[2024-01-24 14:13:01,693] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:13:01,695] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:13:01,695] [INFO] DQC Reference Directory: /var/lib/cwl/stgd25cf250-9153-4910-88cd-f71eee4daa9a/dqc_reference
[2024-01-24 14:13:02,913] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:13:02,914] [INFO] Task started: Prodigal
[2024-01-24 14:13:02,915] [INFO] Running command: gunzip -c /var/lib/cwl/stgfcdc1b4f-c59e-4d5e-8408-fc4c34c0510d/GCF_001458355.1_Tgelatinovorus_CECT4357_Seqman_Prokka_genomic.fna.gz | prodigal -d GCF_001458355.1_Tgelatinovorus_CECT4357_Seqman_Prokka_genomic.fna/cds.fna -a GCF_001458355.1_Tgelatinovorus_CECT4357_Seqman_Prokka_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:13:15,387] [INFO] Task succeeded: Prodigal
[2024-01-24 14:13:15,387] [INFO] Task started: HMMsearch
[2024-01-24 14:13:15,387] [INFO] Running command: hmmsearch --tblout GCF_001458355.1_Tgelatinovorus_CECT4357_Seqman_Prokka_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd25cf250-9153-4910-88cd-f71eee4daa9a/dqc_reference/reference_markers.hmm GCF_001458355.1_Tgelatinovorus_CECT4357_Seqman_Prokka_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:13:15,681] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:13:15,683] [INFO] Found 6/6 markers.
[2024-01-24 14:13:15,729] [INFO] Query marker FASTA was written to GCF_001458355.1_Tgelatinovorus_CECT4357_Seqman_Prokka_genomic.fna/markers.fasta
[2024-01-24 14:13:15,730] [INFO] Task started: Blastn
[2024-01-24 14:13:15,730] [INFO] Running command: blastn -query GCF_001458355.1_Tgelatinovorus_CECT4357_Seqman_Prokka_genomic.fna/markers.fasta -db /var/lib/cwl/stgd25cf250-9153-4910-88cd-f71eee4daa9a/dqc_reference/reference_markers.fasta -out GCF_001458355.1_Tgelatinovorus_CECT4357_Seqman_Prokka_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:16,509] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:16,513] [INFO] Selected 16 target genomes.
[2024-01-24 14:13:16,514] [INFO] Target genome list was writen to GCF_001458355.1_Tgelatinovorus_CECT4357_Seqman_Prokka_genomic.fna/target_genomes.txt
[2024-01-24 14:13:16,523] [INFO] Task started: fastANI
[2024-01-24 14:13:16,524] [INFO] Running command: fastANI --query /var/lib/cwl/stgfcdc1b4f-c59e-4d5e-8408-fc4c34c0510d/GCF_001458355.1_Tgelatinovorus_CECT4357_Seqman_Prokka_genomic.fna.gz --refList GCF_001458355.1_Tgelatinovorus_CECT4357_Seqman_Prokka_genomic.fna/target_genomes.txt --output GCF_001458355.1_Tgelatinovorus_CECT4357_Seqman_Prokka_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:13:28,817] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:28,817] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd25cf250-9153-4910-88cd-f71eee4daa9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:13:28,818] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd25cf250-9153-4910-88cd-f71eee4daa9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:13:28,830] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:13:28,831] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:13:28,831] [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
Thalassobius gelatinovorus	strain=CECT 4357	GCA_001458355.1	53501	53501	type	True	100.0	1287	1289	95	conclusive
Thalassobius gelatinovorus	strain=DSM 5887	GCA_900111045.1	53501	53501	type	True	99.9929	1276	1289	95	conclusive
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	82.5516	882	1289	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	82.3014	859	1289	95	below_threshold
Thalassobius autumnalis	strain=CECT 5118	GCA_001458255.1	2072972	2072972	type	True	78.4351	486	1289	95	below_threshold
Thalassobius mediterraneus	strain=DSM 16398	GCA_900156595.1	340021	340021	type	True	78.25	398	1289	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	78.2462	434	1289	95	below_threshold
Ruegeria marisrubri	strain=ZGT118	GCA_001507595.1	1685379	1685379	type	True	77.8335	359	1289	95	below_threshold
Leisingera aquimarina	strain=DSM 24565	GCA_000473165.1	476529	476529	type	True	77.7238	343	1289	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	77.675	323	1289	95	below_threshold
Pseudooceanicola antarcticus	strain=Ar-45	GCA_002786285.1	1247613	1247613	type	True	77.2453	271	1289	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	77.1187	294	1289	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.0075	277	1289	95	below_threshold
Zongyanglinia marina	strain=DSW4-44	GCA_005771405.1	2578117	2578117	type	True	76.9784	185	1289	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.8996	240	1289	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	76.8484	184	1289	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:13:28,833] [INFO] DFAST Taxonomy check result was written to GCF_001458355.1_Tgelatinovorus_CECT4357_Seqman_Prokka_genomic.fna/tc_result.tsv
