013205645.1_ASM1320564v1_genomic.fna/checkm_input GCA_013205645.1_ASM1320564v1_genomic.fna/checkm_result
[2023-06-17 01:08:53,227] [INFO] Task succeeded: CheckM
[2023-06-17 01:08:53,229] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.71%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 01:08:53,251] [INFO] ===== Completeness check finished =====
[2023-06-17 01:08:53,251] [INFO] ===== Start GTDB Search =====
[2023-06-17 01:08:53,252] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013205645.1_ASM1320564v1_genomic.fna/markers.fasta)
[2023-06-17 01:08:53,252] [INFO] Task started: Blastn
[2023-06-17 01:08:53,252] [INFO] Running command: blastn -query GCA_013205645.1_ASM1320564v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg38bc7c2f-fd48-4547-98fa-cd62903581f5/dqc_reference/reference_markers_gtdb.fasta -out GCA_013205645.1_ASM1320564v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 01:08:54,403] [INFO] Task succeeded: Blastn
[2023-06-17 01:08:54,408] [INFO] Selected 21 target genomes.
[2023-06-17 01:08:54,408] [INFO] Target genome list was writen to GCA_013205645.1_ASM1320564v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 01:08:54,470] [INFO] Task started: fastANI
[2023-06-17 01:08:54,470] [INFO] Running command: fastANI --query /var/lib/cwl/stg42a2ee87-67ca-4a03-8ed8-8926857747f9/GCA_013205645.1_ASM1320564v1_genomic.fna.gz --refList GCA_013205645.1_ASM1320564v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013205645.1_ASM1320564v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 01:09:09,491] [INFO] Task succeeded: fastANI
[2023-06-17 01:09:09,511] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 01:09:09,511] [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_013205645.1	s__Polaromonas sp013205645	100.0	603	616	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903941205.1	s__Polaromonas sp903941205	79.1688	291	616	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002379085.1	s__Polaromonas sp002379085	78.7158	255	616	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018780625.1	s__Polaromonas sp018780625	78.5615	224	616	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002379095.1	s__Polaromonas sp002379095	78.5524	257	616	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002278925.1	s__Polaromonas sp002278925	78.4468	260	616	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	99.99	99.98	0.99	0.99	5	-
GCF_000013865.1	s__Polaromonas sp000013865	78.3266	247	616	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000688115.1	s__Polaromonas sp000688115	78.3039	200	616	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103405.1	s__Polaromonas sp900103405	78.2892	261	616	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016000195.1	s__Polaromonas sp016000195	78.2717	217	616	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	98.70	98.70	0.94	0.94	2	-
GCA_012927455.1	s__Polaromonas sp012927455	78.266	233	616	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000282655.1	s__Polaromonas sp000282655	78.1715	262	616	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001598235.1	s__Polaromonas jejuensis	78.1615	249	616	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000709345.1	s__Polaromonas glacialis	78.1567	258	616	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903844825.1	s__Polaromonas sp903844825	77.9933	223	616	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903926695.1	s__Polaromonas sp903926695	77.6242	141	616	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003097105.1	s__Rhodoferax_B sp003097105	77.518	164	616	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104385.1	s__Rhodoferax_B sp900104385	77.4849	168	616	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018993155.1	s__Hydrogenophaga sp018993155	77.2128	141	616	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013387465.1	s__Hydrogenophaga aromaticivorans	77.1115	160	616	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	96.00	95.64	0.87	0.82	12	-
GCF_014489595.1	s__Acidovorax_F monticola	76.7065	133	616	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_F	95.0	97.51	97.51	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-06-17 01:09:09,513] [INFO] GTDB search result was written to GCA_013205645.1_ASM1320564v1_genomic.fna/result_gtdb.tsv
[2023-06-17 01:09:09,514] [INFO] ===== GTDB Search completed =====
[2023-06-17 01:09:09,519] [INFO] DFAST_QC result json was written to GCA_013205645.1_ASM1320564v1_genomic.fna/dqc_result.json
[2023-06-17 01:09:09,520] [INFO] DFAST_QC completed!
[2023-06-17 01:09:09,520] [INFO] Total running time: 0h1m16s