[2024-01-24 15:03:30,219] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:03:30,222] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:03:30,224] [INFO] DQC Reference Directory: /var/lib/cwl/stg7475deeb-0db6-400a-94d8-d09f320063a3/dqc_reference
[2024-01-24 15:03:31,616] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:03:31,617] [INFO] Task started: Prodigal
[2024-01-24 15:03:31,618] [INFO] Running command: gunzip -c /var/lib/cwl/stg6223b886-9980-4687-955e-59cd650ef504/GCF_004920405.1_ASM492040v1_genomic.fna.gz | prodigal -d GCF_004920405.1_ASM492040v1_genomic.fna/cds.fna -a GCF_004920405.1_ASM492040v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:03:46,254] [INFO] Task succeeded: Prodigal
[2024-01-24 15:03:46,254] [INFO] Task started: HMMsearch
[2024-01-24 15:03:46,254] [INFO] Running command: hmmsearch --tblout GCF_004920405.1_ASM492040v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7475deeb-0db6-400a-94d8-d09f320063a3/dqc_reference/reference_markers.hmm GCF_004920405.1_ASM492040v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:03:46,556] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:03:46,557] [INFO] Found 6/6 markers.
[2024-01-24 15:03:46,606] [INFO] Query marker FASTA was written to GCF_004920405.1_ASM492040v1_genomic.fna/markers.fasta
[2024-01-24 15:03:46,607] [INFO] Task started: Blastn
[2024-01-24 15:03:46,607] [INFO] Running command: blastn -query GCF_004920405.1_ASM492040v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7475deeb-0db6-400a-94d8-d09f320063a3/dqc_reference/reference_markers.fasta -out GCF_004920405.1_ASM492040v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:47,629] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:47,645] [INFO] Selected 12 target genomes.
[2024-01-24 15:03:47,645] [INFO] Target genome list was writen to GCF_004920405.1_ASM492040v1_genomic.fna/target_genomes.txt
[2024-01-24 15:03:47,650] [INFO] Task started: fastANI
[2024-01-24 15:03:47,650] [INFO] Running command: fastANI --query /var/lib/cwl/stg6223b886-9980-4687-955e-59cd650ef504/GCF_004920405.1_ASM492040v1_genomic.fna.gz --refList GCF_004920405.1_ASM492040v1_genomic.fna/target_genomes.txt --output GCF_004920405.1_ASM492040v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:04:00,989] [INFO] Task succeeded: fastANI
[2024-01-24 15:04:00,990] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7475deeb-0db6-400a-94d8-d09f320063a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:04:00,990] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7475deeb-0db6-400a-94d8-d09f320063a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:04:01,006] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:04:01,007] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:04:01,007] [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 peli	strain=DSM 17833	GCA_900099645.1	592361	592361	type	True	85.4956	1117	1456	95	below_threshold
Pseudomonas peli	strain=DSM 17833	GCA_012986145.1	592361	592361	type	True	85.4884	1123	1456	95	below_threshold
Pseudomonas guineae	strain=LMG 24016	GCA_900113745.1	425504	425504	type	True	85.3593	1069	1456	95	below_threshold
Pseudomonas tumuqii	strain=LAMW06	GCA_013184545.1	2715755	2715755	type	True	81.8334	878	1456	95	below_threshold
Pseudomonas borbori	strain=DSM 17834	GCA_900115555.1	289003	289003	type	True	81.6621	830	1456	95	below_threshold
Pseudomonas cuatrocienegasensis	strain=CIP 109853	GCA_900110925.1	543360	543360	type	True	81.5699	835	1456	95	below_threshold
Pseudomonas benzenivorans	strain=DSM 8628	GCA_900100495.1	556533	556533	type	True	81.3852	906	1456	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	81.2084	825	1456	95	below_threshold
Pseudomonas ullengensis	strain=UL070	GCA_014174475.1	2759166	2759166	type	True	80.9845	739	1456	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	80.7383	854	1456	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	80.3422	738	1456	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	80.0943	682	1456	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:04:01,008] [INFO] DFAST Taxonomy check result was written to GCF_004920405.1_ASM492040v1_genomic.fna/tc_result.tsv
