[2024-01-24 13:43:27,005] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:43:27,007] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:43:27,007] [INFO] DQC Reference Directory: /var/lib/cwl/stg95d61868-6f48-44fb-9720-7de5fdda38a8/dqc_reference
[2024-01-24 13:43:28,179] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:43:28,180] [INFO] Task started: Prodigal
[2024-01-24 13:43:28,180] [INFO] Running command: gunzip -c /var/lib/cwl/stg610fe91b-e9c3-4add-ad1f-fecaeb596eef/GCF_900129345.1_IMG-taxon_2695420938_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900129345.1_IMG-taxon_2695420938_annotated_assembly_genomic.fna/cds.fna -a GCF_900129345.1_IMG-taxon_2695420938_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:43:39,503] [INFO] Task succeeded: Prodigal
[2024-01-24 13:43:39,503] [INFO] Task started: HMMsearch
[2024-01-24 13:43:39,504] [INFO] Running command: hmmsearch --tblout GCF_900129345.1_IMG-taxon_2695420938_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg95d61868-6f48-44fb-9720-7de5fdda38a8/dqc_reference/reference_markers.hmm GCF_900129345.1_IMG-taxon_2695420938_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:43:39,722] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:43:39,723] [INFO] Found 6/6 markers.
[2024-01-24 13:43:39,755] [INFO] Query marker FASTA was written to GCF_900129345.1_IMG-taxon_2695420938_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:43:39,755] [INFO] Task started: Blastn
[2024-01-24 13:43:39,756] [INFO] Running command: blastn -query GCF_900129345.1_IMG-taxon_2695420938_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg95d61868-6f48-44fb-9720-7de5fdda38a8/dqc_reference/reference_markers.fasta -out GCF_900129345.1_IMG-taxon_2695420938_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:40,628] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:40,631] [INFO] Selected 19 target genomes.
[2024-01-24 13:43:40,631] [INFO] Target genome list was writen to GCF_900129345.1_IMG-taxon_2695420938_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:43:40,643] [INFO] Task started: fastANI
[2024-01-24 13:43:40,644] [INFO] Running command: fastANI --query /var/lib/cwl/stg610fe91b-e9c3-4add-ad1f-fecaeb596eef/GCF_900129345.1_IMG-taxon_2695420938_annotated_assembly_genomic.fna.gz --refList GCF_900129345.1_IMG-taxon_2695420938_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900129345.1_IMG-taxon_2695420938_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:43:56,306] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:56,306] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg95d61868-6f48-44fb-9720-7de5fdda38a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:43:56,306] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg95d61868-6f48-44fb-9720-7de5fdda38a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:43:56,321] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:43:56,321] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:43:56,321] [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
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	100.0	1240	1244	95	conclusive
Ruegeria marisrubri	strain=ZGT118	GCA_001507595.1	1685379	1685379	type	True	84.5699	830	1244	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	82.5066	780	1244	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	81.6337	776	1244	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	81.301	725	1244	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	81.2184	728	1244	95	below_threshold
Ruegeria marina	strain=CGMCC 1.9108	GCA_900101475.1	639004	639004	type	True	80.76	714	1244	95	below_threshold
Ruegeria denitrificans	strain=CECT 5091	GCA_001458295.1	1715692	1715692	type	True	80.6907	726	1244	95	below_threshold
Ruegeria atlantica	strain=CECT 4292	GCA_001458195.1	81569	81569	suspected-type	True	80.1901	704	1244	95	below_threshold
Leisingera aquaemixtae	strain=CECT 8399	GCA_001458395.1	1396826	1396826	type	True	80.0798	656	1244	95	below_threshold
Ruegeria halocynthiae	strain=DSM 27839	GCA_900106805.1	985054	985054	type	True	80.0346	672	1244	95	below_threshold
Leisingera caerulea	strain=DSM 24564	GCA_000473325.1	506591	506591	type	True	79.9764	642	1244	95	below_threshold
Ruegeria faecimaris	strain=DSM 28009	GCA_900182615.1	686389	686389	type	True	79.9718	677	1244	95	below_threshold
