[2024-01-24 10:57:12,794] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:12,797] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:12,797] [INFO] DQC Reference Directory: /var/lib/cwl/stgb3641c48-8424-4009-8f57-9b1029bfe5a2/dqc_reference
[2024-01-24 10:57:14,271] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:14,272] [INFO] Task started: Prodigal
[2024-01-24 10:57:14,272] [INFO] Running command: gunzip -c /var/lib/cwl/stg529f629e-1c41-4d64-ba12-81a95164a5c6/GCF_904061905.1_CIP111764_genomic.fna.gz | prodigal -d GCF_904061905.1_CIP111764_genomic.fna/cds.fna -a GCF_904061905.1_CIP111764_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:31,937] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:31,938] [INFO] Task started: HMMsearch
[2024-01-24 10:57:31,938] [INFO] Running command: hmmsearch --tblout GCF_904061905.1_CIP111764_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb3641c48-8424-4009-8f57-9b1029bfe5a2/dqc_reference/reference_markers.hmm GCF_904061905.1_CIP111764_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:32,320] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:32,322] [INFO] Found 6/6 markers.
[2024-01-24 10:57:32,371] [INFO] Query marker FASTA was written to GCF_904061905.1_CIP111764_genomic.fna/markers.fasta
[2024-01-24 10:57:32,371] [INFO] Task started: Blastn
[2024-01-24 10:57:32,371] [INFO] Running command: blastn -query GCF_904061905.1_CIP111764_genomic.fna/markers.fasta -db /var/lib/cwl/stgb3641c48-8424-4009-8f57-9b1029bfe5a2/dqc_reference/reference_markers.fasta -out GCF_904061905.1_CIP111764_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:33,608] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:33,612] [INFO] Selected 17 target genomes.
[2024-01-24 10:57:33,612] [INFO] Target genome list was writen to GCF_904061905.1_CIP111764_genomic.fna/target_genomes.txt
[2024-01-24 10:57:33,618] [INFO] Task started: fastANI
[2024-01-24 10:57:33,618] [INFO] Running command: fastANI --query /var/lib/cwl/stg529f629e-1c41-4d64-ba12-81a95164a5c6/GCF_904061905.1_CIP111764_genomic.fna.gz --refList GCF_904061905.1_CIP111764_genomic.fna/target_genomes.txt --output GCF_904061905.1_CIP111764_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:01,051] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:01,052] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb3641c48-8424-4009-8f57-9b1029bfe5a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:01,052] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb3641c48-8424-4009-8f57-9b1029bfe5a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:01,075] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:58:01,076] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:01,076] [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 carbonaria	strain=CIP 111764	GCA_904061905.1	2762745	2762745	type	True	100.0	1791	1797	95	conclusive
Pseudomonas thermotolerans	strain=DSM 14292	GCA_000364625.1	157784	157784	type	True	87.2323	1037	1797	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	86.5198	1136	1797	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	85.9318	1104	1797	95	below_threshold
Pseudomonas citronellolis	strain=LMG 18378	GCA_900112375.1	53408	53408	type	True	84.4331	1207	1797	95	below_threshold
Pseudomonas citronellolis	strain=DSM 50332	GCA_004745455.1	53408	53408	type	True	84.4227	1216	1797	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	84.4165	974	1797	95	below_threshold
Pseudomonas delhiensis	strain=CCM 7361	GCA_900099945.1	366289	366289	type	True	84.4001	1193	1797	95	below_threshold
Pseudomonas citronellolis	strain=NBRC 103043	GCA_002091555.1	53408	53408	type	True	84.3899	1203	1797	95	below_threshold
Pseudomonas benzenivorans	strain=DSM 8628	GCA_900100495.1	556533	556533	type	True	84.1405	1068	1797	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	83.6284	1006	1797	95	below_threshold
Pseudomonas campi	strain=S1-A32-2	GCA_013200955.2	2731681	2731681	type	True	83.4459	928	1797	95	below_threshold
Pseudomonas ullengensis	strain=UL070	GCA_014174475.1	2759166	2759166	type	True	83.2865	951	1797	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	83.2102	768	1797	95	below_threshold
Pseudomonas indica	strain=NBRC 103045	GCA_002091635.1	137658	137658	type	True	83.0027	1004	1797	95	below_threshold
Stutzerimonas azotifigens	strain=DSM 17556	GCA_000425625.1	291995	291995	type	True	82.7008	840	1797	95	below_threshold
[Pseudomonas] nosocomialis	strain=A31/70	GCA_005876855.1	1056496	1056496	type	True	82.0716	805	1797	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:01,078] [INFO] DFAST Taxonomy check result was written to GCF_904061905.1_CIP111764_genomic.fna/tc_result.tsv
