[2024-01-24 13:59:42,751] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:59:42,753] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:59:42,753] [INFO] DQC Reference Directory: /var/lib/cwl/stg8a936c83-88dd-40a7-8a77-ddc1d4a41a5d/dqc_reference
[2024-01-24 13:59:44,062] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:59:44,063] [INFO] Task started: Prodigal
[2024-01-24 13:59:44,063] [INFO] Running command: gunzip -c /var/lib/cwl/stgc89fd0f6-a841-487b-8768-3f0d5902d756/GCF_000730565.1_ASM73056v1_genomic.fna.gz | prodigal -d GCF_000730565.1_ASM73056v1_genomic.fna/cds.fna -a GCF_000730565.1_ASM73056v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:00:01,954] [INFO] Task succeeded: Prodigal
[2024-01-24 14:00:01,955] [INFO] Task started: HMMsearch
[2024-01-24 14:00:01,955] [INFO] Running command: hmmsearch --tblout GCF_000730565.1_ASM73056v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8a936c83-88dd-40a7-8a77-ddc1d4a41a5d/dqc_reference/reference_markers.hmm GCF_000730565.1_ASM73056v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:00:02,228] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:00:02,229] [INFO] Found 6/6 markers.
[2024-01-24 14:00:02,268] [INFO] Query marker FASTA was written to GCF_000730565.1_ASM73056v1_genomic.fna/markers.fasta
[2024-01-24 14:00:02,268] [INFO] Task started: Blastn
[2024-01-24 14:00:02,269] [INFO] Running command: blastn -query GCF_000730565.1_ASM73056v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a936c83-88dd-40a7-8a77-ddc1d4a41a5d/dqc_reference/reference_markers.fasta -out GCF_000730565.1_ASM73056v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:00:03,269] [INFO] Task succeeded: Blastn
[2024-01-24 14:00:03,273] [INFO] Selected 17 target genomes.
[2024-01-24 14:00:03,274] [INFO] Target genome list was writen to GCF_000730565.1_ASM73056v1_genomic.fna/target_genomes.txt
[2024-01-24 14:00:03,281] [INFO] Task started: fastANI
[2024-01-24 14:00:03,282] [INFO] Running command: fastANI --query /var/lib/cwl/stgc89fd0f6-a841-487b-8768-3f0d5902d756/GCF_000730565.1_ASM73056v1_genomic.fna.gz --refList GCF_000730565.1_ASM73056v1_genomic.fna/target_genomes.txt --output GCF_000730565.1_ASM73056v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:00:22,538] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:22,539] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8a936c83-88dd-40a7-8a77-ddc1d4a41a5d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:00:22,539] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8a936c83-88dd-40a7-8a77-ddc1d4a41a5d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:00:22,555] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:00:22,555] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:00:22,555] [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 fulva	strain=NBRC 16637	GCA_000730565.1	47880	47880	type	True	100.0	1564	1567	95	conclusive
Pseudomonas fulva	strain=DSM 17717	GCA_000621265.1	47880	47880	type	True	99.9886	1555	1567	95	conclusive
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	84.5831	1090	1567	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	84.5183	1049	1567	95	below_threshold
Pseudomonas parafulva	strain=DSM 17004	GCA_000425765.1	157782	157782	suspected-type	True	84.389	1179	1567	95	below_threshold
Pseudomonas putida	strain=IPO3752	GCA_013387005.1	303	303	suspected-type	True	84.3432	1120	1567	95	below_threshold
Pseudomonas putida	strain=NCTC10936	GCA_900455645.1	303	303	suspected-type	True	84.325	1139	1567	95	below_threshold
Pseudomonas monteilii	strain=NBRC 103158	GCA_000730605.1	76759	76759	type	True	84.285	1105	1567	95	below_threshold
Pseudomonas putida	strain=ATCC 12633	GCA_024508115.1	303	303	suspected-type	True	84.2844	1151	1567	95	below_threshold
Pseudomonas putida	strain=NBRC 14164	GCA_000412675.1	303	303	suspected-type	True	84.282	1152	1567	95	below_threshold
Pseudomonas monteilii	strain=DSM 14164	GCA_000621245.1	76759	76759	type	True	84.2679	1131	1567	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	83.8357	1051	1567	95	below_threshold
Pseudomonas muyukensis	strain=COW39	GCA_019139535.1	2842357	2842357	type	True	83.7459	1055	1567	95	below_threshold
Pseudomonas sichuanensis	strain=WCHPs060039	GCA_003231305.1	2213015	2213015	type	True	83.6357	1036	1567	95	below_threshold
Pseudomonas fakonensis	strain=COW40	GCA_019139895.1	2842355	2842355	type	True	83.6314	1081	1567	95	below_threshold
Pseudomonas xantholysinigenes	strain=RW9S1A	GCA_014268885.2	2745490	2745490	type	True	83.5411	1044	1567	95	below_threshold
Pseudomonas ceruminis	strain=BML-PP028	GCA_013373895.1	2740516	2740516	type	True	83.4872	1067	1567	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:00:22,558] [INFO] DFAST Taxonomy check result was written to GCF_000730565.1_ASM73056v1_genomic.fna/tc_result.tsv
[2024-01-24 14:00:22,559] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:00:22,559] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:00:22,559] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8a936c83-88dd-40a7-8a77-ddc1d4a41a5d/dqc_reference/checkm_data
