[2024-01-24 12:31:34,404] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:34,406] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:34,406] [INFO] DQC Reference Directory: /var/lib/cwl/stgd388f0b5-5502-4155-a1e1-6d65f0b01be8/dqc_reference
[2024-01-24 12:31:35,760] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:35,761] [INFO] Task started: Prodigal
[2024-01-24 12:31:35,761] [INFO] Running command: gunzip -c /var/lib/cwl/stga85efc9a-1282-4c71-8761-2f83915acf00/GCF_000262065.2_KF707_a1_genomic.fna.gz | prodigal -d GCF_000262065.2_KF707_a1_genomic.fna/cds.fna -a GCF_000262065.2_KF707_a1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:55,555] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:55,555] [INFO] Task started: HMMsearch
[2024-01-24 12:31:55,555] [INFO] Running command: hmmsearch --tblout GCF_000262065.2_KF707_a1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd388f0b5-5502-4155-a1e1-6d65f0b01be8/dqc_reference/reference_markers.hmm GCF_000262065.2_KF707_a1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:55,929] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:55,931] [INFO] Found 6/6 markers.
[2024-01-24 12:31:55,990] [INFO] Query marker FASTA was written to GCF_000262065.2_KF707_a1_genomic.fna/markers.fasta
[2024-01-24 12:31:55,991] [INFO] Task started: Blastn
[2024-01-24 12:31:55,991] [INFO] Running command: blastn -query GCF_000262065.2_KF707_a1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd388f0b5-5502-4155-a1e1-6d65f0b01be8/dqc_reference/reference_markers.fasta -out GCF_000262065.2_KF707_a1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:57,041] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:57,045] [INFO] Selected 17 target genomes.
[2024-01-24 12:31:57,045] [INFO] Target genome list was writen to GCF_000262065.2_KF707_a1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:57,053] [INFO] Task started: fastANI
[2024-01-24 12:31:57,054] [INFO] Running command: fastANI --query /var/lib/cwl/stga85efc9a-1282-4c71-8761-2f83915acf00/GCF_000262065.2_KF707_a1_genomic.fna.gz --refList GCF_000262065.2_KF707_a1_genomic.fna/target_genomes.txt --output GCF_000262065.2_KF707_a1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:19,334] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:19,334] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd388f0b5-5502-4155-a1e1-6d65f0b01be8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:19,335] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd388f0b5-5502-4155-a1e1-6d65f0b01be8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:19,360] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:32:19,360] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:32:19,360] [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 furukawaii	strain=KF707	GCA_000262065.3	1149133	1149133	type	True	100.0	2063	2130	95	conclusive
Pseudomonas furukawaii	strain=KF707	GCA_002355475.1	1149133	1149133	type	True	99.9938	2003	2130	95	conclusive
Pseudomonas otitidis	strain=DSM 17224	GCA_900111835.1	319939	319939	suspected-type	True	85.4476	1246	2130	95	below_threshold
Pseudomonas tohonis	strain=TUM18999	GCA_012767755.2	2725477	2725477	type	True	85.3477	1269	2130	95	below_threshold
Pseudomonas citronellolis	strain=NBRC 103043	GCA_002091555.1	53408	53408	type	True	83.3031	1186	2130	95	below_threshold
Pseudomonas citronellolis	strain=DSM 50332	GCA_004745455.1	53408	53408	type	True	83.273	1208	2130	95	below_threshold
Pseudomonas citronellolis	strain=LMG 18378	GCA_900112375.1	53408	53408	type	True	83.1893	1219	2130	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	83.1675	999	2130	95	below_threshold
Pseudomonas alcaligenes	strain=NCTC10367	GCA_900455475.1	43263	43263	type	True	83.1265	960	2130	95	below_threshold
Pseudomonas alcaligenes	strain=NBRC 14159	GCA_000467105.1	43263	43263	type	True	83.0512	934	2130	95	below_threshold
Pseudomonas thermotolerans	strain=DSM 14292	GCA_000364625.1	157784	157784	type	True	82.8737	879	2130	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	82.6819	1008	2130	95	below_threshold
Pseudomonas mangiferae	strain=DMKU BBB3-04	GCA_007109405.1	2593654	2593654	type	True	82.6479	891	2130	95	below_threshold
