[2024-01-24 12:29:18,840] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:18,843] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:18,843] [INFO] DQC Reference Directory: /var/lib/cwl/stg7b93fa6f-9241-492e-9fcd-184a682cc783/dqc_reference
[2024-01-24 12:29:20,037] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:20,038] [INFO] Task started: Prodigal
[2024-01-24 12:29:20,038] [INFO] Running command: gunzip -c /var/lib/cwl/stg81739102-f67c-4fd8-b2c2-2dfe79313cd4/GCF_002563335.1_ASM256333v1_genomic.fna.gz | prodigal -d GCF_002563335.1_ASM256333v1_genomic.fna/cds.fna -a GCF_002563335.1_ASM256333v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:29:38,237] [INFO] Task succeeded: Prodigal
[2024-01-24 12:29:38,238] [INFO] Task started: HMMsearch
[2024-01-24 12:29:38,238] [INFO] Running command: hmmsearch --tblout GCF_002563335.1_ASM256333v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7b93fa6f-9241-492e-9fcd-184a682cc783/dqc_reference/reference_markers.hmm GCF_002563335.1_ASM256333v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:29:38,529] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:29:38,531] [INFO] Found 6/6 markers.
[2024-01-24 12:29:38,586] [INFO] Query marker FASTA was written to GCF_002563335.1_ASM256333v1_genomic.fna/markers.fasta
[2024-01-24 12:29:38,586] [INFO] Task started: Blastn
[2024-01-24 12:29:38,586] [INFO] Running command: blastn -query GCF_002563335.1_ASM256333v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b93fa6f-9241-492e-9fcd-184a682cc783/dqc_reference/reference_markers.fasta -out GCF_002563335.1_ASM256333v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:39,601] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:39,606] [INFO] Selected 15 target genomes.
[2024-01-24 12:29:39,606] [INFO] Target genome list was writen to GCF_002563335.1_ASM256333v1_genomic.fna/target_genomes.txt
[2024-01-24 12:29:39,639] [INFO] Task started: fastANI
[2024-01-24 12:29:39,639] [INFO] Running command: fastANI --query /var/lib/cwl/stg81739102-f67c-4fd8-b2c2-2dfe79313cd4/GCF_002563335.1_ASM256333v1_genomic.fna.gz --refList GCF_002563335.1_ASM256333v1_genomic.fna/target_genomes.txt --output GCF_002563335.1_ASM256333v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:29:59,216] [INFO] Task succeeded: fastANI
[2024-01-24 12:29:59,216] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7b93fa6f-9241-492e-9fcd-184a682cc783/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:29:59,217] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7b93fa6f-9241-492e-9fcd-184a682cc783/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:29:59,239] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:29:59,239] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:29:59,240] [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 aeruginosa	strain=DSM 50071	GCA_001042925.1	287	287	type	True	93.9345	1802	2087	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_012987025.1	287	287	type	True	93.926	1803	2087	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_001045685.1	287	287	type	True	93.9004	1802	2087	95	below_threshold
Pseudomonas aeruginosa	strain=NCTC10332	GCA_001457615.1	287	287	type	True	93.9	1809	2087	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_900167195.1	287	287	type	True	93.8787	1795	2087	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	93.8751	1833	2087	95	below_threshold
Pseudomonas aeruginosa	strain=CCUG 551	GCA_008801675.1	287	287	type	True	93.8576	1804	2087	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	93.8423	1808	2087	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	83.0163	928	2087	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	82.1854	768	2087	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	82.0383	991	2087	95	below_threshold
Pseudomonas flexibilis	strain=ATCC 29606	GCA_000802425.1	706570	706570	type	True	81.55	744	2087	95	below_threshold
Pseudomonas flexibilis	strain=ATCC 29606	GCA_900155995.1	706570	706570	type	True	81.5357	744	2087	95	below_threshold
Pseudomonas salomonii	strain=LMG 22120	GCA_001730645.1	191391	191391	type	True	79.3613	799	2087	95	below_threshold
Pseudomonas salomonii	strain=ICMP 14252	GCA_900107155.1	191391	191391	type	True	79.2667	819	2087	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:29:59,241] [INFO] DFAST Taxonomy check result was written to GCF_002563335.1_ASM256333v1_genomic.fna/tc_result.tsv
[2024-01-24 12:29:59,242] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:29:59,243] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:29:59,243] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7b93fa6f-9241-492e-9fcd-184a682cc783/dqc_reference/checkm_data
[2024-01-24 12:29:59,244] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:29:59,306] [INFO] Task started: CheckM
[2024-01-24 12:29:59,306] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002563335.1_ASM256333v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002563335.1_ASM256333v1_genomic.fna/checkm_input GCF_002563335.1_ASM256333v1_genomic.fna/checkm_result
[2024-01-24 12:30:51,931] [INFO] Task succeeded: CheckM
[2024-01-24 12:30:51,932] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:30:51,963] [INFO] ===== Completeness check finished =====
[2024-01-24 12:30:51,964] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:30:51,964] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002563335.1_ASM256333v1_genomic.fna/markers.fasta)
[2024-01-24 12:30:51,964] [INFO] Task started: Blastn
[2024-01-24 12:30:51,965] [INFO] Running command: blastn -query GCF_002563335.1_ASM256333v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b93fa6f-9241-492e-9fcd-184a682cc783/dqc_reference/reference_markers_gtdb.fasta -out GCF_002563335.1_ASM256333v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:53,803] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:53,808] [INFO] Selected 19 target genomes.
