[2024-01-24 14:19:51,496] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:51,499] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:51,499] [INFO] DQC Reference Directory: /var/lib/cwl/stg0ab86e3c-d8c5-404d-82b8-f3eb65c42a84/dqc_reference
[2024-01-24 14:19:56,937] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:56,940] [INFO] Task started: Prodigal
[2024-01-24 14:19:56,941] [INFO] Running command: gunzip -c /var/lib/cwl/stgcbc6f85e-8d53-4df6-9997-ac0ba17660ac/GCF_000730585.1_ASM73058v1_genomic.fna.gz | prodigal -d GCF_000730585.1_ASM73058v1_genomic.fna/cds.fna -a GCF_000730585.1_ASM73058v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:20:19,723] [INFO] Task succeeded: Prodigal
[2024-01-24 14:20:19,723] [INFO] Task started: HMMsearch
[2024-01-24 14:20:19,723] [INFO] Running command: hmmsearch --tblout GCF_000730585.1_ASM73058v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0ab86e3c-d8c5-404d-82b8-f3eb65c42a84/dqc_reference/reference_markers.hmm GCF_000730585.1_ASM73058v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:20:20,078] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:20:20,079] [INFO] Found 6/6 markers.
[2024-01-24 14:20:20,143] [INFO] Query marker FASTA was written to GCF_000730585.1_ASM73058v1_genomic.fna/markers.fasta
[2024-01-24 14:20:20,143] [INFO] Task started: Blastn
[2024-01-24 14:20:20,143] [INFO] Running command: blastn -query GCF_000730585.1_ASM73058v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ab86e3c-d8c5-404d-82b8-f3eb65c42a84/dqc_reference/reference_markers.fasta -out GCF_000730585.1_ASM73058v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:22,693] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:22,702] [INFO] Selected 13 target genomes.
[2024-01-24 14:20:22,703] [INFO] Target genome list was writen to GCF_000730585.1_ASM73058v1_genomic.fna/target_genomes.txt
[2024-01-24 14:20:22,730] [INFO] Task started: fastANI
[2024-01-24 14:20:22,730] [INFO] Running command: fastANI --query /var/lib/cwl/stgcbc6f85e-8d53-4df6-9997-ac0ba17660ac/GCF_000730585.1_ASM73058v1_genomic.fna.gz --refList GCF_000730585.1_ASM73058v1_genomic.fna/target_genomes.txt --output GCF_000730585.1_ASM73058v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:44,278] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:44,279] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0ab86e3c-d8c5-404d-82b8-f3eb65c42a84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:44,280] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0ab86e3c-d8c5-404d-82b8-f3eb65c42a84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:44,296] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:20:44,296] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:20:44,297] [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 japonica	strain=NBRC 103040	GCA_000730585.1	256466	256466	type	True	100.0	2131	2140	95	conclusive
Pseudomonas japonica	strain=DSM 22348	GCA_900188455.1	256466	256466	type	True	99.9859	2125	2140	95	conclusive
Pseudomonas bharatica	strain=CSV86	GCA_000319305.2	2692112	2692112	type	True	88.2682	1496	2140	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	85.102	1139	2140	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	85.066	1191	2140	95	below_threshold
Pseudomonas brassicae	strain=MAFF 212427	GCA_010671725.1	2708063	2708063	type	True	84.7792	1029	2140	95	below_threshold
Pseudomonas alkylphenolica	strain=KL28	GCA_000746525.1	237609	237609	type	True	84.5696	1149	2140	95	below_threshold
Pseudomonas vranovensis	strain=DSM 16006	GCA_000425805.1	321661	321661	type	True	84.2146	1192	2140	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_021602465.1	2740517	2740517	suspected-type	True	84.0177	1173	2140	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	83.923	1096	2140	95	below_threshold
Pseudomonas chlororaphis subsp. aurantiaca	strain=DSM 19603	GCA_003851835.1	86192	587753	type	True	83.4206	1213	2140	95	below_threshold
Pseudomonas defluvii	strain=WCHP16	GCA_001695625.1	1876757	1876757	type	True	83.0505	948	2140	95	below_threshold
Pseudomonas laurentiana	strain=JCM 32154	GCA_014648275.1	2364649	2364649	type	True	82.8114	1025	2140	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:44,298] [INFO] DFAST Taxonomy check result was written to GCF_000730585.1_ASM73058v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:44,299] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:44,299] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:44,300] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0ab86e3c-d8c5-404d-82b8-f3eb65c42a84/dqc_reference/checkm_data
[2024-01-24 14:20:44,301] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:44,370] [INFO] Task started: CheckM
[2024-01-24 14:20:44,371] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000730585.1_ASM73058v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000730585.1_ASM73058v1_genomic.fna/checkm_input GCF_000730585.1_ASM73058v1_genomic.fna/checkm_result
[2024-01-24 14:22:00,565] [INFO] Task succeeded: CheckM
[2024-01-24 14:22:00,567] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:22:00,591] [INFO] ===== Completeness check finished =====
[2024-01-24 14:22:00,591] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:22:00,592] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000730585.1_ASM73058v1_genomic.fna/markers.fasta)
[2024-01-24 14:22:00,592] [INFO] Task started: Blastn
[2024-01-24 14:22:00,592] [INFO] Running command: blastn -query GCF_000730585.1_ASM73058v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ab86e3c-d8c5-404d-82b8-f3eb65c42a84/dqc_reference/reference_markers_gtdb.fasta -out GCF_000730585.1_ASM73058v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:05,742] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:05,748] [INFO] Selected 8 target genomes.
[2024-01-24 14:22:05,748] [INFO] Target genome list was writen to GCF_000730585.1_ASM73058v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:22:05,757] [INFO] Task started: fastANI
[2024-01-24 14:22:05,757] [INFO] Running command: fastANI --query /var/lib/cwl/stgcbc6f85e-8d53-4df6-9997-ac0ba17660ac/GCF_000730585.1_ASM73058v1_genomic.fna.gz --refList GCF_000730585.1_ASM73058v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000730585.1_ASM73058v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:22:20,330] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:20,356] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:22:20,356] [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_900188455.1	s__Pseudomonas_E japonica	99.9859	2125	2140	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_001941965.1	s__Pseudomonas_E putida_L	89.2681	1561	2140	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_003523465.1	s__Pseudomonas_E sp003523465	88.9416	682	2140	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_000319305.2	s__Pseudomonas_E putida_C	88.3162	1491	2140	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.35	97.35	0.88	0.88	2	-
GCF_900187455.1	s__Pseudomonas_E sp900187455	87.6868	1556	2140	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_003231275.1	s__Pseudomonas_E huaxiensis	87.4145	1537	2140	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.93	95.93	0.85	0.85	2	-
GCF_003105155.1	s__Pseudomonas_E sp003105155	85.3274	1172	2140	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_004214895.1	s__Pseudomonas_E sp004214895	84.7562	1229	2140	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 14:22:20,358] [INFO] GTDB search result was written to GCF_000730585.1_ASM73058v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:22:20,359] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:22:20,365] [INFO] DFAST_QC result json was written to GCF_000730585.1_ASM73058v1_genomic.fna/dqc_result.json
[2024-01-24 14:22:20,365] [INFO] DFAST_QC completed!
[2024-01-24 14:22:20,365] [INFO] Total running time: 0h2m29s