[2024-01-24 11:34:41,524] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:41,526] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:41,526] [INFO] DQC Reference Directory: /var/lib/cwl/stgd4bcd8de-98d1-4536-82e6-e7177794bc8c/dqc_reference
[2024-01-24 11:34:42,935] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:42,936] [INFO] Task started: Prodigal
[2024-01-24 11:34:42,936] [INFO] Running command: gunzip -c /var/lib/cwl/stge949e84c-b6a1-45ab-bc30-6e952e5ad006/GCF_007625165.1_ASM762516v1_genomic.fna.gz | prodigal -d GCF_007625165.1_ASM762516v1_genomic.fna/cds.fna -a GCF_007625165.1_ASM762516v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:34:49,464] [INFO] Task succeeded: Prodigal
[2024-01-24 11:34:49,464] [INFO] Task started: HMMsearch
[2024-01-24 11:34:49,464] [INFO] Running command: hmmsearch --tblout GCF_007625165.1_ASM762516v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd4bcd8de-98d1-4536-82e6-e7177794bc8c/dqc_reference/reference_markers.hmm GCF_007625165.1_ASM762516v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:34:49,696] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:34:49,698] [INFO] Found 6/6 markers.
[2024-01-24 11:34:49,718] [INFO] Query marker FASTA was written to GCF_007625165.1_ASM762516v1_genomic.fna/markers.fasta
[2024-01-24 11:34:49,718] [INFO] Task started: Blastn
[2024-01-24 11:34:49,718] [INFO] Running command: blastn -query GCF_007625165.1_ASM762516v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4bcd8de-98d1-4536-82e6-e7177794bc8c/dqc_reference/reference_markers.fasta -out GCF_007625165.1_ASM762516v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:34:50,590] [INFO] Task succeeded: Blastn
[2024-01-24 11:34:50,594] [INFO] Selected 11 target genomes.
[2024-01-24 11:34:50,594] [INFO] Target genome list was writen to GCF_007625165.1_ASM762516v1_genomic.fna/target_genomes.txt
[2024-01-24 11:34:50,599] [INFO] Task started: fastANI
[2024-01-24 11:34:50,599] [INFO] Running command: fastANI --query /var/lib/cwl/stge949e84c-b6a1-45ab-bc30-6e952e5ad006/GCF_007625165.1_ASM762516v1_genomic.fna.gz --refList GCF_007625165.1_ASM762516v1_genomic.fna/target_genomes.txt --output GCF_007625165.1_ASM762516v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:34:56,376] [INFO] Task succeeded: fastANI
[2024-01-24 11:34:56,377] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd4bcd8de-98d1-4536-82e6-e7177794bc8c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:34:56,377] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd4bcd8de-98d1-4536-82e6-e7177794bc8c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:34:56,387] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:34:56,387] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:34:56,387] [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
Spiribacter vilamensis	strain=DSM 21056	GCA_007625165.1	531306	531306	type	True	100.0	691	691	95	conclusive
Spiribacter vilamensis	strain=DSM 21056	GCA_004217415.1	531306	531306	type	True	99.9957	690	691	95	conclusive
Spiribacter curvatus	strain=UAH-SP71	GCA_000485905.1	1335757	1335757	type	True	83.2939	474	691	95	below_threshold
Spiribacter aquaticus	strain=SP30	GCA_007625215.1	1935996	1935996	type	True	81.3559	433	691	95	below_threshold
Spiribacter salinus	strain=M19-40	GCA_000319575.2	1335746	1335746	type	True	78.0879	176	691	95	below_threshold
Arhodomonas aquaeolei	strain=DSM 8974	GCA_000374645.1	2369	2369	type	True	77.4654	181	691	95	below_threshold
Aquisalimonas asiatica	strain=CGMCC 1.6291	GCA_900110585.1	406100	406100	type	True	77.2878	111	691	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	76.2982	80	691	95	below_threshold
Stutzerimonas frequens	strain=FDAARGOS_877	GCA_016028515.1	2968969	2968969	type	True	76.0983	62	691	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_024448335.1	2968969	2968969	type	True	75.9404	60	691	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	75.9339	60	691	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:34:56,389] [INFO] DFAST Taxonomy check result was written to GCF_007625165.1_ASM762516v1_genomic.fna/tc_result.tsv
[2024-01-24 11:34:56,389] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:34:56,390] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:34:56,390] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd4bcd8de-98d1-4536-82e6-e7177794bc8c/dqc_reference/checkm_data
