[2024-01-24 14:46:55,494] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:55,497] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:55,497] [INFO] DQC Reference Directory: /var/lib/cwl/stged06f60f-be8c-4bf5-aed3-430a88b9f675/dqc_reference
[2024-01-24 14:46:58,013] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:58,015] [INFO] Task started: Prodigal
[2024-01-24 14:46:58,015] [INFO] Running command: gunzip -c /var/lib/cwl/stgf19521ab-cda6-4780-8996-abcfbaaaf192/GCF_028747405.1_ASM2874740v1_genomic.fna.gz | prodigal -d GCF_028747405.1_ASM2874740v1_genomic.fna/cds.fna -a GCF_028747405.1_ASM2874740v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:23,553] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:23,554] [INFO] Task started: HMMsearch
[2024-01-24 14:47:23,554] [INFO] Running command: hmmsearch --tblout GCF_028747405.1_ASM2874740v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stged06f60f-be8c-4bf5-aed3-430a88b9f675/dqc_reference/reference_markers.hmm GCF_028747405.1_ASM2874740v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:23,891] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:23,893] [INFO] Found 6/6 markers.
[2024-01-24 14:47:23,951] [INFO] Query marker FASTA was written to GCF_028747405.1_ASM2874740v1_genomic.fna/markers.fasta
[2024-01-24 14:47:23,952] [INFO] Task started: Blastn
[2024-01-24 14:47:23,952] [INFO] Running command: blastn -query GCF_028747405.1_ASM2874740v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged06f60f-be8c-4bf5-aed3-430a88b9f675/dqc_reference/reference_markers.fasta -out GCF_028747405.1_ASM2874740v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:24,914] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:24,917] [INFO] Selected 10 target genomes.
[2024-01-24 14:47:24,917] [INFO] Target genome list was writen to GCF_028747405.1_ASM2874740v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:24,922] [INFO] Task started: fastANI
[2024-01-24 14:47:24,922] [INFO] Running command: fastANI --query /var/lib/cwl/stgf19521ab-cda6-4780-8996-abcfbaaaf192/GCF_028747405.1_ASM2874740v1_genomic.fna.gz --refList GCF_028747405.1_ASM2874740v1_genomic.fna/target_genomes.txt --output GCF_028747405.1_ASM2874740v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:41,683] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:41,684] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stged06f60f-be8c-4bf5-aed3-430a88b9f675/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:41,684] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stged06f60f-be8c-4bf5-aed3-430a88b9f675/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:41,696] [INFO] Found 10 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 14:47:41,697] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:41,697] [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 chlororaphis subsp. chlororaphis	strain=DSM 50083	GCA_003945765.1	333	587753	type	True	99.9982	2210	2212	95	conclusive
Pseudomonas chlororaphis subsp. chlororaphis	strain=LMG 5004	GCA_001269625.1	333	587753	type	True	99.9967	2197	2212	95	conclusive
Pseudomonas chlororaphis subsp. chlororaphis	strain=DSM 50083	GCA_007858335.1	333	587753	type	True	99.9933	2191	2212	95	conclusive
Pseudomonas chlororaphis subsp. chlororaphis	strain=ATCC 9446	GCA_002095925.1	333	587753	type	True	99.9887	2186	2212	95	conclusive
Pseudomonas chlororaphis subsp. chlororaphis		GCA_900625015.1	333	587753	type	True	99.9861	2191	2212	95	conclusive
Pseudomonas pergaminensis	strain=1008	GCA_024112395.1	2853159	2853159	type	True	84.1358	1367	2212	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	82.7269	1125	2212	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	82.7129	1069	2212	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	82.0675	974	2212	95	below_threshold
Pseudomonas ceruminis	strain=BML-PP028	GCA_013373895.1	2740516	2740516	type	True	81.4625	992	2212	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:41,699] [INFO] DFAST Taxonomy check result was written to GCF_028747405.1_ASM2874740v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:41,700] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:41,700] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:41,700] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stged06f60f-be8c-4bf5-aed3-430a88b9f675/dqc_reference/checkm_data
[2024-01-24 14:47:41,703] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:41,775] [INFO] Task started: CheckM
[2024-01-24 14:47:41,775] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028747405.1_ASM2874740v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028747405.1_ASM2874740v1_genomic.fna/checkm_input GCF_028747405.1_ASM2874740v1_genomic.fna/checkm_result
[2024-01-24 14:48:54,648] [INFO] Task succeeded: CheckM
[2024-01-24 14:48:54,650] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:48:54,674] [INFO] ===== Completeness check finished =====
[2024-01-24 14:48:54,674] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:48:54,675] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028747405.1_ASM2874740v1_genomic.fna/markers.fasta)
[2024-01-24 14:48:54,675] [INFO] Task started: Blastn
[2024-01-24 14:48:54,675] [INFO] Running command: blastn -query GCF_028747405.1_ASM2874740v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged06f60f-be8c-4bf5-aed3-430a88b9f675/dqc_reference/reference_markers_gtdb.fasta -out GCF_028747405.1_ASM2874740v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:56,444] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:56,448] [INFO] Selected 7 target genomes.
[2024-01-24 14:48:56,449] [INFO] Target genome list was writen to GCF_028747405.1_ASM2874740v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:48:56,455] [INFO] Task started: fastANI
[2024-01-24 14:48:56,455] [INFO] Running command: fastANI --query /var/lib/cwl/stgf19521ab-cda6-4780-8996-abcfbaaaf192/GCF_028747405.1_ASM2874740v1_genomic.fna.gz --refList GCF_028747405.1_ASM2874740v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028747405.1_ASM2874740v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:49:10,289] [INFO] Task succeeded: fastANI
[2024-01-24 14:49:10,296] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:49:10,297] [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_003945765.1	s__Pseudomonas_E chlororaphis	99.9982	2210	2212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.91	95.71	0.92	0.83	34	conclusive
GCF_003850345.1	s__Pseudomonas_E chlororaphis_F	94.9976	1970	2212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.16	95.02	0.90	0.86	82	-
GCF_900107395.1	s__Pseudomonas_E sp900107395	93.4842	1866	2212	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_001921865.1	s__Pseudomonas_E chlororaphis_D	91.3858	1775	2212	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_000931465.1	s__Pseudomonas_E sp000931465	91.1784	1813	2212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.57	98.57	0.96	0.96	2	-
GCF_000397205.1	s__Pseudomonas_E protegens	86.7743	1606	2212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.81	97.08	0.96	0.89	76	-
GCF_003363755.1	s__Pseudomonas_E protegens_A	86.2595	1564	2212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.07	97.56	0.94	0.93	12	-
--------------------------------------------------------------------------------
[2024-01-24 14:49:10,298] [INFO] GTDB search result was written to GCF_028747405.1_ASM2874740v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:49:10,299] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:49:10,302] [INFO] DFAST_QC result json was written to GCF_028747405.1_ASM2874740v1_genomic.fna/dqc_result.json
[2024-01-24 14:49:10,302] [INFO] DFAST_QC completed!
[2024-01-24 14:49:10,302] [INFO] Total running time: 0h2m15s