[2024-01-25 19:41:20,870] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:41:20,872] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:41:20,872] [INFO] DQC Reference Directory: /var/lib/cwl/stg2c252fde-97da-4759-aef5-96e8d0273c21/dqc_reference
[2024-01-25 19:41:21,970] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:41:21,971] [INFO] Task started: Prodigal
[2024-01-25 19:41:21,971] [INFO] Running command: gunzip -c /var/lib/cwl/stg4fac0446-539b-40c8-85f6-9e122c8bfc87/GCF_900205755.1_IMG-taxon_2710724120_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900205755.1_IMG-taxon_2710724120_annotated_assembly_genomic.fna/cds.fna -a GCF_900205755.1_IMG-taxon_2710724120_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:41:26,120] [INFO] Task succeeded: Prodigal
[2024-01-25 19:41:26,121] [INFO] Task started: HMMsearch
[2024-01-25 19:41:26,121] [INFO] Running command: hmmsearch --tblout GCF_900205755.1_IMG-taxon_2710724120_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2c252fde-97da-4759-aef5-96e8d0273c21/dqc_reference/reference_markers.hmm GCF_900205755.1_IMG-taxon_2710724120_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:41:26,302] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:41:26,303] [INFO] Found 6/6 markers.
[2024-01-25 19:41:26,322] [INFO] Query marker FASTA was written to GCF_900205755.1_IMG-taxon_2710724120_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 19:41:26,322] [INFO] Task started: Blastn
[2024-01-25 19:41:26,322] [INFO] Running command: blastn -query GCF_900205755.1_IMG-taxon_2710724120_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c252fde-97da-4759-aef5-96e8d0273c21/dqc_reference/reference_markers.fasta -out GCF_900205755.1_IMG-taxon_2710724120_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:41:26,945] [INFO] Task succeeded: Blastn
[2024-01-25 19:41:26,948] [INFO] Selected 19 target genomes.
[2024-01-25 19:41:26,948] [INFO] Target genome list was writen to GCF_900205755.1_IMG-taxon_2710724120_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 19:41:26,982] [INFO] Task started: fastANI
[2024-01-25 19:41:26,982] [INFO] Running command: fastANI --query /var/lib/cwl/stg4fac0446-539b-40c8-85f6-9e122c8bfc87/GCF_900205755.1_IMG-taxon_2710724120_annotated_assembly_genomic.fna.gz --refList GCF_900205755.1_IMG-taxon_2710724120_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900205755.1_IMG-taxon_2710724120_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:41:34,392] [INFO] Task succeeded: fastANI
[2024-01-25 19:41:34,393] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2c252fde-97da-4759-aef5-96e8d0273c21/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:41:34,393] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2c252fde-97da-4759-aef5-96e8d0273c21/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:41:34,402] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:41:34,402] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:41:34,403] [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
Polynucleobacter meluiroseus	strain=AP-Melu-1000-B4	GCA_900205755.1	1938814	1938814	type	True	100.0	625	625	95	conclusive
Polynucleobacter campilacus	strain=MWH-Feld-100	GCA_002206625.1	1743163	1743163	type	True	79.7432	219	625	95	below_threshold
Polynucleobacter sphagniphilus	strain=MWH-Weng1-1	GCA_001953355.1	1743169	1743169	type	True	79.4368	205	625	95	below_threshold
Polynucleobacter arcticus	strain=UK-Long2-W17	GCA_013307205.1	1743165	1743165	type	True	79.3393	225	625	95	below_threshold
Polynucleobacter aenigmaticus	strain=MWH-K35W1	GCA_002206635.1	1743164	1743164	type	True	79.2396	220	625	95	below_threshold
Polynucleobacter hallstattensis	strain=MWH-Hall10	GCA_018881835.1	1855586	1855586	type	True	79.2274	219	625	95	below_threshold
Polynucleobacter paludilacus	strain=MWH-Mekk-C3	GCA_018687595.1	1855895	1855895	type	True	79.2119	162	625	95	below_threshold
Polynucleobacter finlandensis	strain=MWH-Mekk-B1	GCA_018881755.1	1855894	1855894	type	True	79.184	214	625	95	below_threshold
Polynucleobacter corsicus	strain=AP-Melu-1000-A1	GCA_018688255.1	2081042	2081042	type	True	79.1791	219	625	95	below_threshold
Polynucleobacter hirudinilacicola	strain=MWH-EgelM1-30-B4	GCA_002192535.1	1743166	1743166	type	True	79.1064	198	625	95	below_threshold
Polynucleobacter alcilacus	strain=UK-Pondora-W15	GCA_018881545.1	1819739	1819739	type	True	79.069	208	625	95	below_threshold
Polynucleobacter parvulilacunae	strain=Ross1-W9	GCA_018881715.1	1855631	1855631	type	True	79.0269	208	625	95	below_threshold
Polynucleobacter duraquae	strain=MWH-MoK4	GCA_000973625.1	1835254	1835254	type	True	78.9626	220	625	95	below_threshold
Polynucleobacter bastaniensis	strain=AP-Basta-1000A-D1	GCA_018882205.1	2081039	2081039	type	True	78.9625	218	625	95	below_threshold
Polynucleobacter antarcticus	strain=LimPoW16	GCA_013307245.1	1743162	1743162	type	True	78.8543	206	625	95	below_threshold
Polynucleobacter nymphae	strain=AP-Mumm-500A-B3	GCA_018882155.1	2081043	2081043	type	True	78.6709	217	625	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:41:34,404] [INFO] DFAST Taxonomy check result was written to GCF_900205755.1_IMG-taxon_2710724120_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 19:41:34,404] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:41:34,404] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:41:34,405] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2c252fde-97da-4759-aef5-96e8d0273c21/dqc_reference/checkm_data
[2024-01-25 19:41:34,405] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:41:34,426] [INFO] Task started: CheckM