[2024-01-24 10:58:01,078] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:01,079] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:01,079] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb3641c48-8424-4009-8f57-9b1029bfe5a2/dqc_reference/checkm_data
[2024-01-24 10:58:01,080] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:01,133] [INFO] Task started: CheckM
[2024-01-24 10:58:01,133] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_904061905.1_CIP111764_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_904061905.1_CIP111764_genomic.fna/checkm_input GCF_904061905.1_CIP111764_genomic.fna/checkm_result
[2024-01-24 10:58:51,012] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:51,013] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:51,037] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:51,037] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:51,038] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_904061905.1_CIP111764_genomic.fna/markers.fasta)
[2024-01-24 10:58:51,038] [INFO] Task started: Blastn
[2024-01-24 10:58:51,038] [INFO] Running command: blastn -query GCF_904061905.1_CIP111764_genomic.fna/markers.fasta -db /var/lib/cwl/stgb3641c48-8424-4009-8f57-9b1029bfe5a2/dqc_reference/reference_markers_gtdb.fasta -out GCF_904061905.1_CIP111764_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:53,378] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:53,387] [INFO] Selected 18 target genomes.
[2024-01-24 10:58:53,388] [INFO] Target genome list was writen to GCF_904061905.1_CIP111764_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:53,401] [INFO] Task started: fastANI
[2024-01-24 10:58:53,401] [INFO] Running command: fastANI --query /var/lib/cwl/stg529f629e-1c41-4d64-ba12-81a95164a5c6/GCF_904061905.1_CIP111764_genomic.fna.gz --refList GCF_904061905.1_CIP111764_genomic.fna/target_genomes_gtdb.txt --output GCF_904061905.1_CIP111764_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:17,673] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:17,690] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:59:17,690] [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_904061905.1	s__Pseudomonas_E carbonaria	100.0	1791	1797	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_000364625.1	s__Pseudomonas_E thermotolerans	87.233	1036	1797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.25	99.24	0.93	0.93	3	-
GCF_016901015.1	s__Pseudomonas_E sp016901015	86.5065	1137	1797	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_003205495.1	s__Pseudomonas_E alcaligenes_B	84.7838	932	1797	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_003696305.1	s__Pseudomonas_E sp003696305	84.7173	1049	1797	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_902506505.1	s__Pseudomonas_E sp902506505	84.6105	976	1797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.45	95.45	0.88	0.88	2	-
GCF_009799925.1	s__Pseudomonas_E sp009799925	84.5963	980	1797	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_900187975.1	s__Pseudomonas delhiensis	84.5613	1177	1797	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	84.4515	1205	1797	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	84.3273	1088	1797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014490745.1	s__Pseudomonas_E alcaligenes_C	84.2829	1031	1797	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_014851565.1	s__Pseudomonas_E sp014851565	83.921	954	1797	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_017589465.1	s__Pseudomonas sp017589465	83.7894	1032	1797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014851905.1	s__Pseudomonas_E sp014851905	83.5067	945	1797	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_014174475.1	s__Pseudomonas_E sp014174475	83.2838	951	1797	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_002091635.1	s__Pseudomonas_M indica	83.0227	1002	1797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_M	95.0	99.16	98.73	0.94	0.91	4	-
GCF_002890915.1	s__Pseudomonas_A stutzeri_AF	82.9544	879	1797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.35	98.08	0.91	0.89	3	-
GCF_005876855.1	s__Pseudomonas_R nosocomialis	82.0913	803	1797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_R	95.0	98.98	98.95	0.91	0.90	3	-
--------------------------------------------------------------------------------
[2024-01-24 10:59:17,691] [INFO] GTDB search result was written to GCF_904061905.1_CIP111764_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:17,692] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:17,698] [INFO] DFAST_QC result json was written to GCF_904061905.1_CIP111764_genomic.fna/dqc_result.json
[2024-01-24 10:59:17,698] [INFO] DFAST_QC completed!
[2024-01-24 10:59:17,698] [INFO] Total running time: 0h2m5s