[2024-01-24 12:45:10,985] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:45:10,988] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:45:10,988] [INFO] DQC Reference Directory: /var/lib/cwl/stg0b3c6baf-c5b0-4de3-ad18-ce7828bc5636/dqc_reference
[2024-01-24 12:45:13,181] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:45:13,192] [INFO] Task started: Prodigal
[2024-01-24 12:45:13,193] [INFO] Running command: gunzip -c /var/lib/cwl/stga619eddd-74c2-41fd-906f-335bc11367d0/GCF_021602345.1_ASM2160234v1_genomic.fna.gz | prodigal -d GCF_021602345.1_ASM2160234v1_genomic.fna/cds.fna -a GCF_021602345.1_ASM2160234v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:36,717] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:36,718] [INFO] Task started: HMMsearch
[2024-01-24 12:45:36,718] [INFO] Running command: hmmsearch --tblout GCF_021602345.1_ASM2160234v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0b3c6baf-c5b0-4de3-ad18-ce7828bc5636/dqc_reference/reference_markers.hmm GCF_021602345.1_ASM2160234v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:37,044] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:37,045] [INFO] Found 6/6 markers.
[2024-01-24 12:45:37,106] [INFO] Query marker FASTA was written to GCF_021602345.1_ASM2160234v1_genomic.fna/markers.fasta
[2024-01-24 12:45:37,107] [INFO] Task started: Blastn
[2024-01-24 12:45:37,107] [INFO] Running command: blastn -query GCF_021602345.1_ASM2160234v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b3c6baf-c5b0-4de3-ad18-ce7828bc5636/dqc_reference/reference_markers.fasta -out GCF_021602345.1_ASM2160234v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:38,225] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:38,230] [INFO] Selected 13 target genomes.
[2024-01-24 12:45:38,230] [INFO] Target genome list was writen to GCF_021602345.1_ASM2160234v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:38,350] [INFO] Task started: fastANI
[2024-01-24 12:45:38,351] [INFO] Running command: fastANI --query /var/lib/cwl/stga619eddd-74c2-41fd-906f-335bc11367d0/GCF_021602345.1_ASM2160234v1_genomic.fna.gz --refList GCF_021602345.1_ASM2160234v1_genomic.fna/target_genomes.txt --output GCF_021602345.1_ASM2160234v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:59,300] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:59,300] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0b3c6baf-c5b0-4de3-ad18-ce7828bc5636/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:59,301] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0b3c6baf-c5b0-4de3-ad18-ce7828bc5636/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:59,316] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:45:59,316] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:59,316] [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 pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	100.0	2146	2148	95	conclusive
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	94.2891	1791	2148	95	below_threshold
Pseudomonas allokribbensis	strain=IzPS23	GCA_014863605.1	2774460	2774460	type	True	91.7396	1773	2148	95	below_threshold
Pseudomonas kribbensis	strain=46-2	GCA_003352185.1	1628086	1628086	type	True	91.4931	1738	2148	95	below_threshold
Pseudomonas bananamidigenes	strain=BW11P2	GCA_001679645.1	2843610	2843610	type	True	90.3293	1626	2148	95	below_threshold
Pseudomonas koreensis	strain=DSM 16610	GCA_012986595.1	198620	198620	suspected-type	True	88.786	1686	2148	95	below_threshold
Pseudomonas monsensis	strain=PGSB 8459	GCA_014268495.2	2745509	2745509	type	True	88.3789	1669	2148	95	below_threshold
Pseudomonas crudilactis	strain=UCMA 17988	GCA_013433315.1	2697028	2697028	type	True	87.946	1719	2148	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	87.9202	1740	2148	95	below_threshold
Pseudomonas granadensis	strain=LMG 27940	GCA_900105485.1	1421430	1421430	suspected-type	True	87.2775	1617	2148	95	below_threshold
Pseudomonas moorei	strain=CCUG 53114	GCA_008801475.1	395599	395599	type	True	85.8815	1422	2148	95	below_threshold
Pseudomonas lurida	strain=LMG 21995	GCA_002563895.1	244566	244566	type	True	83.5122	1274	2148	95	below_threshold