[2024-01-24 11:34:56,391] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:34:56,413] [INFO] Task started: CheckM
[2024-01-24 11:34:56,414] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007625165.1_ASM762516v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007625165.1_ASM762516v1_genomic.fna/checkm_input GCF_007625165.1_ASM762516v1_genomic.fna/checkm_result
[2024-01-24 11:35:19,920] [INFO] Task succeeded: CheckM
[2024-01-24 11:35:19,921] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:35:19,939] [INFO] ===== Completeness check finished =====
[2024-01-24 11:35:19,939] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:35:19,939] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007625165.1_ASM762516v1_genomic.fna/markers.fasta)
[2024-01-24 11:35:19,939] [INFO] Task started: Blastn
[2024-01-24 11:35:19,940] [INFO] Running command: blastn -query GCF_007625165.1_ASM762516v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4bcd8de-98d1-4536-82e6-e7177794bc8c/dqc_reference/reference_markers_gtdb.fasta -out GCF_007625165.1_ASM762516v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:21,535] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:21,538] [INFO] Selected 11 target genomes.
[2024-01-24 11:35:21,539] [INFO] Target genome list was writen to GCF_007625165.1_ASM762516v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:35:21,546] [INFO] Task started: fastANI
[2024-01-24 11:35:21,546] [INFO] Running command: fastANI --query /var/lib/cwl/stge949e84c-b6a1-45ab-bc30-6e952e5ad006/GCF_007625165.1_ASM762516v1_genomic.fna.gz --refList GCF_007625165.1_ASM762516v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007625165.1_ASM762516v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:35:27,841] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:27,851] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:35:27,851] [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_004217415.1	s__Spiribacter vilamensis	99.9957	690	691	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Nitrococcaceae;g__Spiribacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_000485905.1	s__Spiribacter curvatus	83.2939	474	691	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Nitrococcaceae;g__Spiribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002813635.1	s__Spiribacter roseus	81.3809	422	691	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Nitrococcaceae;g__Spiribacter	95.0	98.20	97.75	0.92	0.91	7	-
GCF_003149435.1	s__E85 sp003149435	78.345	246	691	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Nitrococcaceae;g__E85	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009676705.1	s__Spiribacter sp009676705	78.0736	192	691	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Nitrococcaceae;g__Spiribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374645.1	s__Arhodomonas aquaeolei	77.4453	183	691	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Nitrococcaceae;g__Arhodomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110585.1	s__Aquisalimonas asiatica	77.2878	111	691	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Aquisalimonadaceae;g__Aquisalimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003664325.1	s__Alkalilimnicola mobilis	77.118	120	691	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Halorhodospiraceae;g__Alkalilimnicola	95.0	98.61	98.57	0.90	0.85	3	-
GCA_002798175.1	s__Luteimonas sp002798175	76.9117	62	691	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009295635.1	s__S0819 sp009295635	76.6046	108	691	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__AK92;g__S0819	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014836665.1	s__Luteimonas sp014836665	76.2501	82	691	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:35:27,853] [INFO] GTDB search result was written to GCF_007625165.1_ASM762516v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:35:27,853] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:35:27,856] [INFO] DFAST_QC result json was written to GCF_007625165.1_ASM762516v1_genomic.fna/dqc_result.json
[2024-01-24 11:35:27,857] [INFO] DFAST_QC completed!
[2024-01-24 11:35:27,857] [INFO] Total running time: 0h0m46s