[2024-01-25 18:20:35,775] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:20:35,776] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:20:35,776] [INFO] DQC Reference Directory: /var/lib/cwl/stg53f26901-ee8a-40f5-93e7-b076fd34ea2a/dqc_reference
[2024-01-25 18:20:36,875] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:20:36,875] [INFO] Task started: Prodigal
[2024-01-25 18:20:36,876] [INFO] Running command: gunzip -c /var/lib/cwl/stgc8d20166-8f55-4654-a639-83d9fe2c1570/GCF_900113825.1_IMG-taxon_2671180118_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900113825.1_IMG-taxon_2671180118_annotated_assembly_genomic.fna/cds.fna -a GCF_900113825.1_IMG-taxon_2671180118_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:21:01,998] [INFO] Task succeeded: Prodigal
[2024-01-25 18:21:01,999] [INFO] Task started: HMMsearch
[2024-01-25 18:21:01,999] [INFO] Running command: hmmsearch --tblout GCF_900113825.1_IMG-taxon_2671180118_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg53f26901-ee8a-40f5-93e7-b076fd34ea2a/dqc_reference/reference_markers.hmm GCF_900113825.1_IMG-taxon_2671180118_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:21:02,301] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:21:02,302] [INFO] Found 6/6 markers.
[2024-01-25 18:21:02,358] [INFO] Query marker FASTA was written to GCF_900113825.1_IMG-taxon_2671180118_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 18:21:02,359] [INFO] Task started: Blastn
[2024-01-25 18:21:02,359] [INFO] Running command: blastn -query GCF_900113825.1_IMG-taxon_2671180118_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg53f26901-ee8a-40f5-93e7-b076fd34ea2a/dqc_reference/reference_markers.fasta -out GCF_900113825.1_IMG-taxon_2671180118_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:21:03,142] [INFO] Task succeeded: Blastn
[2024-01-25 18:21:03,144] [INFO] Selected 19 target genomes.
[2024-01-25 18:21:03,144] [INFO] Target genome list was writen to GCF_900113825.1_IMG-taxon_2671180118_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 18:21:03,155] [INFO] Task started: fastANI
[2024-01-25 18:21:03,156] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8d20166-8f55-4654-a639-83d9fe2c1570/GCF_900113825.1_IMG-taxon_2671180118_annotated_assembly_genomic.fna.gz --refList GCF_900113825.1_IMG-taxon_2671180118_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900113825.1_IMG-taxon_2671180118_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:21:29,798] [INFO] Task succeeded: fastANI
[2024-01-25 18:21:29,799] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg53f26901-ee8a-40f5-93e7-b076fd34ea2a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:21:29,799] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg53f26901-ee8a-40f5-93e7-b076fd34ea2a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:21:29,810] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:21:29,810] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:21:29,811] [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
Paraburkholderia megapolitana	strain=LMG 23650	GCA_900113825.1	420953	420953	type	True	100.0	2515	2517	95	conclusive
Paraburkholderia megapolitana	strain=LMG 23650	GCA_007556815.1	420953	420953	type	True	99.9938	2515	2517	95	conclusive
Paraburkholderia acidicola	strain=ATCC 31363	GCA_002362315.1	1912599	1912599	type	True	92.6116	2036	2517	95	below_threshold
Paraburkholderia flava	strain=LD6	GCA_004359985.1	2547393	2547393	type	True	84.3664	1518	2517	95	below_threshold
Paraburkholderia monticola	strain=JC2948	GCA_001580545.1	1399968	1399968	type	True	82.5943	1141	2517	95	below_threshold
Paraburkholderia gardini	strain=LMG 32171	GCA_907164575.1	2823469	2823469	type	True	82.4974	1032	2517	95	below_threshold
Paraburkholderia ultramafica	strain=LMG 28614	GCA_902859915.1	1544867	1544867	type	True	82.4604	1093	2517	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	82.2555	1120	2517	95	below_threshold
Paraburkholderia lacunae	strain=S27	GCA_003353175.1	2211104	2211104	type	True	82.2412	1164	2517	95	below_threshold
Paraburkholderia saeva	strain=LMG 31841	GCA_907164555.1	2777537	2777537	type	True	82.1664	1057	2517	95	below_threshold
Paraburkholderia aromaticivorans	strain=BN5	GCA_002278075.1	2026199	2026199	type	True	82.0349	1152	2517	95	below_threshold
Paraburkholderia nemoris	strain=LMG 31836	GCA_905221015.1	2793076	2793076	type	True	81.8127	1233	2517	95	below_threshold
Paraburkholderia haematera	strain=LMG 31837	GCA_905220975.1	2793077	2793077	type	True	81.6883	1149	2517	95	below_threshold
Paraburkholderia domus	strain=LMG 31832	GCA_905220705.1	2793075	2793075	type	True	81.6498	1151	2517	95	below_threshold
Pandoraea sputorum	strain=DSM 21091	GCA_000814845.2	93222	93222	type	True	78.3068	443	2517	95	below_threshold
Pandoraea morbifera	strain=LMG 31116	GCA_902459575.1	2508300	2508300	type	True	77.961	448	2517	95	below_threshold
Hydrogenophilus thermoluteolus	strain=TH-1	GCA_003574215.1	297	297	type	True	75.7478	51	2517	95	below_threshold
Pseudomonas sagittaria	strain=JCM 18195	GCA_900115715.1	1135990	1135990	type	True	75.738	144	2517	95	below_threshold