Pseudomonas ullengensis	strain=UL070	GCA_014174475.1	2759166	2759166	type	True	82.2458	936	2130	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	82.2286	954	2130	95	below_threshold
Pseudomonas campi	strain=S1-A32-2	GCA_013200955.2	2731681	2731681	type	True	82.1821	897	2130	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	81.8411	745	2130	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:32:19,363] [INFO] DFAST Taxonomy check result was written to GCF_000262065.2_KF707_a1_genomic.fna/tc_result.tsv
[2024-01-24 12:32:19,363] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:19,364] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:19,364] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd388f0b5-5502-4155-a1e1-6d65f0b01be8/dqc_reference/checkm_data
[2024-01-24 12:32:19,366] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:19,431] [INFO] Task started: CheckM
[2024-01-24 12:32:19,432] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000262065.2_KF707_a1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000262065.2_KF707_a1_genomic.fna/checkm_input GCF_000262065.2_KF707_a1_genomic.fna/checkm_result
[2024-01-24 12:33:18,610] [INFO] Task succeeded: CheckM
[2024-01-24 12:33:18,611] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 12:33:18,641] [INFO] ===== Completeness check finished =====
[2024-01-24 12:33:18,642] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:33:18,642] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000262065.2_KF707_a1_genomic.fna/markers.fasta)
[2024-01-24 12:33:18,643] [INFO] Task started: Blastn
[2024-01-24 12:33:18,643] [INFO] Running command: blastn -query GCF_000262065.2_KF707_a1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd388f0b5-5502-4155-a1e1-6d65f0b01be8/dqc_reference/reference_markers_gtdb.fasta -out GCF_000262065.2_KF707_a1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:33:20,617] [INFO] Task succeeded: Blastn
[2024-01-24 12:33:20,622] [INFO] Selected 10 target genomes.
[2024-01-24 12:33:20,623] [INFO] Target genome list was writen to GCF_000262065.2_KF707_a1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:33:20,632] [INFO] Task started: fastANI
[2024-01-24 12:33:20,632] [INFO] Running command: fastANI --query /var/lib/cwl/stga85efc9a-1282-4c71-8761-2f83915acf00/GCF_000262065.2_KF707_a1_genomic.fna.gz --refList GCF_000262065.2_KF707_a1_genomic.fna/target_genomes_gtdb.txt --output GCF_000262065.2_KF707_a1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:33:36,685] [INFO] Task succeeded: fastANI
[2024-01-24 12:33:36,700] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:33:36,701] [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_002355475.1	s__Pseudomonas_F furukawaii	99.9938	2002	2130	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	99.26	98.53	0.90	0.84	3	conclusive
GCF_000412695.1	s__Pseudomonas_F resinovorans_A	87.3017	1472	2130	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008807375.1	s__Pseudomonas_F lalkuanensis	86.919	1411	2130	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000949385.2	s__Pseudomonas_F sp000949385	86.6075	1408	2130	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014700075.1	s__Pseudomonas_F sp014700075	86.597	1395	2130	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013393345.1	s__Pseudomonas_F resinovorans_C	86.2132	1403	2130	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	95.04	95.04	0.90	0.90	2	-
GCF_003626975.1	s__Pseudomonas_F sp003626975	85.5633	1424	2130	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	99.49	99.49	0.93	0.93	2	-
GCF_900111835.1	s__Pseudomonas_F otitidis	85.4451	1245	2130	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	96.35	95.43	0.89	0.84	21	-
GCF_012767755.2	s__Pseudomonas_F sp003234055	85.3268	1266	2130	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_904061905.1	s__Pseudomonas_E carbonaria	83.27	1063	2130	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:33:36,703] [INFO] GTDB search result was written to GCF_000262065.2_KF707_a1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:33:36,703] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:33:36,707] [INFO] DFAST_QC result json was written to GCF_000262065.2_KF707_a1_genomic.fna/dqc_result.json
[2024-01-24 12:33:36,707] [INFO] DFAST_QC completed!
[2024-01-24 12:33:36,708] [INFO] Total running time: 0h2m2s