[2024-01-24 14:07:14,960] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:07:14,962] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:07:14,962] [INFO] DQC Reference Directory: /var/lib/cwl/stg95448970-bee1-4e14-be52-a225a02d011a/dqc_reference
[2024-01-24 14:07:16,295] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:07:16,295] [INFO] Task started: Prodigal
[2024-01-24 14:07:16,296] [INFO] Running command: gunzip -c /var/lib/cwl/stg8850cb91-2372-4277-8ba9-ed89e7ab8b29/GCF_900188035.1_IMG-taxon_2724679734_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900188035.1_IMG-taxon_2724679734_annotated_assembly_genomic.fna/cds.fna -a GCF_900188035.1_IMG-taxon_2724679734_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:07:32,735] [INFO] Task succeeded: Prodigal
[2024-01-24 14:07:32,736] [INFO] Task started: HMMsearch
[2024-01-24 14:07:32,736] [INFO] Running command: hmmsearch --tblout GCF_900188035.1_IMG-taxon_2724679734_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg95448970-bee1-4e14-be52-a225a02d011a/dqc_reference/reference_markers.hmm GCF_900188035.1_IMG-taxon_2724679734_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:07:33,052] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:07:33,054] [INFO] Found 6/6 markers.
[2024-01-24 14:07:33,102] [INFO] Query marker FASTA was written to GCF_900188035.1_IMG-taxon_2724679734_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:07:33,103] [INFO] Task started: Blastn
[2024-01-24 14:07:33,103] [INFO] Running command: blastn -query GCF_900188035.1_IMG-taxon_2724679734_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg95448970-bee1-4e14-be52-a225a02d011a/dqc_reference/reference_markers.fasta -out GCF_900188035.1_IMG-taxon_2724679734_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:34,001] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:34,005] [INFO] Selected 19 target genomes.
[2024-01-24 14:07:34,005] [INFO] Target genome list was writen to GCF_900188035.1_IMG-taxon_2724679734_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:07:34,020] [INFO] Task started: fastANI
[2024-01-24 14:07:34,020] [INFO] Running command: fastANI --query /var/lib/cwl/stg8850cb91-2372-4277-8ba9-ed89e7ab8b29/GCF_900188035.1_IMG-taxon_2724679734_annotated_assembly_genomic.fna.gz --refList GCF_900188035.1_IMG-taxon_2724679734_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900188035.1_IMG-taxon_2724679734_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:07:51,493] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:51,493] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg95448970-bee1-4e14-be52-a225a02d011a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:07:51,494] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg95448970-bee1-4e14-be52-a225a02d011a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:07:51,509] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:07:51,509] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:07:51,510] [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
Puniceibacterium sediminis	strain=DSM 29052	GCA_900188035.1	1608407	1608407	type	True	100.0	1508	1512	95	conclusive
Puniceibacterium antarcticum	strain=SM1211	GCA_002760615.1	1206336	1206336	type	True	82.5308	904	1512	95	below_threshold
Puniceibacterium confluentis	strain=JSSK-17	GCA_007923445.1	1958944	1958944	type	True	81.5907	865	1512	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	78.3277	518	1512	95	below_threshold
Pseudopuniceibacterium antarcticum	strain=HQ09	GCA_014899185.1	2613965	2613965	type	True	78.1553	373	1512	95	below_threshold
Mameliella sediminis	strain=DP3N28-2	GCA_019218285.1	2836866	2836866	type	True	78.1321	422	1512	95	below_threshold
Ruegeria marisrubri	strain=ZGT118	GCA_001507595.1	1685379	1685379	type	True	78.0882	388	1512	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	78.0765	346	1512	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	78.0541	440	1512	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	77.9783	412	1512	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	77.9566	406	1512	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	77.9085	370	1512	95	below_threshold
Pseudooceanicola onchidii	strain=XY-99	GCA_004959925.1	2562279	2562279	type	True	77.8545	372	1512	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	77.6838	410	1512	95	below_threshold
Leisingera aquaemixtae	strain=CECT 8399	GCA_001458395.1	1396826	1396826	type	True	77.6798	364	1512	95	below_threshold
Sagittula marina	strain=DSM 102235	GCA_014196795.1	943940	943940	type	True	77.6361	341	1512	95	below_threshold