[2024-01-24 14:13:28,833] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:13:28,833] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:13:28,833] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd25cf250-9153-4910-88cd-f71eee4daa9a/dqc_reference/checkm_data
[2024-01-24 14:13:28,834] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:13:28,879] [INFO] Task started: CheckM
[2024-01-24 14:13:28,879] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001458355.1_Tgelatinovorus_CECT4357_Seqman_Prokka_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001458355.1_Tgelatinovorus_CECT4357_Seqman_Prokka_genomic.fna/checkm_input GCF_001458355.1_Tgelatinovorus_CECT4357_Seqman_Prokka_genomic.fna/checkm_result
[2024-01-24 14:14:09,225] [INFO] Task succeeded: CheckM
[2024-01-24 14:14:09,226] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:14:09,253] [INFO] ===== Completeness check finished =====
[2024-01-24 14:14:09,253] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:14:09,253] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001458355.1_Tgelatinovorus_CECT4357_Seqman_Prokka_genomic.fna/markers.fasta)
[2024-01-24 14:14:09,254] [INFO] Task started: Blastn
[2024-01-24 14:14:09,254] [INFO] Running command: blastn -query GCF_001458355.1_Tgelatinovorus_CECT4357_Seqman_Prokka_genomic.fna/markers.fasta -db /var/lib/cwl/stgd25cf250-9153-4910-88cd-f71eee4daa9a/dqc_reference/reference_markers_gtdb.fasta -out GCF_001458355.1_Tgelatinovorus_CECT4357_Seqman_Prokka_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:10,447] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:10,452] [INFO] Selected 15 target genomes.
[2024-01-24 14:14:10,452] [INFO] Target genome list was writen to GCF_001458355.1_Tgelatinovorus_CECT4357_Seqman_Prokka_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:14:10,474] [INFO] Task started: fastANI
[2024-01-24 14:14:10,474] [INFO] Running command: fastANI --query /var/lib/cwl/stgfcdc1b4f-c59e-4d5e-8408-fc4c34c0510d/GCF_001458355.1_Tgelatinovorus_CECT4357_Seqman_Prokka_genomic.fna.gz --refList GCF_001458355.1_Tgelatinovorus_CECT4357_Seqman_Prokka_genomic.fna/target_genomes_gtdb.txt --output GCF_001458355.1_Tgelatinovorus_CECT4357_Seqman_Prokka_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:14:21,774] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:21,789] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:14:21,790] [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_001458355.1	s__Thalassobius gelatinovorus	100.0	1286	1289	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	100.00	99.99	0.99	0.99	3	conclusive
GCF_009857745.1	s__Thalassobius mangrovi	82.5487	882	1289	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018219815.1	s__Thalassobius aquimarinus	82.3176	856	1289	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004799325.1	s__Thalassobius vesicularis	78.855	510	1289	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017792425.1	s__Thalassobius sp017792425	78.8062	470	1289	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110775.1	s__Litorimicrobium taeanense	78.6413	500	1289	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litorimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900182725.1	s__Thalassobius litoralis	78.6314	524	1289	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458255.1	s__Thalassobius autumnalis	78.4243	486	1289	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	99.93	99.93	0.99	0.99	2	-
GCA_002708925.1	s__Thalassobius sp002708925	78.4237	424	1289	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	99.91	99.91	0.84	0.84	2	-
GCF_001458435.1	s__Thalassobius mediterraneus	78.2469	405	1289	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001507595.1	s__Ruegeria marisrubri	77.827	358	1289	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	77.7693	333	1289	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001262635.1	s__Aestuariivita boseongensis	77.675	323	1289	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473165.1	s__Leisingera aquimarina	77.6609	342	1289	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000743705.1	s__Ruegeria halocynthiae_B	77.4437	290	1289	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 14:14:21,791] [INFO] GTDB search result was written to GCF_001458355.1_Tgelatinovorus_CECT4357_Seqman_Prokka_genomic.fna/result_gtdb.tsv
[2024-01-24 14:14:21,792] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:14:21,796] [INFO] DFAST_QC result json was written to GCF_001458355.1_Tgelatinovorus_CECT4357_Seqman_Prokka_genomic.fna/dqc_result.json
[2024-01-24 14:14:21,796] [INFO] DFAST_QC completed!
[2024-01-24 14:14:21,796] [INFO] Total running time: 0h1m20s