[2024-01-24 14:30:31,458] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:31,461] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:31,461] [INFO] DQC Reference Directory: /var/lib/cwl/stg6047db73-2cf9-4ca2-9378-20d03e2b9d6f/dqc_reference
[2024-01-24 14:30:33,803] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:33,805] [INFO] Task started: Prodigal
[2024-01-24 14:30:33,806] [INFO] Running command: gunzip -c /var/lib/cwl/stg1e3e1cab-7892-4929-b76d-fdb152dcce83/GCF_004214895.1_ASM421489v1_genomic.fna.gz | prodigal -d GCF_004214895.1_ASM421489v1_genomic.fna/cds.fna -a GCF_004214895.1_ASM421489v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:30:55,495] [INFO] Task succeeded: Prodigal
[2024-01-24 14:30:55,495] [INFO] Task started: HMMsearch
[2024-01-24 14:30:55,496] [INFO] Running command: hmmsearch --tblout GCF_004214895.1_ASM421489v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6047db73-2cf9-4ca2-9378-20d03e2b9d6f/dqc_reference/reference_markers.hmm GCF_004214895.1_ASM421489v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:30:55,899] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:30:55,901] [INFO] Found 6/6 markers.
[2024-01-24 14:30:55,948] [INFO] Query marker FASTA was written to GCF_004214895.1_ASM421489v1_genomic.fna/markers.fasta
[2024-01-24 14:30:55,949] [INFO] Task started: Blastn
[2024-01-24 14:30:55,949] [INFO] Running command: blastn -query GCF_004214895.1_ASM421489v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6047db73-2cf9-4ca2-9378-20d03e2b9d6f/dqc_reference/reference_markers.fasta -out GCF_004214895.1_ASM421489v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:30:56,943] [INFO] Task succeeded: Blastn
[2024-01-24 14:30:56,947] [INFO] Selected 14 target genomes.
[2024-01-24 14:30:56,947] [INFO] Target genome list was writen to GCF_004214895.1_ASM421489v1_genomic.fna/target_genomes.txt
[2024-01-24 14:30:56,957] [INFO] Task started: fastANI
[2024-01-24 14:30:56,958] [INFO] Running command: fastANI --query /var/lib/cwl/stg1e3e1cab-7892-4929-b76d-fdb152dcce83/GCF_004214895.1_ASM421489v1_genomic.fna.gz --refList GCF_004214895.1_ASM421489v1_genomic.fna/target_genomes.txt --output GCF_004214895.1_ASM421489v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:16,763] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:16,763] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6047db73-2cf9-4ca2-9378-20d03e2b9d6f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:16,764] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6047db73-2cf9-4ca2-9378-20d03e2b9d6f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:16,776] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:31:16,776] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:31:16,777] [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 alkylphenolica	strain=KL28	GCA_000746525.1	237609	237609	type	True	86.887	1350	1895	95	below_threshold
Pseudomonas vranovensis	strain=DSM 16006	GCA_000425805.1	321661	321661	type	True	86.4234	1311	1895	95	below_threshold
Pseudomonas brassicae	strain=MAFF 212427	GCA_010671725.1	2708063	2708063	type	True	85.1501	1027	1895	95	below_threshold
Pseudomonas japonica	strain=NBRC 103040	GCA_000730585.1	256466	256466	type	True	84.7141	1250	1895	95	below_threshold
Pseudomonas japonica	strain=DSM 22348	GCA_900188455.1	256466	256466	type	True	84.6418	1248	1895	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	84.4186	1209	1895	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	84.3955	1171	1895	95	below_threshold
Pseudomonas arcuscaelestis	strain=P66	GCA_016881005.1	2710591	2710591	type	True	84.3297	1250	1895	95	below_threshold
Pseudomonas bharatica	strain=CSV86	GCA_000319305.2	2692112	2692112	type	True	84.243	1178	1895	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	83.7454	1102	1895	95	below_threshold
Pseudomonas defluvii	strain=WCHP16	GCA_001695625.1	1876757	1876757	type	True	83.5737	949	1895	95	below_threshold
Pseudomonas ceruminis	strain=BML-PP028	GCA_013373895.1	2740516	2740516	type	True	83.0848	1119	1895	95	below_threshold
