[2024-01-24 13:49:55,347] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:55,350] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:55,350] [INFO] DQC Reference Directory: /var/lib/cwl/stgdf0f9bae-c19c-4948-b371-9cc687e4191a/dqc_reference
[2024-01-24 13:49:56,644] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:56,645] [INFO] Task started: Prodigal
[2024-01-24 13:49:56,645] [INFO] Running command: gunzip -c /var/lib/cwl/stg5ff4a590-37e5-4ea4-9d67-785e21554fa8/GCF_900111045.1_IMG-taxon_2622736435_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900111045.1_IMG-taxon_2622736435_annotated_assembly_genomic.fna/cds.fna -a GCF_900111045.1_IMG-taxon_2622736435_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:10,003] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:10,003] [INFO] Task started: HMMsearch
[2024-01-24 13:50:10,003] [INFO] Running command: hmmsearch --tblout GCF_900111045.1_IMG-taxon_2622736435_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdf0f9bae-c19c-4948-b371-9cc687e4191a/dqc_reference/reference_markers.hmm GCF_900111045.1_IMG-taxon_2622736435_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:10,291] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:10,293] [INFO] Found 6/6 markers.
[2024-01-24 13:50:10,332] [INFO] Query marker FASTA was written to GCF_900111045.1_IMG-taxon_2622736435_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:50:10,333] [INFO] Task started: Blastn
[2024-01-24 13:50:10,333] [INFO] Running command: blastn -query GCF_900111045.1_IMG-taxon_2622736435_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf0f9bae-c19c-4948-b371-9cc687e4191a/dqc_reference/reference_markers.fasta -out GCF_900111045.1_IMG-taxon_2622736435_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:11,091] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:11,093] [INFO] Selected 16 target genomes.
[2024-01-24 13:50:11,094] [INFO] Target genome list was writen to GCF_900111045.1_IMG-taxon_2622736435_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:50:11,102] [INFO] Task started: fastANI
[2024-01-24 13:50:11,102] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ff4a590-37e5-4ea4-9d67-785e21554fa8/GCF_900111045.1_IMG-taxon_2622736435_annotated_assembly_genomic.fna.gz --refList GCF_900111045.1_IMG-taxon_2622736435_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900111045.1_IMG-taxon_2622736435_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:24,296] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:24,296] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdf0f9bae-c19c-4948-b371-9cc687e4191a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:24,296] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdf0f9bae-c19c-4948-b371-9cc687e4191a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:24,311] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:50:24,311] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:24,311] [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=DSM 5887	GCA_900111045.1	53501	53501	type	True	100.0	1305	1306	95	conclusive
Thalassobius gelatinovorus	strain=CECT 4357	GCA_001458355.1	53501	53501	type	True	99.9921	1278	1306	95	conclusive
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	82.5331	907	1306	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	82.247	864	1306	95	below_threshold
Thalassobius autumnalis	strain=CECT 5118	GCA_001458255.1	2072972	2072972	type	True	78.4309	491	1306	95	below_threshold
Thalassobius mediterraneus	strain=DSM 16398	GCA_900156595.1	340021	340021	type	True	78.2842	401	1306	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	78.2836	427	1306	95	below_threshold
Ruegeria marisrubri	strain=ZGT118	GCA_001507595.1	1685379	1685379	type	True	77.8147	353	1306	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	77.5593	346	1306	95	below_threshold
Leisingera aquimarina	strain=DSM 24565	GCA_000473165.1	476529	476529	type	True	77.48	352	1306	95	below_threshold
Pseudooceanicola antarcticus	strain=Ar-45	GCA_002786285.1	1247613	1247613	type	True	77.2043	272	1306	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.1732	261	1306	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	77.1554	292	1306	95	below_threshold
Zongyanglinia marina	strain=DSW4-44	GCA_005771405.1	2578117	2578117	type	True	76.9242	185	1306	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	76.8189	183	1306	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.8006	254	1306	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:24,313] [INFO] DFAST Taxonomy check result was written to GCF_900111045.1_IMG-taxon_2622736435_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:50:24,314] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:24,314] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:24,314] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdf0f9bae-c19c-4948-b371-9cc687e4191a/dqc_reference/checkm_data
[2024-01-24 13:50:24,315] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:24,359] [INFO] Task started: CheckM
[2024-01-24 13:50:24,360] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900111045.1_IMG-taxon_2622736435_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900111045.1_IMG-taxon_2622736435_annotated_assembly_genomic.fna/checkm_input GCF_900111045.1_IMG-taxon_2622736435_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:51:03,957] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:03,959] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:03,981] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:03,981] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:03,982] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900111045.1_IMG-taxon_2622736435_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:51:03,982] [INFO] Task started: Blastn
[2024-01-24 13:51:03,982] [INFO] Running command: blastn -query GCF_900111045.1_IMG-taxon_2622736435_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf0f9bae-c19c-4948-b371-9cc687e4191a/dqc_reference/reference_markers_gtdb.fasta -out GCF_900111045.1_IMG-taxon_2622736435_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:05,176] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:05,180] [INFO] Selected 15 target genomes.
[2024-01-24 13:51:05,181] [INFO] Target genome list was writen to GCF_900111045.1_IMG-taxon_2622736435_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:05,206] [INFO] Task started: fastANI
[2024-01-24 13:51:05,206] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ff4a590-37e5-4ea4-9d67-785e21554fa8/GCF_900111045.1_IMG-taxon_2622736435_annotated_assembly_genomic.fna.gz --refList GCF_900111045.1_IMG-taxon_2622736435_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900111045.1_IMG-taxon_2622736435_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:17,007] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:17,024] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:17,024] [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	99.9921	1278	1306	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	82.5238	908	1306	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	82.2429	865	1306	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	78.9	503	1306	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	78.7915	477	1306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900182725.1	s__Thalassobius litoralis	78.6702	518	1306	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	78.5946	516	1306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litorimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458255.1	s__Thalassobius autumnalis	78.4301	490	1306	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	78.3121	439	1306	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	78.2801	403	1306	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	77.8175	352	1306	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	77.7686	332	1306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000743705.1	s__Ruegeria halocynthiae_B	77.5687	274	1306	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	77.5593	346	1306	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	77.4788	352	1306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:17,026] [INFO] GTDB search result was written to GCF_900111045.1_IMG-taxon_2622736435_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:17,027] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:17,031] [INFO] DFAST_QC result json was written to GCF_900111045.1_IMG-taxon_2622736435_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:51:17,031] [INFO] DFAST_QC completed!
[2024-01-24 13:51:17,031] [INFO] Total running time: 0h1m22s