[2024-01-25 17:40:35,616] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:40:35,618] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:40:35,618] [INFO] DQC Reference Directory: /var/lib/cwl/stgae90baca-79bf-434e-b388-46ad7a9df6e4/dqc_reference
[2024-01-25 17:40:36,761] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:40:36,761] [INFO] Task started: Prodigal
[2024-01-25 17:40:36,762] [INFO] Running command: gunzip -c /var/lib/cwl/stg4dce8121-16c7-451d-9cef-c23bcfea58e5/GCF_002601815.1_ASM260181v1_genomic.fna.gz | prodigal -d GCF_002601815.1_ASM260181v1_genomic.fna/cds.fna -a GCF_002601815.1_ASM260181v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:40:52,919] [INFO] Task succeeded: Prodigal
[2024-01-25 17:40:52,919] [INFO] Task started: HMMsearch
[2024-01-25 17:40:52,919] [INFO] Running command: hmmsearch --tblout GCF_002601815.1_ASM260181v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgae90baca-79bf-434e-b388-46ad7a9df6e4/dqc_reference/reference_markers.hmm GCF_002601815.1_ASM260181v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:40:53,279] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:40:53,280] [INFO] Found 6/6 markers.
[2024-01-25 17:40:53,331] [INFO] Query marker FASTA was written to GCF_002601815.1_ASM260181v1_genomic.fna/markers.fasta
[2024-01-25 17:40:53,331] [INFO] Task started: Blastn
[2024-01-25 17:40:53,332] [INFO] Running command: blastn -query GCF_002601815.1_ASM260181v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgae90baca-79bf-434e-b388-46ad7a9df6e4/dqc_reference/reference_markers.fasta -out GCF_002601815.1_ASM260181v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:40:54,303] [INFO] Task succeeded: Blastn
[2024-01-25 17:40:54,308] [INFO] Selected 15 target genomes.
[2024-01-25 17:40:54,309] [INFO] Target genome list was writen to GCF_002601815.1_ASM260181v1_genomic.fna/target_genomes.txt
[2024-01-25 17:40:54,322] [INFO] Task started: fastANI
[2024-01-25 17:40:54,323] [INFO] Running command: fastANI --query /var/lib/cwl/stg4dce8121-16c7-451d-9cef-c23bcfea58e5/GCF_002601815.1_ASM260181v1_genomic.fna.gz --refList GCF_002601815.1_ASM260181v1_genomic.fna/target_genomes.txt --output GCF_002601815.1_ASM260181v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:41:14,875] [INFO] Task succeeded: fastANI
[2024-01-25 17:41:14,876] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgae90baca-79bf-434e-b388-46ad7a9df6e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:41:14,876] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgae90baca-79bf-434e-b388-46ad7a9df6e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:41:14,886] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:41:14,886] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:41:14,886] [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	93.8986	1819	2097	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_012987025.1	287	287	type	True	93.896	1820	2097	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_001045685.1	287	287	type	True	93.8719	1818	2097	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_900167195.1	287	287	type	True	93.8633	1797	2097	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	93.8624	1855	2097	95	below_threshold
Pseudomonas aeruginosa	strain=CCUG 551	GCA_008801675.1	287	287	type	True	93.8532	1811	2097	95	below_threshold
Pseudomonas aeruginosa	strain=NCTC10332	GCA_001457615.1	287	287	type	True	93.8508	1816	2097	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	93.8431	1827	2097	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	82.8379	945	2097	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	82.3799	760	2097	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	82.0197	1005	2097	95	below_threshold
Pseudomonas flexibilis	strain=ATCC 29606	GCA_000802425.1	706570	706570	type	True	81.6391	731	2097	95	below_threshold
Pseudomonas flexibilis	strain=ATCC 29606	GCA_900155995.1	706570	706570	type	True	81.5708	743	2097	95	below_threshold
Pseudomonas salomonii	strain=LMG 22120	GCA_001730645.1	191391	191391	type	True	79.3305	808	2097	95	below_threshold
Pseudomonas salomonii	strain=ICMP 14252	GCA_900107155.1	191391	191391	type	True	79.2963	810	2097	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:41:14,888] [INFO] DFAST Taxonomy check result was written to GCF_002601815.1_ASM260181v1_genomic.fna/tc_result.tsv
