[2024-01-24 13:40:55,426] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:55,428] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:55,428] [INFO] DQC Reference Directory: /var/lib/cwl/stg17ff0e9e-04d6-4dae-ac73-666601c460a7/dqc_reference
[2024-01-24 13:40:56,668] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:56,668] [INFO] Task started: Prodigal
[2024-01-24 13:40:56,669] [INFO] Running command: gunzip -c /var/lib/cwl/stg20146f43-0372-4501-9232-bbbeea60b02e/GCF_012987025.1_ASM1298702v1_genomic.fna.gz | prodigal -d GCF_012987025.1_ASM1298702v1_genomic.fna/cds.fna -a GCF_012987025.1_ASM1298702v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:12,631] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:12,631] [INFO] Task started: HMMsearch
[2024-01-24 13:41:12,631] [INFO] Running command: hmmsearch --tblout GCF_012987025.1_ASM1298702v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg17ff0e9e-04d6-4dae-ac73-666601c460a7/dqc_reference/reference_markers.hmm GCF_012987025.1_ASM1298702v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:13,016] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:13,017] [INFO] Found 6/6 markers.
[2024-01-24 13:41:13,065] [INFO] Query marker FASTA was written to GCF_012987025.1_ASM1298702v1_genomic.fna/markers.fasta
[2024-01-24 13:41:13,065] [INFO] Task started: Blastn
[2024-01-24 13:41:13,065] [INFO] Running command: blastn -query GCF_012987025.1_ASM1298702v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg17ff0e9e-04d6-4dae-ac73-666601c460a7/dqc_reference/reference_markers.fasta -out GCF_012987025.1_ASM1298702v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:14,096] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:14,108] [INFO] Selected 11 target genomes.
[2024-01-24 13:41:14,109] [INFO] Target genome list was writen to GCF_012987025.1_ASM1298702v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:14,111] [INFO] Task started: fastANI
[2024-01-24 13:41:14,112] [INFO] Running command: fastANI --query /var/lib/cwl/stg20146f43-0372-4501-9232-bbbeea60b02e/GCF_012987025.1_ASM1298702v1_genomic.fna.gz --refList GCF_012987025.1_ASM1298702v1_genomic.fna/target_genomes.txt --output GCF_012987025.1_ASM1298702v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:30,319] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:30,319] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg17ff0e9e-04d6-4dae-ac73-666601c460a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:30,320] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg17ff0e9e-04d6-4dae-ac73-666601c460a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:30,328] [INFO] Found 11 fastANI hits (8 hits with ANI > threshold)
[2024-01-24 13:41:30,328] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:30,328] [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_012987025.1	287	287	type	True	100.0	2080	2082	95	conclusive
Pseudomonas aeruginosa	strain=DSM 50071	GCA_001042925.1	287	287	type	True	100.0	2080	2082	95	conclusive
Pseudomonas aeruginosa	strain=DSM 50071	GCA_001045685.1	287	287	type	True	99.9998	2081	2082	95	conclusive
Pseudomonas aeruginosa	strain=NCTC10332	GCA_001457615.1	287	287	type	True	99.9972	2082	2082	95	conclusive
Pseudomonas aeruginosa	strain=DSM 50071	GCA_900167195.1	287	287	type	True	99.9819	2038	2082	95	conclusive
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	99.399	2022	2082	95	conclusive
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	99.3649	2003	2082	95	conclusive
Pseudomonas aeruginosa	strain=CCUG 551	GCA_008801675.1	287	287	type	True	99.2479	1990	2082	95	conclusive
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	82.6654	921	2082	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	81.8809	972	2082	95	below_threshold
Pseudomonas yangonensis	strain=MY50	GCA_009932725.1	2579922	2579922	type	True	81.2178	917	2082	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:30,329] [INFO] DFAST Taxonomy check result was written to GCF_012987025.1_ASM1298702v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:30,330] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:30,330] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:30,330] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg17ff0e9e-04d6-4dae-ac73-666601c460a7/dqc_reference/checkm_data
[2024-01-24 13:41:30,331] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:30,388] [INFO] Task started: CheckM
[2024-01-24 13:41:30,389] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012987025.1_ASM1298702v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012987025.1_ASM1298702v1_genomic.fna/checkm_input GCF_012987025.1_ASM1298702v1_genomic.fna/checkm_result
[2024-01-24 13:42:13,897] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:13,898] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:13,914] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:13,915] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:13,915] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012987025.1_ASM1298702v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:13,915] [INFO] Task started: Blastn
[2024-01-24 13:42:13,915] [INFO] Running command: blastn -query GCF_012987025.1_ASM1298702v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg17ff0e9e-04d6-4dae-ac73-666601c460a7/dqc_reference/reference_markers_gtdb.fasta -out GCF_012987025.1_ASM1298702v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:16,010] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:16,013] [INFO] Selected 17 target genomes.
[2024-01-24 13:42:16,013] [INFO] Target genome list was writen to GCF_012987025.1_ASM1298702v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:16,022] [INFO] Task started: fastANI
[2024-01-24 13:42:16,022] [INFO] Running command: fastANI --query /var/lib/cwl/stg20146f43-0372-4501-9232-bbbeea60b02e/GCF_012987025.1_ASM1298702v1_genomic.fna.gz --refList GCF_012987025.1_ASM1298702v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012987025.1_ASM1298702v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:38,970] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:38,981] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:38,982] [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_001457615.1	s__Pseudomonas aeruginosa	99.9972	2082	2082	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	99.12	97.38	0.94	0.84	5623	conclusive
GCF_000017205.1	s__Pseudomonas aeruginosa_A	94.0226	1851	2082	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	99.07	98.78	0.93	0.80	42	-
GCF_900187975.1	s__Pseudomonas delhiensis	84.8617	1336	2082	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.078	98.79	97.59	0.94	0.89	3	-
GCF_900112375.1	s__Pseudomonas citronellolis	84.6302	1362	2082	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.078	97.44	97.08	0.86	0.82	26	-
GCF_900103845.1	s__Pseudomonas jinjuensis	84.5813	1170	2082	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_017589465.1	s__Pseudomonas sp017589465	84.3038	1093	2082	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204515.1	s__Pseudomonas nitritireducens_A	83.9081	1311	2082	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	83.888	1218	2082	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002091755.1	s__Pseudomonas nitroreducens	83.5679	1255	2082	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	98.47	95.19	0.93	0.83	16	-
GCF_003205495.1	s__Pseudomonas_E alcaligenes_B	82.8905	898	2082	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_012767755.2	s__Pseudomonas_F sp003234055	82.8315	1243	2082	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	96.89	96.11	0.89	0.88	3	-
GCF_003696305.1	s__Pseudomonas_E sp003696305	82.7279	1022	2082	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	82.3823	557	2082	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	82.3759	756	2082	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_900105885.1	s__Pseudomonas_K guangdongensis	82.3224	693	2082	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_000761545.1	s__Pseudomonas_E sp000761545	82.2368	944	2082	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	82.2098	854	2082	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:38,983] [INFO] GTDB search result was written to GCF_012987025.1_ASM1298702v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:38,984] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:38,986] [INFO] DFAST_QC result json was written to GCF_012987025.1_ASM1298702v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:38,986] [INFO] DFAST_QC completed!
[2024-01-24 13:42:38,987] [INFO] Total running time: 0h1m44s