Ruegeria conchae	strain=TW15	GCA_000192475.2	981384	981384	suspected-type	True	79.9352	635	1244	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.8674	425	1244	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.8157	429	1244	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	78.2068	369	1244	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	78.0256	408	1244	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.9226	391	1244	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:43:56,323] [INFO] DFAST Taxonomy check result was written to GCF_900129345.1_IMG-taxon_2695420938_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:43:56,323] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:43:56,323] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:43:56,324] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg95d61868-6f48-44fb-9720-7de5fdda38a8/dqc_reference/checkm_data
[2024-01-24 13:43:56,325] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:43:56,362] [INFO] Task started: CheckM
[2024-01-24 13:43:56,362] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900129345.1_IMG-taxon_2695420938_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900129345.1_IMG-taxon_2695420938_annotated_assembly_genomic.fna/checkm_input GCF_900129345.1_IMG-taxon_2695420938_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:44:36,065] [INFO] Task succeeded: CheckM
[2024-01-24 13:44:36,066] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:44:36,080] [INFO] ===== Completeness check finished =====
[2024-01-24 13:44:36,080] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:44:36,081] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900129345.1_IMG-taxon_2695420938_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:44:36,081] [INFO] Task started: Blastn
[2024-01-24 13:44:36,081] [INFO] Running command: blastn -query GCF_900129345.1_IMG-taxon_2695420938_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg95d61868-6f48-44fb-9720-7de5fdda38a8/dqc_reference/reference_markers_gtdb.fasta -out GCF_900129345.1_IMG-taxon_2695420938_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:44:37,589] [INFO] Task succeeded: Blastn
[2024-01-24 13:44:37,592] [INFO] Selected 12 target genomes.
[2024-01-24 13:44:37,592] [INFO] Target genome list was writen to GCF_900129345.1_IMG-taxon_2695420938_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:44:37,621] [INFO] Task started: fastANI
[2024-01-24 13:44:37,621] [INFO] Running command: fastANI --query /var/lib/cwl/stg610fe91b-e9c3-4add-ad1f-fecaeb596eef/GCF_900129345.1_IMG-taxon_2695420938_annotated_assembly_genomic.fna.gz --refList GCF_900129345.1_IMG-taxon_2695420938_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900129345.1_IMG-taxon_2695420938_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:44:48,233] [INFO] Task succeeded: fastANI
[2024-01-24 13:44:48,243] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:44:48,243] [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_900129345.1	s__Ruegeria intermedia	100.0	1240	1244	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000161775.1	s__Ruegeria lacuscaerulensis	93.0434	990	1244	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.98	99.98	1.00	1.00	2	-
GCF_013032855.1	s__Ruegeria arenilitoris	90.1825	925	1244	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	97.27	95.93	0.96	0.94	31	-
GCF_001507595.1	s__Ruegeria marisrubri	84.5606	831	1244	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938215.1	s__Ruegeria sediminis	82.5018	781	1244	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013031405.1	s__Ruegeria sp013031405	82.0191	829	1244	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013030985.1	s__Ruegeria arenilitoris_B	81.9751	838	1244	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.15	99.15	0.92	0.92	2	-
GCF_013032025.1	s__Ruegeria atlantica_C	81.6901	761	1244	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	100.00	100.00	0.99	0.99	2	-
GCF_009363615.1	s__Ruegeria sp009363615	81.6138	775	1244	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	97.20	96.03	0.88	0.85	16	-
GCF_017743975.1	s__Ruegeria sp017743975	80.8309	735	1244	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_903914075.1	s__Ruegeria sp903914075	80.7369	680	1244	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	95.16	95.09	0.87	0.84	7	-
GCF_013033965.1	s__Ruegeria atlantica_D	80.4999	712	1244	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:44:48,247] [INFO] GTDB search result was written to GCF_900129345.1_IMG-taxon_2695420938_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:44:48,247] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:44:48,252] [INFO] DFAST_QC result json was written to GCF_900129345.1_IMG-taxon_2695420938_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:44:48,253] [INFO] DFAST_QC completed!
[2024-01-24 13:44:48,253] [INFO] Total running time: 0h1m21s