[2024-01-24 14:05:34,161] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:34,162] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:34,162] [INFO] DQC Reference Directory: /var/lib/cwl/stgcc6ff843-2477-40b8-9deb-a741963bb8b8/dqc_reference
[2024-01-24 14:05:35,522] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:35,522] [INFO] Task started: Prodigal
[2024-01-24 14:05:35,523] [INFO] Running command: gunzip -c /var/lib/cwl/stg0cfdbb36-d17c-48e7-9b4a-4e6536a50912/GCF_900114705.1_IMG-taxon_2597490347_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900114705.1_IMG-taxon_2597490347_annotated_assembly_genomic.fna/cds.fna -a GCF_900114705.1_IMG-taxon_2597490347_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:55,633] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:55,633] [INFO] Task started: HMMsearch
[2024-01-24 14:05:55,633] [INFO] Running command: hmmsearch --tblout GCF_900114705.1_IMG-taxon_2597490347_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcc6ff843-2477-40b8-9deb-a741963bb8b8/dqc_reference/reference_markers.hmm GCF_900114705.1_IMG-taxon_2597490347_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:56,042] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:56,043] [INFO] Found 6/6 markers.
[2024-01-24 14:05:56,095] [INFO] Query marker FASTA was written to GCF_900114705.1_IMG-taxon_2597490347_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:05:56,095] [INFO] Task started: Blastn
[2024-01-24 14:05:56,095] [INFO] Running command: blastn -query GCF_900114705.1_IMG-taxon_2597490347_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgcc6ff843-2477-40b8-9deb-a741963bb8b8/dqc_reference/reference_markers.fasta -out GCF_900114705.1_IMG-taxon_2597490347_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:57,188] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:57,194] [INFO] Selected 22 target genomes.
[2024-01-24 14:05:57,194] [INFO] Target genome list was writen to GCF_900114705.1_IMG-taxon_2597490347_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:05:57,206] [INFO] Task started: fastANI
[2024-01-24 14:05:57,206] [INFO] Running command: fastANI --query /var/lib/cwl/stg0cfdbb36-d17c-48e7-9b4a-4e6536a50912/GCF_900114705.1_IMG-taxon_2597490347_annotated_assembly_genomic.fna.gz --refList GCF_900114705.1_IMG-taxon_2597490347_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900114705.1_IMG-taxon_2597490347_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:29,604] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:29,605] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcc6ff843-2477-40b8-9deb-a741963bb8b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:29,605] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcc6ff843-2477-40b8-9deb-a741963bb8b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:29,623] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:06:29,623] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:06:29,624] [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
Rugamonas brunnea	strain=LX20W	GCA_014042345.1	2758569	2758569	type	True	84.3906	1297	2233	95	below_threshold
Rugamonas rivuli	strain=FT103W	GCA_009380165.1	2743358	2743358	type	True	84.3134	1388	2233	95	below_threshold
Duganella aceris	strain=SAP-35	GCA_011090165.1	2703883	2703883	type	True	84.1011	1326	2233	95	below_threshold
Rugamonas aquatica	strain=FT29W	GCA_009380215.1	2743357	2743357	type	True	84.0482	1390	2233	95	below_threshold
Rugamonas fusca	strain=FT3S	GCA_014042365.1	2758568	2758568	type	True	84.0161	1289	2233	95	below_threshold
Rugamonas apoptosis	strain=LX47W	GCA_014042355.1	2758570	2758570	type	True	83.7816	1302	2233	95	below_threshold
Pseudoduganella namucuonensis	strain=CGMCC 1.11014	GCA_900116645.1	1035707	1035707	type	True	83.6587	1357	2233	95	below_threshold
Duganella callida	strain=DN04	GCA_004614165.1	2561932	2561932	type	True	83.0025	1156	2233	95	below_threshold
Duganella phyllosphaerae	strain=T54	GCA_001758785.1	762836	762836	type	True	82.506	1094	2233	95	below_threshold
Massilia glaciei	strain=B448-2	GCA_003011895.2	1524097	1524097	type	True	81.8838	996	2233	95	below_threshold
Massilia eurypsychrophila	strain=JCM 30074	GCA_002760655.1	1485217	1485217	type	True	81.8108	1052	2233	95	below_threshold
Massilia soli	strain=R798	GCA_016809835.2	2792854	2792854	type	True	81.5636	919	2233	95	below_threshold
Janthinobacterium psychrotolerans	strain=S3-2	GCA_001677885.1	1747903	1747903	type	True	81.5291	1099	2233	95	below_threshold
Janthinobacterium agaricidamnosum	strain=NBRC 102515	GCA_001571185.1	55508	55508	type	True	81.2599	1023	2233	95	below_threshold
Massilia frigida	strain=CCM 8695	GCA_011682175.1	2609281	2609281	type	True	81.1516	1146	2233	95	below_threshold
Massilia violaceinigra	strain=B2	GCA_002752675.1	2045208	2045208	type	True	80.9304	1121	2233	95	below_threshold
Aquabacterium olei	strain=NBRC 110486	GCA_003100395.1	1296669	1296669	type	True	77.5692	429	2233	95	below_threshold
Pelomonas saccharophila	strain=DSM 654	GCA_004342485.1	304	304	type	True	77.0208	687	2233	95	below_threshold
Roseateles depolymerans	strain=DSM 11813	GCA_003387155.1	76731	76731	type	True	77.0112	434	2233	95	below_threshold
Pelomonas puraquae	strain=CCUG 52769	GCA_002205845.1	431059	431059	type	True	76.9486	589	2233	95	below_threshold
Aquamicrobium defluvii	strain=DSM 11603	GCA_004363725.1	69279	69279	type	True	75.5544	146	2233	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:29,625] [INFO] DFAST Taxonomy check result was written to GCF_900114705.1_IMG-taxon_2597490347_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:06:29,626] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:29,626] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:29,626] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcc6ff843-2477-40b8-9deb-a741963bb8b8/dqc_reference/checkm_data
