[2024-01-24 13:01:18,797] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:18,798] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:18,799] [INFO] DQC Reference Directory: /var/lib/cwl/stg12e54783-d9a8-4d76-9701-ef7c227937ac/dqc_reference
[2024-01-24 13:01:20,062] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:20,066] [INFO] Task started: Prodigal
[2024-01-24 13:01:20,067] [INFO] Running command: gunzip -c /var/lib/cwl/stg5453a839-75a0-4cf7-b8f1-e64617abb8be/GCF_900115035.1_IMG-taxon_2663762756_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900115035.1_IMG-taxon_2663762756_annotated_assembly_genomic.fna/cds.fna -a GCF_900115035.1_IMG-taxon_2663762756_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:33,145] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:33,146] [INFO] Task started: HMMsearch
[2024-01-24 13:01:33,146] [INFO] Running command: hmmsearch --tblout GCF_900115035.1_IMG-taxon_2663762756_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg12e54783-d9a8-4d76-9701-ef7c227937ac/dqc_reference/reference_markers.hmm GCF_900115035.1_IMG-taxon_2663762756_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:33,434] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:33,435] [INFO] Found 6/6 markers.
[2024-01-24 13:01:33,477] [INFO] Query marker FASTA was written to GCF_900115035.1_IMG-taxon_2663762756_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:01:33,477] [INFO] Task started: Blastn
[2024-01-24 13:01:33,477] [INFO] Running command: blastn -query GCF_900115035.1_IMG-taxon_2663762756_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg12e54783-d9a8-4d76-9701-ef7c227937ac/dqc_reference/reference_markers.fasta -out GCF_900115035.1_IMG-taxon_2663762756_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:34,371] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:34,375] [INFO] Selected 15 target genomes.
[2024-01-24 13:01:34,375] [INFO] Target genome list was writen to GCF_900115035.1_IMG-taxon_2663762756_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:01:34,381] [INFO] Task started: fastANI
[2024-01-24 13:01:34,382] [INFO] Running command: fastANI --query /var/lib/cwl/stg5453a839-75a0-4cf7-b8f1-e64617abb8be/GCF_900115035.1_IMG-taxon_2663762756_annotated_assembly_genomic.fna.gz --refList GCF_900115035.1_IMG-taxon_2663762756_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900115035.1_IMG-taxon_2663762756_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:46,251] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:46,251] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg12e54783-d9a8-4d76-9701-ef7c227937ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:46,252] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg12e54783-d9a8-4d76-9701-ef7c227937ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:46,265] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:01:46,265] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:01:46,265] [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
Thioclava dalianensis	strain=CGMCC 1.12325	GCA_900115035.1	1185766	1185766	type	True	100.0	1376	1379	95	conclusive
Thioclava dalianensis	strain=DLFJ1-1	GCA_000715505.1	1185766	1185766	type	True	99.9562	1330	1379	95	conclusive
Thioclava atlantica	strain=13D2W-2	GCA_000737065.1	1317124	1317124	type	True	81.7669	735	1379	95	below_threshold
Thioclava electrotropha	strain=Elox9	GCA_002085925.2	1549850	1549850	type	True	81.4401	775	1379	95	below_threshold
Thioclava pacifica	strain=DSM 10166	GCA_000714535.1	285109	285109	type	True	81.2784	694	1379	95	below_threshold
Thioclava sediminum	strain=TAW-CT134	GCA_002020355.1	1915319	1915319	type	True	81.2366	745	1379	95	below_threshold
Thioclava indica	strain=DT23-4	GCA_000714545.1	1353528	1353528	type	True	81.1112	719	1379	95	below_threshold
Thioclava nitratireducens	strain=25B10_4	GCA_001940525.2	1915078	1915078	type	True	80.8612	744	1379	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	78.1525	396	1379	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	77.9433	352	1379	95	below_threshold
Pararhodobacter aggregans	strain=D1-19	GCA_003075525.1	404875	404875	type	True	77.6151	364	1379	95	below_threshold
Pararhodobacter aggregans	strain=DSM 18938	GCA_003054005.1	404875	404875	type	True	77.5819	364	1379	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	77.404	337	1379	95	below_threshold
Paracoccus salsus	strain=EGI L200073	GCA_021556615.1	2911061	2911061	type	True	77.3449	294	1379	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	77.3082	293	1379	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:46,267] [INFO] DFAST Taxonomy check result was written to GCF_900115035.1_IMG-taxon_2663762756_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:01:46,267] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:46,267] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:46,267] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg12e54783-d9a8-4d76-9701-ef7c227937ac/dqc_reference/checkm_data
