[2024-01-24 14:06:29,677] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:29,679] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:29,679] [INFO] DQC Reference Directory: /var/lib/cwl/stg96541603-24d2-4279-a8c1-3388d620be01/dqc_reference
[2024-01-24 14:06:31,050] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:31,051] [INFO] Task started: Prodigal
[2024-01-24 14:06:31,051] [INFO] Running command: gunzip -c /var/lib/cwl/stga723d9b3-6c9a-417b-badc-1277b6b17ca2/GCF_002925845.1_ASM292584v1_genomic.fna.gz | prodigal -d GCF_002925845.1_ASM292584v1_genomic.fna/cds.fna -a GCF_002925845.1_ASM292584v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:44,164] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:44,165] [INFO] Task started: HMMsearch
[2024-01-24 14:06:44,165] [INFO] Running command: hmmsearch --tblout GCF_002925845.1_ASM292584v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg96541603-24d2-4279-a8c1-3388d620be01/dqc_reference/reference_markers.hmm GCF_002925845.1_ASM292584v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:44,497] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:44,498] [INFO] Found 6/6 markers.
[2024-01-24 14:06:44,539] [INFO] Query marker FASTA was written to GCF_002925845.1_ASM292584v1_genomic.fna/markers.fasta
[2024-01-24 14:06:44,540] [INFO] Task started: Blastn
[2024-01-24 14:06:44,540] [INFO] Running command: blastn -query GCF_002925845.1_ASM292584v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg96541603-24d2-4279-a8c1-3388d620be01/dqc_reference/reference_markers.fasta -out GCF_002925845.1_ASM292584v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:45,543] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:45,548] [INFO] Selected 22 target genomes.
[2024-01-24 14:06:45,549] [INFO] Target genome list was writen to GCF_002925845.1_ASM292584v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:45,579] [INFO] Task started: fastANI
[2024-01-24 14:06:45,580] [INFO] Running command: fastANI --query /var/lib/cwl/stga723d9b3-6c9a-417b-badc-1277b6b17ca2/GCF_002925845.1_ASM292584v1_genomic.fna.gz --refList GCF_002925845.1_ASM292584v1_genomic.fna/target_genomes.txt --output GCF_002925845.1_ASM292584v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:07:03,363] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:03,364] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg96541603-24d2-4279-a8c1-3388d620be01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:07:03,364] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg96541603-24d2-4279-a8c1-3388d620be01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:07:03,381] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:07:03,382] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:07:03,382] [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
Roseovarius nitratireducens	strain=TFZ	GCA_002925845.1	2044597	2044597	type	True	100.0	1271	1278	95	conclusive
Roseovarius tolerans	strain=DSM 11457	GCA_900109855.1	74031	74031	type	True	82.3188	752	1278	95	below_threshold
Roseovarius azorensis	strain=DSM 100674	GCA_900109455.1	1287727	1287727	type	True	80.5385	704	1278	95	below_threshold
Roseovarius halotolerans	strain=CECT 8110	GCA_900172255.1	505353	505353	type	True	79.656	557	1278	95	below_threshold
Roseovarius halotolerans	strain=DSM 29507	GCA_003634925.1	505353	505353	type	True	79.6273	560	1278	95	below_threshold
Roseovarius mucosus	strain=DSM 17069	GCA_000768555.3	215743	215743	type	True	79.5701	632	1278	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	79.3157	504	1278	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	79.0394	484	1278	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	79.0015	546	1278	95	below_threshold
Roseovarius nubinhibens	strain=ISM	GCA_000152625.1	314263	314263	type	True	78.8965	495	1278	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.8316	455	1278	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	78.6282	475	1278	95	below_threshold
Salibaculum halophilum	strain=WDS1C4	GCA_002094885.1	1914408	1914408	type	True	78.6028	412	1278	95	below_threshold
Roseovarius lutimaris	strain=DSM 28463	GCA_900115165.1	1005928	1005928	type	True	78.4317	531	1278	95	below_threshold
Roseivivax marinus	strain=DSM 27511	GCA_900109705.1	1379903	1379903	type	True	78.3305	418	1278	95	below_threshold
Pelagivirga dicentrarchi	strain=YLY04	GCA_003316635.1	2250573	2250573	type	True	78.1956	396	1278	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	78.1602	379	1278	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	77.9309	366	1278	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	77.6785	339	1278	95	below_threshold