[2024-01-24 14:06:29,628] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:29,692] [INFO] Task started: CheckM
[2024-01-24 14:06:29,692] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900114705.1_IMG-taxon_2597490347_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900114705.1_IMG-taxon_2597490347_annotated_assembly_genomic.fna/checkm_input GCF_900114705.1_IMG-taxon_2597490347_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:07:26,551] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:26,553] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:26,571] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:26,572] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:26,572] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900114705.1_IMG-taxon_2597490347_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:07:26,572] [INFO] Task started: Blastn
[2024-01-24 14:07:26,572] [INFO] Running command: blastn -query GCF_900114705.1_IMG-taxon_2597490347_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgcc6ff843-2477-40b8-9deb-a741963bb8b8/dqc_reference/reference_markers_gtdb.fasta -out GCF_900114705.1_IMG-taxon_2597490347_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:28,365] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:28,368] [INFO] Selected 24 target genomes.
[2024-01-24 14:07:28,369] [INFO] Target genome list was writen to GCF_900114705.1_IMG-taxon_2597490347_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:28,411] [INFO] Task started: fastANI
[2024-01-24 14:07:28,411] [INFO] Running command: fastANI --query /var/lib/cwl/stg0cfdbb36-d17c-48e7-9b4a-4e6536a50912/GCF_900114705.1_IMG-taxon_2597490347_annotated_assembly_genomic.fna.gz --refList GCF_900114705.1_IMG-taxon_2597490347_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900114705.1_IMG-taxon_2597490347_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:08:09,360] [INFO] Task succeeded: fastANI
[2024-01-24 14:08:09,376] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:08:09,376] [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_900114705.1	s__Rugamonas rubra	100.0	2232	2233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rugamonas	95.0	96.24	96.24	0.86	0.86	2	conclusive
GCF_016461825.1	s__Rugamonas sp016461825	92.8003	1799	2233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rugamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003416985.1	s__Duganella sp003416985	84.8572	1411	2233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	97.63	95.41	0.92	0.79	7	-
GCA_000381565.1	s__Duganella sp000381565	84.6425	1429	2233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	95.03	95.03	0.82	0.82	2	-
GCF_013375995.1	s__Duganella sp013375995	84.485	1352	2233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014042345.1	s__LX47W sp014042345	84.434	1291	2233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__LX47W	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003416895.1	s__Duganella sp003416895	84.3537	1388	2233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	99.92	99.92	0.99	0.99	2	-
GCF_017833525.1	s__Duganella sp017833525	84.2231	1393	2233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000344615.1	s__Janthinobacterium sp000344615	84.1172	1314	2233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Janthinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011090165.1	s__Duganella aceris	84.1065	1325	2233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013284265.1	s__Rugamonas sp013284265	84.0963	1387	2233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rugamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014042365.1	s__LX47W sp014042365	84.0105	1291	2233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__LX47W	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110275.1	s__Duganella sp900110275	83.907	1336	2233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014379395.1	s__Janthinobacterium sp014379395	83.7713	583	2233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Janthinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116645.1	s__Pseudoduganella namucuonensis	83.6661	1355	2233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013376005.1	s__Duganella sp013376005	83.4336	1292	2233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009674565.1	s__Duganella rivi	83.2768	1254	2233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.1471	N/A	N/A	N/A	N/A	1	-
GCF_015352985.1	s__Noviherbaspirillum malthae	79.2413	620	2233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001598255.1	s__Mitsuaria chitosanitabida	77.3965	661	2233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mitsuaria	95.0	99.05	99.05	0.96	0.96	2	-
GCF_004342485.1	s__Pelomonas saccharophila	77.0211	689	2233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900119315.1	s__Actinoplanes sp900119315	74.8192	419	2233	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:08:09,378] [INFO] GTDB search result was written to GCF_900114705.1_IMG-taxon_2597490347_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:08:09,379] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:08:09,383] [INFO] DFAST_QC result json was written to GCF_900114705.1_IMG-taxon_2597490347_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:08:09,383] [INFO] DFAST_QC completed!
[2024-01-24 14:08:09,384] [INFO] Total running time: 0h2m35s