[2024-01-24 13:01:46,268] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:46,308] [INFO] Task started: CheckM
[2024-01-24 13:01:46,308] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900115035.1_IMG-taxon_2663762756_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900115035.1_IMG-taxon_2663762756_annotated_assembly_genomic.fna/checkm_input GCF_900115035.1_IMG-taxon_2663762756_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:02:27,230] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:27,232] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:27,260] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:27,261] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:27,261] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900115035.1_IMG-taxon_2663762756_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:02:27,262] [INFO] Task started: Blastn
[2024-01-24 13:02:27,262] [INFO] Running command: blastn -query GCF_900115035.1_IMG-taxon_2663762756_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg12e54783-d9a8-4d76-9701-ef7c227937ac/dqc_reference/reference_markers_gtdb.fasta -out GCF_900115035.1_IMG-taxon_2663762756_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:28,973] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:28,977] [INFO] Selected 15 target genomes.
[2024-01-24 13:02:28,978] [INFO] Target genome list was writen to GCF_900115035.1_IMG-taxon_2663762756_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:28,990] [INFO] Task started: fastANI
[2024-01-24 13:02:28,991] [INFO] Running command: fastANI --query /var/lib/cwl/stg5453a839-75a0-4cf7-b8f1-e64617abb8be/GCF_900115035.1_IMG-taxon_2663762756_annotated_assembly_genomic.fna.gz --refList GCF_900115035.1_IMG-taxon_2663762756_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900115035.1_IMG-taxon_2663762756_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:40,922] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:40,942] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:02:40,942] [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_000715505.1	s__Thioclava dalianensis	99.9562	1330	1379	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_000737065.1	s__Thioclava atlantica	81.7725	734	1379	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002085925.2	s__Thioclava electrotropha	81.4294	774	1379	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	96.2561	N/A	N/A	N/A	N/A	1	-
GCF_000714535.1	s__Thioclava pacifica	81.2685	695	1379	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002563775.1	s__Thioclava sp002563775	81.263	743	1379	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	95.0406	95.45	95.45	0.86	0.86	2	-
GCF_002020355.1	s__Thioclava sediminum	81.2287	746	1379	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	96.2561	96.53	96.29	0.92	0.90	8	-
GCF_009296265.1	s__Thioclava sp009296265	81.1373	750	1379	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	96.2474	N/A	N/A	N/A	N/A	1	-
GCF_000714545.1	s__Thioclava indica	81.1142	718	1379	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002020135.1	s__Thioclava marina	81.0161	686	1379	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	95.0	98.70	98.47	0.89	0.86	6	-
GCF_001940525.2	s__Thioclava nitratireducens	80.8639	743	1379	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	95.0	98.60	98.50	0.92	0.89	7	-
GCA_016937195.1	s__Thioclava sp016937195	80.7584	573	1379	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017303295.1	s__Pararhodobacter sp017303295	77.9797	376	1379	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106675.1	s__Acidimangrovimonas indica	77.866	375	1379	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Acidimangrovimonas	95.0	99.99	99.99	1.00	0.99	3	-
GCF_003075525.1	s__Pararhodobacter aggregans	77.6072	365	1379	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003863335.1	s__Wagnerdoeblera faecalis	76.8321	250	1379	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wagnerdoeblera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:02:40,944] [INFO] GTDB search result was written to GCF_900115035.1_IMG-taxon_2663762756_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:40,945] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:40,949] [INFO] DFAST_QC result json was written to GCF_900115035.1_IMG-taxon_2663762756_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:02:40,949] [INFO] DFAST_QC completed!
[2024-01-24 13:02:40,949] [INFO] Total running time: 0h1m22s