[2024-01-24 12:30:53,808] [INFO] Target genome list was writen to GCF_002563335.1_ASM256333v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:30:53,840] [INFO] Task started: fastANI
[2024-01-24 12:30:53,840] [INFO] Running command: fastANI --query /var/lib/cwl/stg81739102-f67c-4fd8-b2c2-2dfe79313cd4/GCF_002563335.1_ASM256333v1_genomic.fna.gz --refList GCF_002563335.1_ASM256333v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002563335.1_ASM256333v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:31:18,002] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:18,024] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:31:18,025] [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_000017205.1	s__Pseudomonas aeruginosa_A	98.8633	1964	2087	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	99.07	98.78	0.93	0.80	42	conclusive
GCF_001457615.1	s__Pseudomonas aeruginosa	93.891	1809	2087	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	99.12	97.38	0.94	0.84	5623	-
GCF_900187975.1	s__Pseudomonas delhiensis	85.1219	1333	2087	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.078	98.79	97.59	0.94	0.89	3	-
GCF_900103845.1	s__Pseudomonas jinjuensis	85.0428	1146	2087	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900112375.1	s__Pseudomonas citronellolis	84.9266	1319	2087	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.078	97.44	97.08	0.86	0.82	26	-
GCF_014204515.1	s__Pseudomonas nitritireducens_A	84.0592	1299	2087	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017491605.1	s__Pseudomonas sp017491605	84.0228	1191	2087	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009189165.1	s__Pseudomonas sp009189165	83.7782	1189	2087	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018398425.1	s__Pseudomonas_E lalucatii	83.0343	926	2087	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.68	99.28	0.97	0.92	4	-
GCF_003696305.1	s__Pseudomonas_E sp003696305	82.9265	1032	2087	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_004801855.1	s__Pseudomonas_K sp004801855	82.7296	759	2087	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	98.38	98.38	0.89	0.89	2	-
GCF_900100495.1	s__Pseudomonas_E benzenivorans	82.6517	1053	2087	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002483005.1	s__Pseudomonas_E sp002483005	82.5421	554	2087	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_900104805.1	s__Pseudomonas_K oryzae	82.4506	856	2087	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_900105885.1	s__Pseudomonas_K guangdongensis	82.4062	732	2087	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	98.99	98.99	0.99	0.99	2	-
GCF_000016565.1	s__Pseudomonas_E mendocina_A	82.0512	981	2087	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.76	97.37	0.90	0.88	7	-
GCF_014522265.1	s__Pseudomonas_B oryzihabitans_D	80.4627	766	2087	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	96.63	95.05	0.89	0.84	6	-
GCF_900115905.1	s__Pseudomonas_D formosensis	79.0942	448	2087	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	98.74	98.74	0.94	0.94	2	-
GCF_900111735.1	s__Pseudomonas_E graminis	78.9995	655	2087	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.28	98.01	0.93	0.92	4	-
--------------------------------------------------------------------------------
[2024-01-24 12:31:18,026] [INFO] GTDB search result was written to GCF_002563335.1_ASM256333v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:31:18,029] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:31:18,032] [INFO] DFAST_QC result json was written to GCF_002563335.1_ASM256333v1_genomic.fna/dqc_result.json
[2024-01-24 12:31:18,032] [INFO] DFAST_QC completed!
[2024-01-24 12:31:18,033] [INFO] Total running time: 0h1m59s