Pseudomonas brassicae	strain=MAFF 212427	GCA_010671725.1	2708063	2708063	type	True	82.2244	893	2148	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:59,319] [INFO] DFAST Taxonomy check result was written to GCF_021602345.1_ASM2160234v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:59,320] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:59,320] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:59,320] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0b3c6baf-c5b0-4de3-ad18-ce7828bc5636/dqc_reference/checkm_data
[2024-01-24 12:45:59,321] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:59,386] [INFO] Task started: CheckM
[2024-01-24 12:45:59,386] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021602345.1_ASM2160234v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021602345.1_ASM2160234v1_genomic.fna/checkm_input GCF_021602345.1_ASM2160234v1_genomic.fna/checkm_result
[2024-01-24 12:47:11,559] [INFO] Task succeeded: CheckM
[2024-01-24 12:47:11,561] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:47:11,590] [INFO] ===== Completeness check finished =====
[2024-01-24 12:47:11,590] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:47:11,591] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021602345.1_ASM2160234v1_genomic.fna/markers.fasta)
[2024-01-24 12:47:11,591] [INFO] Task started: Blastn
[2024-01-24 12:47:11,591] [INFO] Running command: blastn -query GCF_021602345.1_ASM2160234v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b3c6baf-c5b0-4de3-ad18-ce7828bc5636/dqc_reference/reference_markers_gtdb.fasta -out GCF_021602345.1_ASM2160234v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:13,502] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:13,506] [INFO] Selected 9 target genomes.
[2024-01-24 12:47:13,506] [INFO] Target genome list was writen to GCF_021602345.1_ASM2160234v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:47:14,061] [INFO] Task started: fastANI
[2024-01-24 12:47:14,062] [INFO] Running command: fastANI --query /var/lib/cwl/stga619eddd-74c2-41fd-906f-335bc11367d0/GCF_021602345.1_ASM2160234v1_genomic.fna.gz --refList GCF_021602345.1_ASM2160234v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021602345.1_ASM2160234v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:47:29,766] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:29,788] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:47:29,788] [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_010448615.1	s__Pseudomonas_E sp001655595	96.2825	1887	2148	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.61	96.24	0.94	0.90	22	conclusive
GCF_004006335.1	s__Pseudomonas_E sp002112885	94.5885	1854	2148	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.01	95.48	0.92	0.90	14	-
GCF_001594225.2	s__Pseudomonas_E glycinae	94.5465	1831	2148	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.56	95.98	0.93	0.88	9	-
GCF_003352875.1	s__Pseudomonas_E fluorescens_BF	94.011	1823	2148	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_014863585.1	s__Pseudomonas_E gozinkensis	93.8761	1822	2148	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_002113125.1	s__Pseudomonas_E sp002113125	93.83	1827	2148	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	1.00	2	-
GCF_012974785.1	s__Pseudomonas_E fluorescens_BT	92.1208	1786	2148	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.87	98.87	0.96	0.96	2	-
GCF_014863605.1	s__Pseudomonas_E allokribbensis	91.7188	1775	2148	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.79	97.76	0.93	0.92	10	-
GCF_003352185.1	s__Pseudomonas_E kribbensis	91.4964	1738	2148	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.22	95.68	0.92	0.89	10	-
--------------------------------------------------------------------------------
[2024-01-24 12:47:29,790] [INFO] GTDB search result was written to GCF_021602345.1_ASM2160234v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:47:29,791] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:47:29,795] [INFO] DFAST_QC result json was written to GCF_021602345.1_ASM2160234v1_genomic.fna/dqc_result.json
[2024-01-24 12:47:29,795] [INFO] DFAST_QC completed!
[2024-01-24 12:47:29,795] [INFO] Total running time: 0h2m19s