[2024-01-24 13:09:34,033] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:34,035] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:34,035] [INFO] DQC Reference Directory: /var/lib/cwl/stg521f4b6e-fcc7-42ea-aad6-b20a6b416779/dqc_reference
[2024-01-24 13:09:35,393] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:35,394] [INFO] Task started: Prodigal
[2024-01-24 13:09:35,394] [INFO] Running command: gunzip -c /var/lib/cwl/stg601f663f-65ce-4414-903d-add7981b2860/GCF_000689415.1_PKB13_genomic.fna.gz | prodigal -d GCF_000689415.1_PKB13_genomic.fna/cds.fna -a GCF_000689415.1_PKB13_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:53,841] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:53,842] [INFO] Task started: HMMsearch
[2024-01-24 13:09:53,842] [INFO] Running command: hmmsearch --tblout GCF_000689415.1_PKB13_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg521f4b6e-fcc7-42ea-aad6-b20a6b416779/dqc_reference/reference_markers.hmm GCF_000689415.1_PKB13_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:09:54,139] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:09:54,140] [INFO] Found 6/6 markers.
[2024-01-24 13:09:54,198] [INFO] Query marker FASTA was written to GCF_000689415.1_PKB13_genomic.fna/markers.fasta
[2024-01-24 13:09:54,199] [INFO] Task started: Blastn
[2024-01-24 13:09:54,199] [INFO] Running command: blastn -query GCF_000689415.1_PKB13_genomic.fna/markers.fasta -db /var/lib/cwl/stg521f4b6e-fcc7-42ea-aad6-b20a6b416779/dqc_reference/reference_markers.fasta -out GCF_000689415.1_PKB13_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:55,179] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:55,182] [INFO] Selected 13 target genomes.
[2024-01-24 13:09:55,182] [INFO] Target genome list was writen to GCF_000689415.1_PKB13_genomic.fna/target_genomes.txt
[2024-01-24 13:09:55,188] [INFO] Task started: fastANI
[2024-01-24 13:09:55,188] [INFO] Running command: fastANI --query /var/lib/cwl/stg601f663f-65ce-4414-903d-add7981b2860/GCF_000689415.1_PKB13_genomic.fna.gz --refList GCF_000689415.1_PKB13_genomic.fna/target_genomes.txt --output GCF_000689415.1_PKB13_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:16,137] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:16,137] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg521f4b6e-fcc7-42ea-aad6-b20a6b416779/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:16,138] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg521f4b6e-fcc7-42ea-aad6-b20a6b416779/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:16,150] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:10:16,150] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:16,150] [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 knackmussii	strain=B13	GCA_000689415.1	65741	65741	type	True	100.0	2036	2054	95	conclusive
Pseudomonas delhiensis	strain=CCM 7361	GCA_900099945.1	366289	366289	type	True	88.9228	1460	2054	95	below_threshold
Pseudomonas delhiensis	strain=RLD-1	GCA_900187975.1	366289	366289	type	True	88.8984	1475	2054	95	below_threshold
Pseudomonas citronellolis	strain=DSM 50332	GCA_004745455.1	53408	53408	type	True	88.844	1543	2054	95	below_threshold
Pseudomonas citronellolis	strain=LMG 18378	GCA_900112375.1	53408	53408	type	True	88.8334	1532	2054	95	below_threshold
Pseudomonas citronellolis	strain=NBRC 103043	GCA_002091555.1	53408	53408	type	True	88.8301	1524	2054	95	below_threshold
Pseudomonas jinjuensis	strain=JCM 21621	GCA_900103845.1	198616	198616	type	True	86.0298	1248	2054	95	below_threshold
Pseudomonas nitroreducens	strain=NBRC 12694	GCA_002091755.1	46680	46680	suspected-type	True	85.9307	1396	2054	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	82.8274	1048	2054	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	82.8131	931	2054	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	81.2921	748	2054	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_002891015.1	2968968	2968968	type	True	81.2033	745	2054	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_024448505.1	2968968	2968968	type	True	81.1113	737	2054	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:16,152] [INFO] DFAST Taxonomy check result was written to GCF_000689415.1_PKB13_genomic.fna/tc_result.tsv
[2024-01-24 13:10:16,153] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:16,153] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:16,153] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg521f4b6e-fcc7-42ea-aad6-b20a6b416779/dqc_reference/checkm_data
[2024-01-24 13:10:16,154] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:16,211] [INFO] Task started: CheckM
[2024-01-24 13:10:16,211] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000689415.1_PKB13_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000689415.1_PKB13_genomic.fna/checkm_input GCF_000689415.1_PKB13_genomic.fna/checkm_result
[2024-01-24 13:11:07,837] [INFO] Task succeeded: CheckM
[2024-01-24 13:11:07,838] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:11:07,854] [INFO] ===== Completeness check finished =====
[2024-01-24 13:11:07,854] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:11:07,855] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000689415.1_PKB13_genomic.fna/markers.fasta)
[2024-01-24 13:11:07,855] [INFO] Task started: Blastn
[2024-01-24 13:11:07,855] [INFO] Running command: blastn -query GCF_000689415.1_PKB13_genomic.fna/markers.fasta -db /var/lib/cwl/stg521f4b6e-fcc7-42ea-aad6-b20a6b416779/dqc_reference/reference_markers_gtdb.fasta -out GCF_000689415.1_PKB13_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:11:09,492] [INFO] Task succeeded: Blastn
[2024-01-24 13:11:09,495] [INFO] Selected 13 target genomes.
[2024-01-24 13:11:09,495] [INFO] Target genome list was writen to GCF_000689415.1_PKB13_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:11:09,503] [INFO] Task started: fastANI
[2024-01-24 13:11:09,503] [INFO] Running command: fastANI --query /var/lib/cwl/stg601f663f-65ce-4414-903d-add7981b2860/GCF_000689415.1_PKB13_genomic.fna.gz --refList GCF_000689415.1_PKB13_genomic.fna/target_genomes_gtdb.txt --output GCF_000689415.1_PKB13_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:11:31,214] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:31,225] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:11:31,225] [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_000689415.1	s__Pseudomonas knackmussii	100.0	2038	2054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	98.27	98.27	0.91	0.91	2	conclusive
GCF_900187975.1	s__Pseudomonas delhiensis	88.8887	1476	2054	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	88.8723	1529	2054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.078	97.44	97.08	0.86	0.82	26	-
GCF_900099785.1	s__Pseudomonas panipatensis	86.9621	1455	2054	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	86.5881	1398	2054	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	86.4422	1302	2054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002452115.1	s__Pseudomonas nitroreducens_B	86.3148	1258	2054	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	86.2484	1420	2054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008807415.1	s__Pseudomonas sp002079985	86.2194	1474	2054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	97.48	95.53	0.92	0.91	9	-
GCF_000955805.1	s__Pseudomonas sp000955805	86.1951	1455	2054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	99.94	99.94	0.99	0.99	2	-
GCF_009189165.1	s__Pseudomonas sp009189165	86.1403	1433	2054	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	86.0415	1247	2054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_016919445.1	s__Pseudomonas sp016919445	85.8844	1430	2054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:11:31,227] [INFO] GTDB search result was written to GCF_000689415.1_PKB13_genomic.fna/result_gtdb.tsv
[2024-01-24 13:11:31,228] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:11:31,231] [INFO] DFAST_QC result json was written to GCF_000689415.1_PKB13_genomic.fna/dqc_result.json
[2024-01-24 13:11:31,231] [INFO] DFAST_QC completed!
[2024-01-24 13:11:31,231] [INFO] Total running time: 0h1m57s