[2023-06-12 22:41:16,783] [INFO] DFAST_QC pipeline started.
[2023-06-12 22:41:16,787] [INFO] DFAST_QC version: 0.5.7
[2023-06-12 22:41:16,787] [INFO] DQC Reference Directory: /var/lib/cwl/stg8b36c5a0-109f-4634-8478-c50e90e2589f/dqc_reference
[2023-06-12 22:41:19,166] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-12 22:41:19,167] [INFO] Task started: Prodigal
[2023-06-12 22:41:19,167] [INFO] Running command: gunzip -c /var/lib/cwl/stgccc9a10f-50c7-4e8f-b482-78d5fd42d8db/GCA_947449895.1_Jr-20nov17-85_genomic.fna.gz | prodigal -d GCA_947449895.1_Jr-20nov17-85_genomic.fna/cds.fna -a GCA_947449895.1_Jr-20nov17-85_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-12 22:41:27,594] [INFO] Task succeeded: Prodigal
[2023-06-12 22:41:27,595] [INFO] Task started: HMMsearch
[2023-06-12 22:41:27,595] [INFO] Running command: hmmsearch --tblout GCA_947449895.1_Jr-20nov17-85_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8b36c5a0-109f-4634-8478-c50e90e2589f/dqc_reference/reference_markers.hmm GCA_947449895.1_Jr-20nov17-85_genomic.fna/protein.faa > /dev/null
[2023-06-12 22:41:27,822] [INFO] Task succeeded: HMMsearch
[2023-06-12 22:41:27,824] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgccc9a10f-50c7-4e8f-b482-78d5fd42d8db/GCA_947449895.1_Jr-20nov17-85_genomic.fna.gz]
[2023-06-12 22:41:27,853] [INFO] Query marker FASTA was written to GCA_947449895.1_Jr-20nov17-85_genomic.fna/markers.fasta
[2023-06-12 22:41:27,854] [INFO] Task started: Blastn
[2023-06-12 22:41:27,854] [INFO] Running command: blastn -query GCA_947449895.1_Jr-20nov17-85_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b36c5a0-109f-4634-8478-c50e90e2589f/dqc_reference/reference_markers.fasta -out GCA_947449895.1_Jr-20nov17-85_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-12 22:41:28,551] [INFO] Task succeeded: Blastn
[2023-06-12 22:41:28,555] [INFO] Selected 20 target genomes.
[2023-06-12 22:41:28,556] [INFO] Target genome list was writen to GCA_947449895.1_Jr-20nov17-85_genomic.fna/target_genomes.txt
[2023-06-12 22:41:28,570] [INFO] Task started: fastANI
[2023-06-12 22:41:28,570] [INFO] Running command: fastANI --query /var/lib/cwl/stgccc9a10f-50c7-4e8f-b482-78d5fd42d8db/GCA_947449895.1_Jr-20nov17-85_genomic.fna.gz --refList GCA_947449895.1_Jr-20nov17-85_genomic.fna/target_genomes.txt --output GCA_947449895.1_Jr-20nov17-85_genomic.fna/fastani_result.tsv --threads 1
[2023-06-12 22:41:44,146] [INFO] Task succeeded: fastANI
[2023-06-12 22:41:44,146] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8b36c5a0-109f-4634-8478-c50e90e2589f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-12 22:41:44,147] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8b36c5a0-109f-4634-8478-c50e90e2589f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-12 22:41:44,165] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-06-12 22:41:44,165] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-12 22:41:44,165] [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	78.6069	289	807	95	below_threshold
Polaromonas jejuensis	strain=NBRC 106434	GCA_001598235.1	457502	457502	type	True	78.1714	310	807	95	below_threshold
Polaromonas eurypsychrophila	strain=CGMCC 1.15322	GCA_014641715.1	1614635	1614635	type	True	77.9764	299	807	95	below_threshold
Limnohabitans radicicola	strain=JUR4	GCA_014837235.1	2771427	2771427	type	True	77.0705	183	807	95	below_threshold
Hydrogenophaga aromaticivorans	strain=D2P1	GCA_013387465.1	2610898	2610898	type	True	77.002	195	807	95	below_threshold
Rhodoferax lacus	strain=IMCC26218	GCA_003415675.1	2184758	2184758	type	True	77.0017	180	807	95	below_threshold
Curvibacter lanceolatus	strain=ATCC 14669	GCA_000381265.1	86182	86182	type	True	76.9843	198	807	95	below_threshold
Acidovorax radicis	strain=N35	GCA_000204195.2	758826	758826	type	True	76.9658	169	807	95	below_threshold
Limnohabitans planktonicus	strain=II-D5	GCA_001270065.2	540060	540060	type	True	76.9579	173	807	95	below_threshold
Curvibacter gracilis	strain=ATCC BAA-807	GCA_000518645.1	230310	230310	type	True	76.936	199	807	95	below_threshold
Ramlibacter tataouinensis	strain=TTB310	GCA_000215705.1	94132	94132	type	True	76.8059	191	807	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	76.743	161	807	95	below_threshold
Acidovorax delafieldii	strain=DSM 64	GCA_007993815.1	47920	47920	type	True	76.7162	170	807	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	76.6832	174	807	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	76.6355	174	807	95	below_threshold
Variovorax gossypii	strain=DSM 100435	GCA_003965815.1	1679495	1679495	type	True	76.5106	161	807	95	below_threshold
Ramlibacter algicola	strain=CrO1	GCA_016641735.1	2795217	2795217	type	True	76.5007	141	807	95	below_threshold
Delftia acidovorans	strain=FDAARGOS_997	GCA_016127415.1	80866	80866	type	True	76.4791	164	807	95	below_threshold
