[2024-01-24 13:48:43,630] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:48:43,632] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:48:43,632] [INFO] DQC Reference Directory: /var/lib/cwl/stg1fdbed93-1c5c-4775-a078-5c1ccc83297a/dqc_reference
[2024-01-24 13:48:44,882] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:48:44,883] [INFO] Task started: Prodigal
[2024-01-24 13:48:44,883] [INFO] Running command: gunzip -c /var/lib/cwl/stgd9017808-5b26-4a3e-a801-d63243490168/GCF_007795095.1_ASM779509v1_genomic.fna.gz | prodigal -d GCF_007795095.1_ASM779509v1_genomic.fna/cds.fna -a GCF_007795095.1_ASM779509v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:48:53,530] [INFO] Task succeeded: Prodigal
[2024-01-24 13:48:53,531] [INFO] Task started: HMMsearch
[2024-01-24 13:48:53,531] [INFO] Running command: hmmsearch --tblout GCF_007795095.1_ASM779509v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1fdbed93-1c5c-4775-a078-5c1ccc83297a/dqc_reference/reference_markers.hmm GCF_007795095.1_ASM779509v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:48:53,786] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:48:53,787] [INFO] Found 6/6 markers.
[2024-01-24 13:48:53,812] [INFO] Query marker FASTA was written to GCF_007795095.1_ASM779509v1_genomic.fna/markers.fasta
[2024-01-24 13:48:53,813] [INFO] Task started: Blastn
[2024-01-24 13:48:53,813] [INFO] Running command: blastn -query GCF_007795095.1_ASM779509v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1fdbed93-1c5c-4775-a078-5c1ccc83297a/dqc_reference/reference_markers.fasta -out GCF_007795095.1_ASM779509v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:48:54,854] [INFO] Task succeeded: Blastn
[2024-01-24 13:48:54,857] [INFO] Selected 10 target genomes.
[2024-01-24 13:48:54,858] [INFO] Target genome list was writen to GCF_007795095.1_ASM779509v1_genomic.fna/target_genomes.txt
[2024-01-24 13:48:54,865] [INFO] Task started: fastANI
[2024-01-24 13:48:54,865] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9017808-5b26-4a3e-a801-d63243490168/GCF_007795095.1_ASM779509v1_genomic.fna.gz --refList GCF_007795095.1_ASM779509v1_genomic.fna/target_genomes.txt --output GCF_007795095.1_ASM779509v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:02,987] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:02,988] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1fdbed93-1c5c-4775-a078-5c1ccc83297a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:02,988] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1fdbed93-1c5c-4775-a078-5c1ccc83297a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:03,001] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:03,001] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:03,001] [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
Luteimonas granuli	strain=Gr-4	GCA_007795095.1	1176533	1176533	type	True	100.0	972	972	95	conclusive
Luteimonas padinae	strain=KCTC 52403	GCA_014652935.1	1714359	1714359	type	True	87.3737	722	972	95	below_threshold
Luteimonas colneyensis	strain=Sa2BVA3	GCA_014836665.1	2762230	2762230	type	True	87.2248	731	972	95	below_threshold
Luteimonas arsenica	strain=26-35	GCA_004352825.1	1586242	1586242	type	True	86.9994	720	972	95	below_threshold
Luteimonas terricola	strain=BZ92r	GCA_004352845.1	645597	645597	type	True	86.6114	718	972	95	below_threshold
Luteimonas terricola	strain=CGMCC 1.8985	GCA_014645675.1	645597	645597	type	True	86.4851	739	972	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	82.4336	519	972	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	82.1043	593	972	95	below_threshold
Luteimonas viscosa	strain=XBU10	GCA_008244685.1	1132694	1132694	type	True	81.873	640	972	95	below_threshold
Luteimonas salinisoli	strain=SJ-92	GCA_013425525.1	2752307	2752307	type	True	81.7793	642	972	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:03,003] [INFO] DFAST Taxonomy check result was written to GCF_007795095.1_ASM779509v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:03,003] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:03,003] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:03,004] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1fdbed93-1c5c-4775-a078-5c1ccc83297a/dqc_reference/checkm_data
[2024-01-24 13:49:03,005] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:03,033] [INFO] Task started: CheckM
[2024-01-24 13:49:03,033] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007795095.1_ASM779509v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007795095.1_ASM779509v1_genomic.fna/checkm_input GCF_007795095.1_ASM779509v1_genomic.fna/checkm_result
[2024-01-24 13:49:52,147] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:52,149] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:49:52,167] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:52,168] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:52,168] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007795095.1_ASM779509v1_genomic.fna/markers.fasta)
[2024-01-24 13:49:52,169] [INFO] Task started: Blastn
[2024-01-24 13:49:52,169] [INFO] Running command: blastn -query GCF_007795095.1_ASM779509v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1fdbed93-1c5c-4775-a078-5c1ccc83297a/dqc_reference/reference_markers_gtdb.fasta -out GCF_007795095.1_ASM779509v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:54,302] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:54,307] [INFO] Selected 7 target genomes.
[2024-01-24 13:49:54,308] [INFO] Target genome list was writen to GCF_007795095.1_ASM779509v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:54,313] [INFO] Task started: fastANI
[2024-01-24 13:49:54,313] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9017808-5b26-4a3e-a801-d63243490168/GCF_007795095.1_ASM779509v1_genomic.fna.gz --refList GCF_007795095.1_ASM779509v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007795095.1_ASM779509v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:00,124] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:00,131] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:00,132] [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_007795095.1	s__Luteimonas granuli	100.0	972	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014652935.1	s__Luteimonas padinae	87.369	723	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014836665.1	s__Luteimonas sp014836665	87.1899	733	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004352825.1	s__Luteimonas arsenica	86.9853	721	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004352845.1	s__Luteimonas terricola	86.6114	718	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_016615955.1	s__Luteimonas sp016615955	86.3118	720	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	99.39	98.78	0.97	0.95	3	-
GCA_004297225.1	s__Luteimonas_B sp004297225	81.1137	451	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:00,143] [INFO] GTDB search result was written to GCF_007795095.1_ASM779509v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:00,144] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:00,149] [INFO] DFAST_QC result json was written to GCF_007795095.1_ASM779509v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:00,150] [INFO] DFAST_QC completed!
[2024-01-24 13:50:00,150] [INFO] Total running time: 0h1m17s