Roseitranquillus sediminis	strain=MCCB 386	GCA_016918935.1	2809051	2809051	type	True	77.6089	316	1278	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	77.2308	380	1278	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	77.1574	371	1278	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:07:03,384] [INFO] DFAST Taxonomy check result was written to GCF_002925845.1_ASM292584v1_genomic.fna/tc_result.tsv
[2024-01-24 14:07:03,385] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:07:03,385] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:07:03,385] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg96541603-24d2-4279-a8c1-3388d620be01/dqc_reference/checkm_data
[2024-01-24 14:07:03,387] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:07:03,427] [INFO] Task started: CheckM
[2024-01-24 14:07:03,427] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002925845.1_ASM292584v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002925845.1_ASM292584v1_genomic.fna/checkm_input GCF_002925845.1_ASM292584v1_genomic.fna/checkm_result
[2024-01-24 14:07:42,241] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:42,242] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:42,262] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:42,262] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:42,263] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002925845.1_ASM292584v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:42,263] [INFO] Task started: Blastn
[2024-01-24 14:07:42,263] [INFO] Running command: blastn -query GCF_002925845.1_ASM292584v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg96541603-24d2-4279-a8c1-3388d620be01/dqc_reference/reference_markers_gtdb.fasta -out GCF_002925845.1_ASM292584v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:43,986] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:43,989] [INFO] Selected 11 target genomes.
[2024-01-24 14:07:43,990] [INFO] Target genome list was writen to GCF_002925845.1_ASM292584v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:44,015] [INFO] Task started: fastANI
[2024-01-24 14:07:44,015] [INFO] Running command: fastANI --query /var/lib/cwl/stga723d9b3-6c9a-417b-badc-1277b6b17ca2/GCF_002925845.1_ASM292584v1_genomic.fna.gz --refList GCF_002925845.1_ASM292584v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002925845.1_ASM292584v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:53,369] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:53,385] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:53,386] [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_002925845.1	s__Roseovarius nitratireducens	100.0	1272	1278	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	96.60	96.60	0.90	0.90	2	conclusive
GCA_016278295.1	s__Roseovarius sp016278295	93.0656	747	1278	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002421985.1	s__Roseovarius sp002421985	83.9866	663	1278	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002720475.1	s__Roseovarius sp002720475	82.8532	548	1278	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.80	99.74	0.82	0.71	3	-
GCA_014359765.1	s__Roseovarius sp014359765	82.5251	616	1278	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109855.1	s__Roseovarius tolerans	82.3605	749	1278	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	96.73	96.73	0.86	0.86	2	-
GCA_002842985.1	s__Roseovarius sp002842985	82.0859	737	1278	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002072155.1	s__Roseovarius sp002072155	82.0808	777	1278	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018069895.1	s__Roseovarius sp018069895	81.7522	720	1278	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.42	99.42	0.86	0.86	2	-
GCF_003651245.1	s__Roseovarius spongiae	79.7168	565	1278	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001314705.1	s__Aquicoccus sp001314705	78.9586	452	1278	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aquicoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:53,387] [INFO] GTDB search result was written to GCF_002925845.1_ASM292584v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:53,388] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:53,392] [INFO] DFAST_QC result json was written to GCF_002925845.1_ASM292584v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:53,393] [INFO] DFAST_QC completed!
[2024-01-24 14:07:53,393] [INFO] Total running time: 0h1m24s