[2024-01-24 14:00:22,561] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:00:22,611] [INFO] Task started: CheckM
[2024-01-24 14:00:22,612] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000730565.1_ASM73056v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000730565.1_ASM73056v1_genomic.fna/checkm_input GCF_000730565.1_ASM73056v1_genomic.fna/checkm_result
[2024-01-24 14:01:15,511] [INFO] Task succeeded: CheckM
[2024-01-24 14:01:15,513] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:01:15,532] [INFO] ===== Completeness check finished =====
[2024-01-24 14:01:15,532] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:01:15,533] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000730565.1_ASM73056v1_genomic.fna/markers.fasta)
[2024-01-24 14:01:15,533] [INFO] Task started: Blastn
[2024-01-24 14:01:15,533] [INFO] Running command: blastn -query GCF_000730565.1_ASM73056v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a936c83-88dd-40a7-8a77-ddc1d4a41a5d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000730565.1_ASM73056v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:01:17,401] [INFO] Task succeeded: Blastn
[2024-01-24 14:01:17,405] [INFO] Selected 20 target genomes.
[2024-01-24 14:01:17,405] [INFO] Target genome list was writen to GCF_000730565.1_ASM73056v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:01:17,430] [INFO] Task started: fastANI
[2024-01-24 14:01:17,430] [INFO] Running command: fastANI --query /var/lib/cwl/stgc89fd0f6-a841-487b-8768-3f0d5902d756/GCF_000730565.1_ASM73056v1_genomic.fna.gz --refList GCF_000730565.1_ASM73056v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000730565.1_ASM73056v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:01:40,885] [INFO] Task succeeded: fastANI
[2024-01-24 14:01:40,901] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:01:40,901] [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_000730565.1	s__Pseudomonas_E fulva	100.0	1564	1567	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.00	95.45	0.93	0.89	89	conclusive
GCF_002021815.1	s__Pseudomonas_E parafulva_B	93.9177	1397	1567	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.79	97.25	0.94	0.89	23	-
GCF_003331055.1	s__Pseudomonas_E sp003331055	84.7291	1076	1567	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_001642705.1	s__Pseudomonas_E sp001642705	84.6447	1149	1567	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.26	95.01	0.89	0.85	3	-
GCF_000935045.1	s__Pseudomonas_E sp000935045	84.6323	1115	1567	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_013373935.1	s__Pseudomonas_E sp002438125	84.5298	1048	1567	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.14	98.14	0.84	0.84	2	-
GCF_015680405.1	s__Pseudomonas_E pudica	84.506	1106	1567	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0481	98.52	95.23	0.90	0.83	12	-
GCF_002165135.1	s__Pseudomonas_E sp002165135	84.4774	1104	1567	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_000730605.1	s__Pseudomonas_E monteilii	84.2863	1105	1567	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.80	95.46	0.86	0.79	45	-
GCF_000412675.1	s__Pseudomonas_E putida	84.2858	1152	1567	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.61	97.45	0.89	0.83	24	-
GCF_016658545.1	s__Pseudomonas_E sp016658545	84.2496	1123	1567	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_017744435.1	s__Pseudomonas_E sp017744435	84.1484	1077	1567	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_002112505.1	s__Pseudomonas_E sp002112505	84.0873	1145	1567	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	0.99	6	-
GCF_009391885.1	s__Pseudomonas_E sp009391885	84.0631	1085	1567	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_009932375.1	s__Pseudomonas_E juntendi	83.8477	1047	1567	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.06	97.13	0.84	0.79	41	-
GCF_016648105.1	s__Pseudomonas_E sp016648105	83.8087	1060	1567	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_019139535.1	s__Pseudomonas_E sp019139535	83.7416	1055	1567	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_003231305.1	s__Pseudomonas_E sichuanensis	83.6295	1036	1567	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.11	95.79	0.86	0.83	4	-
GCF_004519305.1	s__Pseudomonas_E sp004519305	83.4686	1037	1567	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_004357765.1	s__Pseudomonas_E putida_U	83.3052	1025	1567	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.43	99.43	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:01:40,902] [INFO] GTDB search result was written to GCF_000730565.1_ASM73056v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:01:40,903] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:01:40,908] [INFO] DFAST_QC result json was written to GCF_000730565.1_ASM73056v1_genomic.fna/dqc_result.json
[2024-01-24 14:01:40,908] [INFO] DFAST_QC completed!
[2024-01-24 14:01:40,908] [INFO] Total running time: 0h1m58s