Delftia acidovorans	strain=NBRC 14950	GCA_001598795.1	80866	80866	type	True	76.4303	163	807	95	below_threshold
Rhodoferax aquaticus	strain=Gr-4	GCA_006974105.1	2527691	2527691	type	True	76.406	110	807	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-12 22:41:44,167] [INFO] DFAST Taxonomy check result was written to GCA_947449895.1_Jr-20nov17-85_genomic.fna/tc_result.tsv
[2023-06-12 22:41:44,168] [INFO] ===== Taxonomy check completed =====
[2023-06-12 22:41:44,168] [INFO] ===== Start completeness check using CheckM =====
[2023-06-12 22:41:44,168] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8b36c5a0-109f-4634-8478-c50e90e2589f/dqc_reference/checkm_data
[2023-06-12 22:41:44,170] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-12 22:41:44,205] [INFO] Task started: CheckM
[2023-06-12 22:41:44,206] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947449895.1_Jr-20nov17-85_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947449895.1_Jr-20nov17-85_genomic.fna/checkm_input GCA_947449895.1_Jr-20nov17-85_genomic.fna/checkm_result
[2023-06-12 22:42:13,708] [INFO] Task succeeded: CheckM
[2023-06-12 22:42:13,709] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 41.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-12 22:42:13,729] [INFO] ===== Completeness check finished =====
[2023-06-12 22:42:13,730] [INFO] ===== Start GTDB Search =====
[2023-06-12 22:42:13,731] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947449895.1_Jr-20nov17-85_genomic.fna/markers.fasta)
[2023-06-12 22:42:13,731] [INFO] Task started: Blastn
[2023-06-12 22:42:13,731] [INFO] Running command: blastn -query GCA_947449895.1_Jr-20nov17-85_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b36c5a0-109f-4634-8478-c50e90e2589f/dqc_reference/reference_markers_gtdb.fasta -out GCA_947449895.1_Jr-20nov17-85_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-12 22:42:14,910] [INFO] Task succeeded: Blastn
[2023-06-12 22:42:14,915] [INFO] Selected 17 target genomes.
[2023-06-12 22:42:14,916] [INFO] Target genome list was writen to GCA_947449895.1_Jr-20nov17-85_genomic.fna/target_genomes_gtdb.txt
[2023-06-12 22:42:14,927] [INFO] Task started: fastANI
[2023-06-12 22:42:14,927] [INFO] Running command: fastANI --query /var/lib/cwl/stgccc9a10f-50c7-4e8f-b482-78d5fd42d8db/GCA_947449895.1_Jr-20nov17-85_genomic.fna.gz --refList GCA_947449895.1_Jr-20nov17-85_genomic.fna/target_genomes_gtdb.txt --output GCA_947449895.1_Jr-20nov17-85_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-12 22:42:27,119] [INFO] Task succeeded: fastANI
[2023-06-12 22:42:27,139] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-12 22:42:27,140] [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	86.8707	393	807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903941205.1	s__Polaromonas sp903941205	78.9779	332	807	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	78.5139	244	807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	98.70	98.70	0.94	0.94	2	-
GCA_018780625.1	s__Polaromonas sp018780625	78.5104	266	807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003711205.1	s__Polaromonas sp003711205	78.476	298	807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000709345.1	s__Polaromonas glacialis	78.4303	273	807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000013865.1	s__Polaromonas sp000013865	78.2425	292	807	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	78.1837	309	807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010365105.1	s__Polaromonas sp010365105	78.1255	272	807	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	78.1184	277	807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012927455.1	s__Polaromonas sp012927455	78.0008	292	807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014641715.1	s__Polaromonas eurypsychrophila	77.9772	299	807	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	77.8976	286	807	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	77.8205	254	807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002381615.1	s__Polaromonas sp002381615	77.7453	249	807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013387465.1	s__Hydrogenophaga aromaticivorans	76.9887	196	807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	96.00	95.64	0.87	0.82	12	-
GCF_016428875.1	s__Xylophilus sp016428875	76.967	180	807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Xylophilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-12 22:42:27,142] [INFO] GTDB search result was written to GCA_947449895.1_Jr-20nov17-85_genomic.fna/result_gtdb.tsv
[2023-06-12 22:42:27,143] [INFO] ===== GTDB Search completed =====
[2023-06-12 22:42:27,147] [INFO] DFAST_QC result json was written to GCA_947449895.1_Jr-20nov17-85_genomic.fna/dqc_result.json
[2023-06-12 22:42:27,148] [INFO] DFAST_QC completed!
[2023-06-12 22:42:27,148] [INFO] Total running time: 0h1m10s