Pseudomonas eucalypticola	strain=NP-1	GCA_013374995.1	2599595	2599595	type	True	82.4245	972	1895	95	below_threshold
Pseudomonas allokribbensis	strain=IzPS23	GCA_014863605.1	2774460	2774460	type	True	82.1762	1112	1895	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:16,779] [INFO] DFAST Taxonomy check result was written to GCF_004214895.1_ASM421489v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:16,779] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:16,779] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:16,780] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6047db73-2cf9-4ca2-9378-20d03e2b9d6f/dqc_reference/checkm_data
[2024-01-24 14:31:16,781] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:16,836] [INFO] Task started: CheckM
[2024-01-24 14:31:16,836] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004214895.1_ASM421489v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004214895.1_ASM421489v1_genomic.fna/checkm_input GCF_004214895.1_ASM421489v1_genomic.fna/checkm_result
[2024-01-24 14:32:21,618] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:21,619] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:21,641] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:21,641] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:21,641] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004214895.1_ASM421489v1_genomic.fna/markers.fasta)
[2024-01-24 14:32:21,642] [INFO] Task started: Blastn
[2024-01-24 14:32:21,642] [INFO] Running command: blastn -query GCF_004214895.1_ASM421489v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6047db73-2cf9-4ca2-9378-20d03e2b9d6f/dqc_reference/reference_markers_gtdb.fasta -out GCF_004214895.1_ASM421489v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:23,213] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:23,218] [INFO] Selected 8 target genomes.
[2024-01-24 14:32:23,218] [INFO] Target genome list was writen to GCF_004214895.1_ASM421489v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:23,226] [INFO] Task started: fastANI
[2024-01-24 14:32:23,226] [INFO] Running command: fastANI --query /var/lib/cwl/stg1e3e1cab-7892-4929-b76d-fdb152dcce83/GCF_004214895.1_ASM421489v1_genomic.fna.gz --refList GCF_004214895.1_ASM421489v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004214895.1_ASM421489v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:35,383] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:35,393] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:35,394] [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_004214895.1	s__Pseudomonas_E sp004214895	100.0	1894	1895	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900497695.1	s__Pseudomonas_E wadenswilerensis	90.9434	1583	1895	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.26	99.26	0.95	0.95	2	-
GCF_000800615.1	s__Pseudomonas_E putida_F	90.8759	1560	1895	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.83	99.76	0.97	0.96	3	-
GCF_018417635.1	s__Pseudomonas_E sp900101695	90.752	1547	1895	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.49	97.27	0.95	0.94	5	-
GCF_000259195.1	s__Pseudomonas_E donghuensis	90.5635	1525	1895	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.33	99.30	0.94	0.92	5	-
GCF_009932335.1	s__Pseudomonas_E asiatica	83.7557	1212	1895	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0481	97.98	96.05	0.89	0.79	58	-
GCF_013179515.1	s__Pseudomonas_E sp013179515	83.3275	1056	1895	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.93	98.93	0.82	0.82	2	-
GCF_003671955.1	s__Pseudomonas_E hunanensis	83.1648	1150	1895	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.33	95.26	0.86	0.79	88	-
--------------------------------------------------------------------------------
[2024-01-24 14:32:35,396] [INFO] GTDB search result was written to GCF_004214895.1_ASM421489v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:35,397] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:35,403] [INFO] DFAST_QC result json was written to GCF_004214895.1_ASM421489v1_genomic.fna/dqc_result.json
[2024-01-24 14:32:35,403] [INFO] DFAST_QC completed!
[2024-01-24 14:32:35,403] [INFO] Total running time: 0h2m4s