[2024-01-24 13:46:18,386] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:18,389] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:18,390] [INFO] DQC Reference Directory: /var/lib/cwl/stg842a6224-c688-4c0e-abde-648ac7967e9e/dqc_reference
[2024-01-24 13:46:19,667] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:19,667] [INFO] Task started: Prodigal
[2024-01-24 13:46:19,668] [INFO] Running command: gunzip -c /var/lib/cwl/stgf5764c0a-d0c3-43eb-ac06-57cdef240a9c/GCF_014164785.1_ASM1416478v1_genomic.fna.gz | prodigal -d GCF_014164785.1_ASM1416478v1_genomic.fna/cds.fna -a GCF_014164785.1_ASM1416478v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:33,237] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:33,238] [INFO] Task started: HMMsearch
[2024-01-24 13:46:33,238] [INFO] Running command: hmmsearch --tblout GCF_014164785.1_ASM1416478v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg842a6224-c688-4c0e-abde-648ac7967e9e/dqc_reference/reference_markers.hmm GCF_014164785.1_ASM1416478v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:33,590] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:33,592] [INFO] Found 6/6 markers.
[2024-01-24 13:46:33,632] [INFO] Query marker FASTA was written to GCF_014164785.1_ASM1416478v1_genomic.fna/markers.fasta
[2024-01-24 13:46:33,632] [INFO] Task started: Blastn
[2024-01-24 13:46:33,632] [INFO] Running command: blastn -query GCF_014164785.1_ASM1416478v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg842a6224-c688-4c0e-abde-648ac7967e9e/dqc_reference/reference_markers.fasta -out GCF_014164785.1_ASM1416478v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:34,711] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:34,714] [INFO] Selected 13 target genomes.
[2024-01-24 13:46:34,714] [INFO] Target genome list was writen to GCF_014164785.1_ASM1416478v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:34,721] [INFO] Task started: fastANI
[2024-01-24 13:46:34,721] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5764c0a-d0c3-43eb-ac06-57cdef240a9c/GCF_014164785.1_ASM1416478v1_genomic.fna.gz --refList GCF_014164785.1_ASM1416478v1_genomic.fna/target_genomes.txt --output GCF_014164785.1_ASM1416478v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:50,180] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:50,181] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg842a6224-c688-4c0e-abde-648ac7967e9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:50,181] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg842a6224-c688-4c0e-abde-648ac7967e9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:50,196] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:50,196] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:50,197] [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 guryensis	strain=SR9	GCA_014164785.1	2759165	2759165	type	True	100.0	1426	1427	95	conclusive
Pseudomonas campi	strain=S1-A32-2	GCA_013200955.2	2731681	2731681	type	True	93.2745	1269	1427	95	below_threshold
Pseudomonas ullengensis	strain=UL070	GCA_014174475.1	2759166	2759166	type	True	86.5169	1076	1427	95	below_threshold
Pseudomonas alcaligenes	strain=NBRC 14159	GCA_000467105.1	43263	43263	type	True	85.9477	1103	1427	95	below_threshold
Pseudomonas alcaligenes	strain=NCTC10367	GCA_900455475.1	43263	43263	type	True	85.9185	1112	1427	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	83.7734	860	1427	95	below_threshold
Pseudomonas benzenivorans	strain=DSM 8628	GCA_900100495.1	556533	556533	type	True	83.5396	941	1427	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	83.3618	890	1427	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	83.1418	934	1427	95	below_threshold
Pseudomonas guguanensis	strain=JCM 18416	GCA_900104265.1	1198456	1198456	type	True	83.0455	937	1427	95	below_threshold
Pseudomonas yangonensis	strain=MY50	GCA_009932725.1	2579922	2579922	type	True	82.4538	863	1427	95	below_threshold
Pseudomonas otitidis	strain=DSM 17224	GCA_900111835.1	319939	319939	suspected-type	True	82.4397	936	1427	95	below_threshold
Pseudomonas kuykendallii	strain=NRRL B-59562	GCA_900106975.1	1007099	1007099	type	True	82.1268	804	1427	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:50,198] [INFO] DFAST Taxonomy check result was written to GCF_014164785.1_ASM1416478v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:50,199] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:50,199] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:50,199] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg842a6224-c688-4c0e-abde-648ac7967e9e/dqc_reference/checkm_data
[2024-01-24 13:46:50,200] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:50,252] [INFO] Task started: CheckM
[2024-01-24 13:46:50,252] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014164785.1_ASM1416478v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014164785.1_ASM1416478v1_genomic.fna/checkm_input GCF_014164785.1_ASM1416478v1_genomic.fna/checkm_result
[2024-01-24 13:47:32,388] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:32,390] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:32,411] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:32,411] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:32,412] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014164785.1_ASM1416478v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:32,412] [INFO] Task started: Blastn
[2024-01-24 13:47:32,412] [INFO] Running command: blastn -query GCF_014164785.1_ASM1416478v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg842a6224-c688-4c0e-abde-648ac7967e9e/dqc_reference/reference_markers_gtdb.fasta -out GCF_014164785.1_ASM1416478v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:34,391] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:34,395] [INFO] Selected 9 target genomes.
[2024-01-24 13:47:34,395] [INFO] Target genome list was writen to GCF_014164785.1_ASM1416478v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:34,399] [INFO] Task started: fastANI
[2024-01-24 13:47:34,400] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5764c0a-d0c3-43eb-ac06-57cdef240a9c/GCF_014164785.1_ASM1416478v1_genomic.fna.gz --refList GCF_014164785.1_ASM1416478v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014164785.1_ASM1416478v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:45,033] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:45,045] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:45,045] [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_014164785.1	s__Pseudomonas_E sp014164785	100.0	1426	1427	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_013200955.2	s__Pseudomonas_E campi	93.2809	1269	1427	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_009799925.1	s__Pseudomonas_E sp009799925	89.6912	1093	1427	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	89.3838	1097	1427	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_014174475.1	s__Pseudomonas_E sp014174475	86.5304	1075	1427	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_000467105.1	s__Pseudomonas_E alcaligenes	85.9463	1101	1427	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.23	96.43	0.89	0.81	8	-
GCF_014851905.1	s__Pseudomonas_E sp014851905	85.6776	1027	1427	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_900156545.1	s__Pseudomonas_E alcaligenes_A	85.5067	1071	1427	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.95	95.95	0.92	0.92	2	-
GCF_900106975.1	s__Pseudomonas_O kuykendallii	82.1367	803	1427	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_O	95.0	96.83	96.68	0.93	0.91	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:45,047] [INFO] GTDB search result was written to GCF_014164785.1_ASM1416478v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:45,048] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:45,053] [INFO] DFAST_QC result json was written to GCF_014164785.1_ASM1416478v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:45,053] [INFO] DFAST_QC completed!
[2024-01-24 13:47:45,054] [INFO] Total running time: 0h1m27s