[2024-01-25 17:41:14,889] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:41:14,889] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:41:14,889] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgae90baca-79bf-434e-b388-46ad7a9df6e4/dqc_reference/checkm_data
[2024-01-25 17:41:14,890] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:41:14,955] [INFO] Task started: CheckM
[2024-01-25 17:41:14,955] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002601815.1_ASM260181v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002601815.1_ASM260181v1_genomic.fna/checkm_input GCF_002601815.1_ASM260181v1_genomic.fna/checkm_result
[2024-01-25 17:42:03,494] [INFO] Task succeeded: CheckM
[2024-01-25 17:42:03,495] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:42:03,518] [INFO] ===== Completeness check finished =====
[2024-01-25 17:42:03,519] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:42:03,520] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002601815.1_ASM260181v1_genomic.fna/markers.fasta)
[2024-01-25 17:42:03,520] [INFO] Task started: Blastn
[2024-01-25 17:42:03,520] [INFO] Running command: blastn -query GCF_002601815.1_ASM260181v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgae90baca-79bf-434e-b388-46ad7a9df6e4/dqc_reference/reference_markers_gtdb.fasta -out GCF_002601815.1_ASM260181v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:42:05,497] [INFO] Task succeeded: Blastn
[2024-01-25 17:42:05,500] [INFO] Selected 19 target genomes.
[2024-01-25 17:42:05,500] [INFO] Target genome list was writen to GCF_002601815.1_ASM260181v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:42:05,522] [INFO] Task started: fastANI
[2024-01-25 17:42:05,522] [INFO] Running command: fastANI --query /var/lib/cwl/stg4dce8121-16c7-451d-9cef-c23bcfea58e5/GCF_002601815.1_ASM260181v1_genomic.fna.gz --refList GCF_002601815.1_ASM260181v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002601815.1_ASM260181v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:42:30,612] [INFO] Task succeeded: fastANI
[2024-01-25 17:42:30,623] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:42:30,624] [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	98.8499	1982	2097	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	93.8578	1815	2097	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	85.0646	1345	2097	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	85.0489	1315	2097	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	84.9593	1162	2097	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_017491605.1	s__Pseudomonas sp017491605	84.1352	1199	2097	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	84.0713	1296	2097	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	83.8934	1181	2097	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003696305.1	s__Pseudomonas_E sp003696305	82.9777	1034	2097	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_018398425.1	s__Pseudomonas_E lalucatii	82.8562	946	2097	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_004801855.1	s__Pseudomonas_K sp004801855	82.7734	764	2097	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	82.6431	1050	2097	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	82.5134	562	2097	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_900105885.1	s__Pseudomonas_K guangdongensis	82.4649	720	2097	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_900104805.1	s__Pseudomonas_K oryzae	82.4433	861	2097	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_000016565.1	s__Pseudomonas_E mendocina_A	82.142	985	2097	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	80.4626	781	2097	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	79.17	436	2097	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	78.9146	670	2097	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.28	98.01	0.93	0.92	4	-
--------------------------------------------------------------------------------
[2024-01-25 17:42:30,625] [INFO] GTDB search result was written to GCF_002601815.1_ASM260181v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:42:30,625] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:42:30,630] [INFO] DFAST_QC result json was written to GCF_002601815.1_ASM260181v1_genomic.fna/dqc_result.json
[2024-01-25 17:42:30,631] [INFO] DFAST_QC completed!
[2024-01-25 17:42:30,631] [INFO] Total running time: 0h1m55s