[2024-01-25 19:41:34,427] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900205755.1_IMG-taxon_2710724120_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900205755.1_IMG-taxon_2710724120_annotated_assembly_genomic.fna/checkm_input GCF_900205755.1_IMG-taxon_2710724120_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 19:41:53,161] [INFO] Task succeeded: CheckM
[2024-01-25 19:41:53,162] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:41:53,180] [INFO] ===== Completeness check finished =====
[2024-01-25 19:41:53,180] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:41:53,180] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900205755.1_IMG-taxon_2710724120_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 19:41:53,180] [INFO] Task started: Blastn
[2024-01-25 19:41:53,180] [INFO] Running command: blastn -query GCF_900205755.1_IMG-taxon_2710724120_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c252fde-97da-4759-aef5-96e8d0273c21/dqc_reference/reference_markers_gtdb.fasta -out GCF_900205755.1_IMG-taxon_2710724120_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:41:54,259] [INFO] Task succeeded: Blastn
[2024-01-25 19:41:54,262] [INFO] Selected 25 target genomes.
[2024-01-25 19:41:54,262] [INFO] Target genome list was writen to GCF_900205755.1_IMG-taxon_2710724120_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:41:54,295] [INFO] Task started: fastANI
[2024-01-25 19:41:54,295] [INFO] Running command: fastANI --query /var/lib/cwl/stg4fac0446-539b-40c8-85f6-9e122c8bfc87/GCF_900205755.1_IMG-taxon_2710724120_annotated_assembly_genomic.fna.gz --refList GCF_900205755.1_IMG-taxon_2710724120_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900205755.1_IMG-taxon_2710724120_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:42:04,221] [INFO] Task succeeded: fastANI
[2024-01-25 19:42:04,235] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:42:04,236] [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_900205755.1	s__Polynucleobacter meluiroseus	100.0	625	625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018882405.1	s__Polynucleobacter sp018882405	79.6383	214	625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000342265.1	s__Polynucleobacter sp000342265	79.4427	220	625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018687355.1	s__Polynucleobacter sp018687355	79.326	192	625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001830325.1	s__Polynucleobacter sp001830325	79.3185	211	625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_018688495.1	s__Polynucleobacter sp018688495	79.2926	204	625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	97.81	97.81	0.94	0.94	2	-
GCF_018688335.1	s__Polynucleobacter sp018688335	79.2925	219	625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	95.20	95.20	0.89	0.89	2	-
GCF_018882325.1	s__Polynucleobacter sp018882325	79.2818	238	625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018881795.1	s__Polynucleobacter sp018881795	79.2516	197	625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002206635.1	s__Polynucleobacter aenigmaticus	79.2508	219	625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018882335.1	s__Polynucleobacter sp018882335	79.2482	214	625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018882085.1	s__Polynucleobacter sp018882085	79.2331	212	625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018688255.1	s__Polynucleobacter sp018688255	79.1901	218	625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018687675.1	s__Polynucleobacter sp018687675	79.185	225	625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018882055.1	s__Polynucleobacter sp018882055	79.1632	220	625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018881755.1	s__Polynucleobacter sp903953215	79.1622	215	625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	98.19	97.38	0.93	0.86	15	-
GCF_018687495.1	s__Polynucleobacter sp018687495	79.1266	191	625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	97.99	97.99	0.89	0.89	2	-
GCF_018688375.1	s__Polynucleobacter sp018688375	79.1102	229	625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018881545.1	s__Polynucleobacter sp018881545	79.092	206	625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018881605.1	s__Polynucleobacter sp018881605	79.0644	194	625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018881635.1	s__Polynucleobacter sp018881635	79.0547	194	625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018882245.1	s__Polynucleobacter sp018882245	79.0233	216	625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903846025.1	s__Polynucleobacter sp903846025	78.3105	186	625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	99.61	99.36	0.89	0.81	20	-
GCA_903827075.1	s__Polynucleobacter sp903827075	78.2262	215	625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	99.13	99.03	0.84	0.82	6	-
GCA_903843235.1	s__Polynucleobacter sp903843235	78.0747	149	625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	99.64	99.31	0.88	0.84	5	-
--------------------------------------------------------------------------------
[2024-01-25 19:42:04,237] [INFO] GTDB search result was written to GCF_900205755.1_IMG-taxon_2710724120_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 19:42:04,238] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:42:04,242] [INFO] DFAST_QC result json was written to GCF_900205755.1_IMG-taxon_2710724120_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 19:42:04,242] [INFO] DFAST_QC completed!
[2024-01-25 19:42:04,242] [INFO] Total running time: 0h0m43s