[2024-01-24 13:22:14,468] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:14,470] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:14,471] [INFO] DQC Reference Directory: /var/lib/cwl/stgb1ed984d-267f-4578-a914-7e1034f239de/dqc_reference
[2024-01-24 13:22:15,707] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:15,708] [INFO] Task started: Prodigal
[2024-01-24 13:22:15,709] [INFO] Running command: gunzip -c /var/lib/cwl/stg1d2b9e1f-a00e-40a1-8057-f1a2cd353193/GCF_001042895.1_G8684_genomic.fna.gz | prodigal -d GCF_001042895.1_G8684_genomic.fna/cds.fna -a GCF_001042895.1_G8684_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:32,354] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:32,354] [INFO] Task started: HMMsearch
[2024-01-24 13:22:32,354] [INFO] Running command: hmmsearch --tblout GCF_001042895.1_G8684_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb1ed984d-267f-4578-a914-7e1034f239de/dqc_reference/reference_markers.hmm GCF_001042895.1_G8684_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:32,817] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:32,819] [INFO] Found 6/6 markers.
[2024-01-24 13:22:32,927] [INFO] Query marker FASTA was written to GCF_001042895.1_G8684_genomic.fna/markers.fasta
[2024-01-24 13:22:32,927] [INFO] Task started: Blastn
[2024-01-24 13:22:32,928] [INFO] Running command: blastn -query GCF_001042895.1_G8684_genomic.fna/markers.fasta -db /var/lib/cwl/stgb1ed984d-267f-4578-a914-7e1034f239de/dqc_reference/reference_markers.fasta -out GCF_001042895.1_G8684_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:33,930] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:33,934] [INFO] Selected 12 target genomes.
[2024-01-24 13:22:33,934] [INFO] Target genome list was writen to GCF_001042895.1_G8684_genomic.fna/target_genomes.txt
[2024-01-24 13:22:33,942] [INFO] Task started: fastANI
[2024-01-24 13:22:33,942] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d2b9e1f-a00e-40a1-8057-f1a2cd353193/GCF_001042895.1_G8684_genomic.fna.gz --refList GCF_001042895.1_G8684_genomic.fna/target_genomes.txt --output GCF_001042895.1_G8684_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:50,329] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:50,329] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb1ed984d-267f-4578-a914-7e1034f239de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:50,330] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb1ed984d-267f-4578-a914-7e1034f239de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:50,341] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:22:50,341] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:50,341] [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 deceptionensis	strain=DSM 26521	GCA_001042895.1	882211	882211	type	True	100.0	1677	1677	95	conclusive
Pseudomonas deceptionensis	strain=LMG 25555	GCA_900106095.1	882211	882211	type	True	99.9982	1676	1677	95	conclusive
Pseudomonas psychrophila	strain=CCUG 53877	GCA_008801485.1	122355	122355	type	True	89.1978	1400	1677	95	below_threshold
Pseudomonas psychrophila	strain=DSM 17535	GCA_001043005.1	122355	122355	type	True	89.1763	1410	1677	95	below_threshold
Pseudomonas fragi	strain=NBRC 3458	GCA_002091615.1	296	296	type	True	87.8387	1327	1677	95	below_threshold
Pseudomonas fragi	strain=NRRL B-727	GCA_900105835.1	296	296	type	True	87.8341	1328	1677	95	below_threshold
Pseudomonas helleri	strain=DSM 29165	GCA_001043025.1	1608996	1608996	type	True	85.0061	1132	1677	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	81.9334	945	1677	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	81.859	952	1677	95	below_threshold
Pseudomonas lurida	strain=LMG 21995	GCA_002563895.1	244566	244566	type	True	81.8288	939	1677	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	81.7145	922	1677	95	below_threshold
Pseudomonas izuensis	strain=IzPS43_3003	GCA_009861505.1	2684212	2684212	type	True	81.7037	931	1677	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:50,343] [INFO] DFAST Taxonomy check result was written to GCF_001042895.1_G8684_genomic.fna/tc_result.tsv
[2024-01-24 13:22:50,343] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:50,344] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:50,344] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb1ed984d-267f-4578-a914-7e1034f239de/dqc_reference/checkm_data
[2024-01-24 13:22:50,345] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:50,398] [INFO] Task started: CheckM
[2024-01-24 13:22:50,398] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001042895.1_G8684_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001042895.1_G8684_genomic.fna/checkm_input GCF_001042895.1_G8684_genomic.fna/checkm_result
[2024-01-24 13:23:41,595] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:41,600] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:41,627] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:41,628] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:41,628] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001042895.1_G8684_genomic.fna/markers.fasta)
[2024-01-24 13:23:41,629] [INFO] Task started: Blastn
[2024-01-24 13:23:41,629] [INFO] Running command: blastn -query GCF_001042895.1_G8684_genomic.fna/markers.fasta -db /var/lib/cwl/stgb1ed984d-267f-4578-a914-7e1034f239de/dqc_reference/reference_markers_gtdb.fasta -out GCF_001042895.1_G8684_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:43,655] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:43,659] [INFO] Selected 10 target genomes.
[2024-01-24 13:23:43,659] [INFO] Target genome list was writen to GCF_001042895.1_G8684_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:43,673] [INFO] Task started: fastANI
[2024-01-24 13:23:43,673] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d2b9e1f-a00e-40a1-8057-f1a2cd353193/GCF_001042895.1_G8684_genomic.fna.gz --refList GCF_001042895.1_G8684_genomic.fna/target_genomes_gtdb.txt --output GCF_001042895.1_G8684_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:57,390] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:57,399] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:57,400] [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_900106095.1	s__Pseudomonas_E deceptionensis	99.9982	1676	1677	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_001043005.1	s__Pseudomonas_E psychrophila	89.185	1409	1677	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.62	99.23	0.96	0.92	7	-
GCF_002269505.1	s__Pseudomonas_E fragi_D	87.858	1311	1677	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.09	96.09	0.88	0.88	2	-
GCF_900105835.1	s__Pseudomonas_E fragi	87.8341	1328	1677	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.76	96.96	0.94	0.89	28	-
GCF_900618535.1	s__Pseudomonas_E bubulae	87.5462	1320	1677	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.12	98.96	0.92	0.87	18	-
GCF_904063065.1	s__Pseudomonas_E paraversuta	86.3383	1257	1677	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.24	99.22	0.95	0.95	9	-
GCF_001294575.1	s__Pseudomonas_E versuta	86.2229	1266	1677	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.68	99.38	0.97	0.97	3	-
GCF_001043025.1	s__Pseudomonas_E helleri	85.0041	1132	1677	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.29	96.40	0.86	0.80	22	-
GCF_006438915.1	s__Pseudomonas_E arsenicoxydans_A	82.1991	949	1677	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_000968015.1	s__Pseudomonas_E fluorescens_W	82.0762	947	1677	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.19	96.19	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:57,401] [INFO] GTDB search result was written to GCF_001042895.1_G8684_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:57,402] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:57,405] [INFO] DFAST_QC result json was written to GCF_001042895.1_G8684_genomic.fna/dqc_result.json
[2024-01-24 13:23:57,405] [INFO] DFAST_QC completed!
[2024-01-24 13:23:57,406] [INFO] Total running time: 0h1m43s