Hydrogenophilus thiooxidans	strain=SS56	GCA_019049855.1	2820326	2820326	type	True	75.338	55	2517	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:21:29,812] [INFO] DFAST Taxonomy check result was written to GCF_900113825.1_IMG-taxon_2671180118_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 18:21:29,812] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:21:29,813] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:21:29,813] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg53f26901-ee8a-40f5-93e7-b076fd34ea2a/dqc_reference/checkm_data
[2024-01-25 18:21:29,813] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:21:29,883] [INFO] Task started: CheckM
[2024-01-25 18:21:29,883] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900113825.1_IMG-taxon_2671180118_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900113825.1_IMG-taxon_2671180118_annotated_assembly_genomic.fna/checkm_input GCF_900113825.1_IMG-taxon_2671180118_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 18:22:41,044] [INFO] Task succeeded: CheckM
[2024-01-25 18:22:41,045] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:22:41,067] [INFO] ===== Completeness check finished =====
[2024-01-25 18:22:41,067] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:22:41,068] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900113825.1_IMG-taxon_2671180118_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 18:22:41,068] [INFO] Task started: Blastn
[2024-01-25 18:22:41,069] [INFO] Running command: blastn -query GCF_900113825.1_IMG-taxon_2671180118_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg53f26901-ee8a-40f5-93e7-b076fd34ea2a/dqc_reference/reference_markers_gtdb.fasta -out GCF_900113825.1_IMG-taxon_2671180118_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:22:42,402] [INFO] Task succeeded: Blastn
[2024-01-25 18:22:42,406] [INFO] Selected 19 target genomes.
[2024-01-25 18:22:42,406] [INFO] Target genome list was writen to GCF_900113825.1_IMG-taxon_2671180118_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:22:42,444] [INFO] Task started: fastANI
[2024-01-25 18:22:42,444] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8d20166-8f55-4654-a639-83d9fe2c1570/GCF_900113825.1_IMG-taxon_2671180118_annotated_assembly_genomic.fna.gz --refList GCF_900113825.1_IMG-taxon_2671180118_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900113825.1_IMG-taxon_2671180118_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:23:09,859] [INFO] Task succeeded: fastANI
[2024-01-25 18:23:09,870] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:23:09,870] [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_007556815.1	s__Paraburkholderia megapolitana	99.9938	2515	2517	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_002362315.1	s__Paraburkholderia acidophila	92.6062	2037	2517	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004359985.1	s__Paraburkholderia sp004359985	84.3558	1520	2517	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011752995.1	s__Paraburkholderia sp011752995	82.5862	1101	2517	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.23	99.21	0.92	0.90	4	-
GCF_001580545.1	s__Paraburkholderia monticola	82.5821	1143	2517	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902859915.1	s__Paraburkholderia ultramafica	82.4715	1092	2517	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177725.1	s__Paraburkholderia susongensis	82.4365	1169	2517	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013366925.1	s__Paraburkholderia youngii	82.3142	1146	2517	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	97.48	97.40	0.88	0.87	5	-
GCF_014397785.1	s__Paraburkholderia sp014397785	82.2633	1118	2517	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003353175.1	s__Paraburkholderia lacunae	82.2351	1164	2517	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003443895.1	s__Paraburkholderia phosphatilytica	82.0443	1212	2517	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002278075.1	s__Paraburkholderia aromaticivorans	82.0351	1152	2517	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142845.1	s__Paraburkholderia phenazinium_A	81.9356	1312	2517	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104845.1	s__Paraburkholderia caballeronis	81.8921	1072	2517	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.48	98.95	0.97	0.92	9	-
GCF_905220975.1	s__Paraburkholderia sp905220975	81.6864	1149	2517	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003574215.1	s__Hydrogenophilus thermoluteolus	75.7478	51	2517	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Hydrogenophilus	95.0	98.30	98.30	0.97	0.97	2	-
GCF_900115715.1	s__Pseudomonas_K sagittaria	75.7449	143	2517	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019049855.1	s__Hydrogenophilus sp019049855	75.338	55	2517	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Hydrogenophilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:23:09,872] [INFO] GTDB search result was written to GCF_900113825.1_IMG-taxon_2671180118_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 18:23:09,872] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:23:09,875] [INFO] DFAST_QC result json was written to GCF_900113825.1_IMG-taxon_2671180118_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 18:23:09,875] [INFO] DFAST_QC completed!
[2024-01-25 18:23:09,876] [INFO] Total running time: 0h2m34s