[2024-01-24 15:04:01,009] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:04:01,009] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:04:01,009] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7475deeb-0db6-400a-94d8-d09f320063a3/dqc_reference/checkm_data
[2024-01-24 15:04:01,011] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:04:01,053] [INFO] Task started: CheckM
[2024-01-24 15:04:01,054] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004920405.1_ASM492040v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004920405.1_ASM492040v1_genomic.fna/checkm_input GCF_004920405.1_ASM492040v1_genomic.fna/checkm_result
[2024-01-24 15:04:44,838] [INFO] Task succeeded: CheckM
[2024-01-24 15:04:44,839] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:04:44,861] [INFO] ===== Completeness check finished =====
[2024-01-24 15:04:44,862] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:04:44,862] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004920405.1_ASM492040v1_genomic.fna/markers.fasta)
[2024-01-24 15:04:44,863] [INFO] Task started: Blastn
[2024-01-24 15:04:44,863] [INFO] Running command: blastn -query GCF_004920405.1_ASM492040v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7475deeb-0db6-400a-94d8-d09f320063a3/dqc_reference/reference_markers_gtdb.fasta -out GCF_004920405.1_ASM492040v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:04:46,580] [INFO] Task succeeded: Blastn
[2024-01-24 15:04:46,584] [INFO] Selected 12 target genomes.
[2024-01-24 15:04:46,584] [INFO] Target genome list was writen to GCF_004920405.1_ASM492040v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:04:46,593] [INFO] Task started: fastANI
[2024-01-24 15:04:46,593] [INFO] Running command: fastANI --query /var/lib/cwl/stg6223b886-9980-4687-955e-59cd650ef504/GCF_004920405.1_ASM492040v1_genomic.fna.gz --refList GCF_004920405.1_ASM492040v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004920405.1_ASM492040v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:04:59,515] [INFO] Task succeeded: fastANI
[2024-01-24 15:04:59,530] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:04:59,530] [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_004920405.1	s__Pseudomonas_E leptonychotis	100.0	1454	1456	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
GCA_002840155.1	s__Pseudomonas_E sp002840155	86.4489	1197	1456	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018827205.1	s__Pseudomonas_E sp018827205	86.0065	1040	1456	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.54	99.51	0.89	0.88	4	-
GCF_900099645.1	s__Pseudomonas_E peli	85.5037	1116	1456	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.85	96.04	0.90	0.85	7	-
GCF_900113745.1	s__Pseudomonas_E guineae	85.3308	1072	1456	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018816095.1	s__Pseudomonas_E sp018816095	84.8526	917	1456	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.20	96.15	0.83	0.82	4	-
GCA_017886405.1	s__Pseudomonas_E sp017886405	83.9587	684	1456	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002354655.1	s__Pseudomonas_E sp002354655	82.7571	935	1456	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.84	99.84	0.95	0.95	2	-
GCA_001465025.1	s__Pseudomonas_E sp001465025	82.628	878	1456	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.96	95.96	0.61	0.61	2	-
GCF_013184545.1	s__Pseudomonas_E sp013184545	81.8339	878	1456	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_002025205.1	s__Pseudomonas_E sp002025205	81.7395	882	1456	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_900115555.1	s__Pseudomonas_E borbori	81.6664	829	1456	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 15:04:59,532] [INFO] GTDB search result was written to GCF_004920405.1_ASM492040v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:04:59,532] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:04:59,536] [INFO] DFAST_QC result json was written to GCF_004920405.1_ASM492040v1_genomic.fna/dqc_result.json
[2024-01-24 15:04:59,536] [INFO] DFAST_QC completed!
[2024-01-24 15:04:59,536] [INFO] Total running time: 0h1m29s