Thalassorhabdomicrobium marinisediminis	strain=BH-SD16	GCA_003072065.1	2170577	2170577	type	True	77.4713	285	1512	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.3933	278	1512	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	77.1068	268	1512	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:07:51,511] [INFO] DFAST Taxonomy check result was written to GCF_900188035.1_IMG-taxon_2724679734_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:07:51,512] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:07:51,512] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:07:51,512] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg95448970-bee1-4e14-be52-a225a02d011a/dqc_reference/checkm_data
[2024-01-24 14:07:51,513] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:07:51,601] [INFO] Task started: CheckM
[2024-01-24 14:07:51,602] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900188035.1_IMG-taxon_2724679734_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900188035.1_IMG-taxon_2724679734_annotated_assembly_genomic.fna/checkm_input GCF_900188035.1_IMG-taxon_2724679734_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:08:42,503] [INFO] Task succeeded: CheckM
[2024-01-24 14:08:42,504] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:08:42,526] [INFO] ===== Completeness check finished =====
[2024-01-24 14:08:42,526] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:08:42,527] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900188035.1_IMG-taxon_2724679734_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:08:42,527] [INFO] Task started: Blastn
[2024-01-24 14:08:42,527] [INFO] Running command: blastn -query GCF_900188035.1_IMG-taxon_2724679734_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg95448970-bee1-4e14-be52-a225a02d011a/dqc_reference/reference_markers_gtdb.fasta -out GCF_900188035.1_IMG-taxon_2724679734_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:08:43,885] [INFO] Task succeeded: Blastn
[2024-01-24 14:08:43,890] [INFO] Selected 17 target genomes.
[2024-01-24 14:08:43,890] [INFO] Target genome list was writen to GCF_900188035.1_IMG-taxon_2724679734_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:08:43,904] [INFO] Task started: fastANI
[2024-01-24 14:08:43,904] [INFO] Running command: fastANI --query /var/lib/cwl/stg8850cb91-2372-4277-8ba9-ed89e7ab8b29/GCF_900188035.1_IMG-taxon_2724679734_annotated_assembly_genomic.fna.gz --refList GCF_900188035.1_IMG-taxon_2724679734_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900188035.1_IMG-taxon_2724679734_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:08:59,844] [INFO] Task succeeded: fastANI
[2024-01-24 14:08:59,861] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:08:59,861] [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_900188035.1	s__Puniceibacterium sediminis	100.0	1508	1512	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002760615.1	s__Puniceibacterium antarcticum	82.5219	905	1512	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007923445.1	s__Puniceibacterium confluentis	81.5994	864	1512	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001038505.1	s__Puniceibacterium sp001038505	79.6492	631	1512	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003344785.1	s__Puniceibacterium profundi	79.2277	622	1512	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014637725.1	s__Marivita lacus	78.4044	466	1512	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100085.1	s__Salipiger marinus	78.3206	519	1512	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.13	98.13	0.95	0.95	2	-
GCF_001975705.1	s__Salipiger abyssi	78.1387	508	1512	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001507595.1	s__Ruegeria marisrubri	78.0882	388	1512	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102075.1	s__Salipiger thiooxidans	78.0574	439	1512	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	97.34	95.88	0.90	0.85	6	-
GCF_003335545.1	s__Ascidiaceihabitans sp003335545	77.9909	412	1512	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000442255.1	s__Salipiger mucosus	77.9906	414	1512	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002814095.1	s__Sagittula sp002814095	77.8654	479	1512	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000521865.1	s__Roseivivax isoporae	77.6829	411	1512	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002222635.1	s__Ascidiaceihabitans pseudonitzschiae_A	77.5756	356	1512	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.92	99.92	0.96	0.96	2	-
GCF_003072065.1	s__Thalassorhabdomicrobium marinisediminis	77.502	282	1512	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassorhabdomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017390475.1	s__Yoonia sp017390475	77.0864	252	1512	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:08:59,863] [INFO] GTDB search result was written to GCF_900188035.1_IMG-taxon_2724679734_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:08:59,864] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:08:59,868] [INFO] DFAST_QC result json was written to GCF_900188035.1_IMG-taxon_2724679734_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:08:59,869] [INFO] DFAST_QC completed!
[2024-01-24 14:08:59,869] [INFO] Total running time: 0h1m45s