[2024-01-24 15:27:21,814] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:27:21,818] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:27:21,819] [INFO] DQC Reference Directory: /var/lib/cwl/stge784165a-930c-45ff-8fda-d4ffff4444dc/dqc_reference
[2024-01-24 15:27:23,236] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:27:23,238] [INFO] Task started: Prodigal
[2024-01-24 15:27:23,238] [INFO] Running command: gunzip -c /var/lib/cwl/stgfc0df3c2-2057-4107-ac68-c8a8fb97bc16/GCF_004745455.1_ASM474545v1_genomic.fna.gz | prodigal -d GCF_004745455.1_ASM474545v1_genomic.fna/cds.fna -a GCF_004745455.1_ASM474545v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:45,388] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:45,389] [INFO] Task started: HMMsearch
[2024-01-24 15:27:45,389] [INFO] Running command: hmmsearch --tblout GCF_004745455.1_ASM474545v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge784165a-930c-45ff-8fda-d4ffff4444dc/dqc_reference/reference_markers.hmm GCF_004745455.1_ASM474545v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:45,726] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:45,727] [INFO] Found 6/6 markers.
[2024-01-24 15:27:45,784] [INFO] Query marker FASTA was written to GCF_004745455.1_ASM474545v1_genomic.fna/markers.fasta
[2024-01-24 15:27:45,785] [INFO] Task started: Blastn
[2024-01-24 15:27:45,785] [INFO] Running command: blastn -query GCF_004745455.1_ASM474545v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge784165a-930c-45ff-8fda-d4ffff4444dc/dqc_reference/reference_markers.fasta -out GCF_004745455.1_ASM474545v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:46,955] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:46,959] [INFO] Selected 10 target genomes.
[2024-01-24 15:27:46,960] [INFO] Target genome list was writen to GCF_004745455.1_ASM474545v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:46,964] [INFO] Task started: fastANI
[2024-01-24 15:27:46,965] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc0df3c2-2057-4107-ac68-c8a8fb97bc16/GCF_004745455.1_ASM474545v1_genomic.fna.gz --refList GCF_004745455.1_ASM474545v1_genomic.fna/target_genomes.txt --output GCF_004745455.1_ASM474545v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:28:31,568] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:31,569] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge784165a-930c-45ff-8fda-d4ffff4444dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:28:31,569] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge784165a-930c-45ff-8fda-d4ffff4444dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:28:31,582] [INFO] Found 10 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 15:28:31,583] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 15:28:31,583] [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 citronellolis	strain=DSM 50332	GCA_004745455.1	53408	53408	type	True	100.0	2404	2435	95	inconclusive
Pseudomonas citronellolis	strain=LMG 18378	GCA_900112375.1	53408	53408	type	True	99.9833	2350	2435	95	inconclusive
Pseudomonas citronellolis	strain=NBRC 103043	GCA_002091555.1	53408	53408	type	True	99.9751	2323	2435	95	inconclusive
Pseudomonas delhiensis	strain=RLD-1	GCA_900187975.1	366289	366289	type	True	95.1085	1913	2435	95	inconclusive
Pseudomonas delhiensis	strain=CCM 7361	GCA_900099945.1	366289	366289	type	True	95.0838	1912	2435	95	inconclusive
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	83.571	1028	2435	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	83.078	1081	2435	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	82.9975	1052	2435	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	82.9938	1137	2435	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	82.7885	874	2435	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:28:31,584] [INFO] DFAST Taxonomy check result was written to GCF_004745455.1_ASM474545v1_genomic.fna/tc_result.tsv
[2024-01-24 15:28:31,585] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:28:31,585] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:28:31,585] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge784165a-930c-45ff-8fda-d4ffff4444dc/dqc_reference/checkm_data
[2024-01-24 15:28:31,586] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:28:31,653] [INFO] Task started: CheckM
[2024-01-24 15:28:31,653] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004745455.1_ASM474545v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004745455.1_ASM474545v1_genomic.fna/checkm_input GCF_004745455.1_ASM474545v1_genomic.fna/checkm_result
[2024-01-24 15:29:31,360] [INFO] Task succeeded: CheckM
[2024-01-24 15:29:31,361] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:29:31,387] [INFO] ===== Completeness check finished =====
[2024-01-24 15:29:31,387] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:29:31,388] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004745455.1_ASM474545v1_genomic.fna/markers.fasta)
[2024-01-24 15:29:31,388] [INFO] Task started: Blastn
[2024-01-24 15:29:31,388] [INFO] Running command: blastn -query GCF_004745455.1_ASM474545v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge784165a-930c-45ff-8fda-d4ffff4444dc/dqc_reference/reference_markers_gtdb.fasta -out GCF_004745455.1_ASM474545v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:29:33,601] [INFO] Task succeeded: Blastn
[2024-01-24 15:29:33,608] [INFO] Selected 10 target genomes.
[2024-01-24 15:29:33,608] [INFO] Target genome list was writen to GCF_004745455.1_ASM474545v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:29:33,615] [INFO] Task started: fastANI
[2024-01-24 15:29:33,615] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc0df3c2-2057-4107-ac68-c8a8fb97bc16/GCF_004745455.1_ASM474545v1_genomic.fna.gz --refList GCF_004745455.1_ASM474545v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004745455.1_ASM474545v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:30:02,307] [INFO] Task succeeded: fastANI
[2024-01-24 15:30:02,320] [INFO] Found 10 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 15:30:02,320] [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_900112375.1	s__Pseudomonas citronellolis	99.9833	2350	2435	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.078	97.44	97.08	0.86	0.82	26	inconclusive
GCF_900187975.1	s__Pseudomonas delhiensis	95.1565	1908	2435	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.078	98.79	97.59	0.94	0.89	3	inconclusive
GCF_000689415.1	s__Pseudomonas knackmussii	88.7549	1572	2435	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	98.27	98.27	0.91	0.91	2	-
GCF_900099785.1	s__Pseudomonas panipatensis	87.5418	1481	2435	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	87.176	1482	2435	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	87.0732	1613	2435	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000349845.1	s__Pseudomonas sp000349845	87.0697	1444	2435	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103845.1	s__Pseudomonas jinjuensis	86.8939	1384	2435	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	86.1505	1324	2435	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000017205.1	s__Pseudomonas aeruginosa_A	84.9532	1378	2435	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	99.07	98.78	0.93	0.80	42	-
--------------------------------------------------------------------------------
[2024-01-24 15:30:02,322] [INFO] GTDB search result was written to GCF_004745455.1_ASM474545v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:30:02,322] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:30:02,325] [INFO] DFAST_QC result json was written to GCF_004745455.1_ASM474545v1_genomic.fna/dqc_result.json
[2024-01-24 15:30:02,326] [INFO] DFAST_QC completed!
[2024-01-24 15:30:02,326] [INFO] Total running time: 0h2m41s