[2024-01-24 12:30:49,302] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:30:49,304] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:30:49,304] [INFO] DQC Reference Directory: /var/lib/cwl/stg4a38b134-8d3c-4c54-b25e-49a2eb102c0c/dqc_reference
[2024-01-24 12:30:50,494] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:30:50,495] [INFO] Task started: Prodigal
[2024-01-24 12:30:50,495] [INFO] Running command: gunzip -c /var/lib/cwl/stge167f042-43d0-4a51-9e48-78f76d2cbf20/GCF_900102335.1_IMG-taxon_2671180043_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900102335.1_IMG-taxon_2671180043_annotated_assembly_genomic.fna/cds.fna -a GCF_900102335.1_IMG-taxon_2671180043_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:04,386] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:04,387] [INFO] Task started: HMMsearch
[2024-01-24 12:31:04,387] [INFO] Running command: hmmsearch --tblout GCF_900102335.1_IMG-taxon_2671180043_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4a38b134-8d3c-4c54-b25e-49a2eb102c0c/dqc_reference/reference_markers.hmm GCF_900102335.1_IMG-taxon_2671180043_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:04,683] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:04,685] [INFO] Found 6/6 markers.
[2024-01-24 12:31:04,728] [INFO] Query marker FASTA was written to GCF_900102335.1_IMG-taxon_2671180043_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:31:04,728] [INFO] Task started: Blastn
[2024-01-24 12:31:04,728] [INFO] Running command: blastn -query GCF_900102335.1_IMG-taxon_2671180043_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a38b134-8d3c-4c54-b25e-49a2eb102c0c/dqc_reference/reference_markers.fasta -out GCF_900102335.1_IMG-taxon_2671180043_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:05,780] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:05,784] [INFO] Selected 11 target genomes.
[2024-01-24 12:31:05,785] [INFO] Target genome list was writen to GCF_900102335.1_IMG-taxon_2671180043_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:31:05,791] [INFO] Task started: fastANI
[2024-01-24 12:31:05,791] [INFO] Running command: fastANI --query /var/lib/cwl/stge167f042-43d0-4a51-9e48-78f76d2cbf20/GCF_900102335.1_IMG-taxon_2671180043_annotated_assembly_genomic.fna.gz --refList GCF_900102335.1_IMG-taxon_2671180043_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900102335.1_IMG-taxon_2671180043_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:18,781] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:18,782] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4a38b134-8d3c-4c54-b25e-49a2eb102c0c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:18,782] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4a38b134-8d3c-4c54-b25e-49a2eb102c0c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:18,796] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:31:18,797] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:31:18,797] [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
Pseudomonas flavescens	strain=LMG 18387	GCA_900100535.1	29435	29435	type	True	85.8244	1191	1509	95	below_threshold
Pseudomonas flavescens	strain=NBRC 103044	GCA_002091575.1	29435	29435	type	True	85.7733	1189	1509	95	below_threshold
Pseudomonas argentinensis	strain=LMG 22563	GCA_900113905.1	289370	289370	type	True	85.4651	1204	1509	95	below_threshold
Pseudomonas argentinensis	strain=CCUG 50743	GCA_008801645.1	289370	289370	type	True	85.3903	1202	1509	95	below_threshold
Pseudomonas punonensis	strain=CECT 8089	GCA_900142655.1	1220495	1220495	type	True	85.2275	1184	1509	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	81.6472	738	1509	95	below_threshold
Pseudomonas brassicae	strain=MAFF 212427	GCA_010671725.1	2708063	2708063	type	True	80.3495	592	1509	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	79.6839	680	1509	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	79.6836	667	1509	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	79.4937	608	1509	95	below_threshold
Pseudomonas lurida	strain=LMG 21995	GCA_002563895.1	244566	244566	type	True	79.4605	630	1509	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:18,799] [INFO] DFAST Taxonomy check result was written to GCF_900102335.1_IMG-taxon_2671180043_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:31:18,799] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:18,800] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:18,800] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4a38b134-8d3c-4c54-b25e-49a2eb102c0c/dqc_reference/checkm_data
[2024-01-24 12:31:18,801] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:18,844] [INFO] Task started: CheckM
[2024-01-24 12:31:18,844] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900102335.1_IMG-taxon_2671180043_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900102335.1_IMG-taxon_2671180043_annotated_assembly_genomic.fna/checkm_input GCF_900102335.1_IMG-taxon_2671180043_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:32:01,801] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:01,802] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:01,824] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:01,824] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:01,825] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900102335.1_IMG-taxon_2671180043_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:32:01,825] [INFO] Task started: Blastn
[2024-01-24 12:32:01,825] [INFO] Running command: blastn -query GCF_900102335.1_IMG-taxon_2671180043_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a38b134-8d3c-4c54-b25e-49a2eb102c0c/dqc_reference/reference_markers_gtdb.fasta -out GCF_900102335.1_IMG-taxon_2671180043_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:03,711] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:03,715] [INFO] Selected 11 target genomes.
[2024-01-24 12:32:03,715] [INFO] Target genome list was writen to GCF_900102335.1_IMG-taxon_2671180043_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:03,730] [INFO] Task started: fastANI
[2024-01-24 12:32:03,731] [INFO] Running command: fastANI --query /var/lib/cwl/stge167f042-43d0-4a51-9e48-78f76d2cbf20/GCF_900102335.1_IMG-taxon_2671180043_annotated_assembly_genomic.fna.gz --refList GCF_900102335.1_IMG-taxon_2671180043_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900102335.1_IMG-taxon_2671180043_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:17,387] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:17,406] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:17,407] [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_900102335.1	s__Pseudomonas_E seleniipraecipitans	100.0	1508	1509	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.06	98.05	0.91	0.90	3	conclusive
GCF_013408425.1	s__Pseudomonas_E fulva_A	86.5599	1269	1509	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.00	99.00	0.95	0.95	2	-
GCF_004327285.1	s__Pseudomonas_E daroniae	86.2463	1169	1509	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.54	98.61	0.97	0.93	4	-
GCF_900100535.1	s__Pseudomonas_E flavescens	85.8335	1190	1509	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001839655.1	s__Pseudomonas_E argentinensis_B	85.5661	1206	1509	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003253735.1	s__Pseudomonas_E sp003253735	85.507	1235	1509	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.17	98.17	0.95	0.95	2	-
GCF_900113905.1	s__Pseudomonas_E argentinensis	85.4743	1203	1509	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000213805.1	s__Pseudomonas_E fulva_B	85.331	1171	1509	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.53	96.12	0.92	0.90	6	-
GCF_900142655.1	s__Pseudomonas_E punonensis	85.2301	1183	1509	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001945395.1	s__Pseudomonas_E sp001945395	85.018	1196	1509	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004327355.1	s__Pseudomonas_E dryadis	83.8844	1083	1509	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.58	99.16	0.96	0.92	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:17,410] [INFO] GTDB search result was written to GCF_900102335.1_IMG-taxon_2671180043_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:17,411] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:17,414] [INFO] DFAST_QC result json was written to GCF_900102335.1_IMG-taxon_2671180043_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:32:17,414] [INFO] DFAST_QC completed!
[2024-01-24 12:32:17,414] [INFO] Total running time: 0h1m28s