[2024-01-24 13:57:44,637] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:44,642] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:44,642] [INFO] DQC Reference Directory: /var/lib/cwl/stg5c74b4f5-b6f3-4801-84b2-46ae3d07c0eb/dqc_reference
[2024-01-24 13:57:45,954] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:45,954] [INFO] Task started: Prodigal
[2024-01-24 13:57:45,955] [INFO] Running command: gunzip -c /var/lib/cwl/stgc85f233b-0fc3-4f21-a960-3bb1c4893a78/GCF_900142425.1_IMG-taxon_2698536702_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900142425.1_IMG-taxon_2698536702_annotated_assembly_genomic.fna/cds.fna -a GCF_900142425.1_IMG-taxon_2698536702_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:56,865] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:56,865] [INFO] Task started: HMMsearch
[2024-01-24 13:57:56,866] [INFO] Running command: hmmsearch --tblout GCF_900142425.1_IMG-taxon_2698536702_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5c74b4f5-b6f3-4801-84b2-46ae3d07c0eb/dqc_reference/reference_markers.hmm GCF_900142425.1_IMG-taxon_2698536702_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:57,160] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:57,161] [INFO] Found 6/6 markers.
[2024-01-24 13:57:57,193] [INFO] Query marker FASTA was written to GCF_900142425.1_IMG-taxon_2698536702_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:57:57,193] [INFO] Task started: Blastn
[2024-01-24 13:57:57,193] [INFO] Running command: blastn -query GCF_900142425.1_IMG-taxon_2698536702_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c74b4f5-b6f3-4801-84b2-46ae3d07c0eb/dqc_reference/reference_markers.fasta -out GCF_900142425.1_IMG-taxon_2698536702_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:58,000] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:58,004] [INFO] Selected 11 target genomes.
[2024-01-24 13:57:58,004] [INFO] Target genome list was writen to GCF_900142425.1_IMG-taxon_2698536702_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:57:58,009] [INFO] Task started: fastANI
[2024-01-24 13:57:58,009] [INFO] Running command: fastANI --query /var/lib/cwl/stgc85f233b-0fc3-4f21-a960-3bb1c4893a78/GCF_900142425.1_IMG-taxon_2698536702_annotated_assembly_genomic.fna.gz --refList GCF_900142425.1_IMG-taxon_2698536702_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900142425.1_IMG-taxon_2698536702_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:06,740] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:06,741] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5c74b4f5-b6f3-4801-84b2-46ae3d07c0eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:06,741] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5c74b4f5-b6f3-4801-84b2-46ae3d07c0eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:06,757] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:58:06,757] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:06,758] [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
Octadecabacter temperatus	strain=DSM 26878	GCA_900142425.1	1458307	1458307	type	True	100.0	1086	1086	95	conclusive
Octadecabacter temperatus	strain=SB1	GCA_001187845.1	1458307	1458307	type	True	99.9976	1086	1086	95	conclusive
Octadecabacter ascidiaceicola	strain=CECT 8868	GCA_900185015.1	1655543	1655543	type	True	83.5832	772	1086	95	below_threshold
Octadecabacter arcticus	strain=238	GCA_000155735.2	53946	53946	type	True	78.4995	443	1086	95	below_threshold
Octadecabacter antarcticus	strain=307	GCA_000155675.2	1217908	1217908	type	True	78.3226	433	1086	95	below_threshold
Thalassorhabdomicrobium marinisediminis	strain=BH-SD16	GCA_003072065.1	2170577	2170577	type	True	77.2374	238	1086	95	below_threshold
Celeribacter litoreus	strain=ASW11-22	GCA_020165855.1	2876714	2876714	type	True	76.7351	103	1086	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	76.2823	56	1086	95	below_threshold
Pseudogemmobacter hezensis	strain=D13-10-4-6	GCA_013155295.1	2737662	2737662	type	True	76.1784	55	1086	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:06,761] [INFO] DFAST Taxonomy check result was written to GCF_900142425.1_IMG-taxon_2698536702_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:58:06,762] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:06,762] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:06,762] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5c74b4f5-b6f3-4801-84b2-46ae3d07c0eb/dqc_reference/checkm_data
[2024-01-24 13:58:06,766] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:06,808] [INFO] Task started: CheckM
[2024-01-24 13:58:06,808] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900142425.1_IMG-taxon_2698536702_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900142425.1_IMG-taxon_2698536702_annotated_assembly_genomic.fna/checkm_input GCF_900142425.1_IMG-taxon_2698536702_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:58:44,197] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:44,198] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:44,218] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:44,219] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:44,219] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900142425.1_IMG-taxon_2698536702_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:58:44,220] [INFO] Task started: Blastn
[2024-01-24 13:58:44,220] [INFO] Running command: blastn -query GCF_900142425.1_IMG-taxon_2698536702_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c74b4f5-b6f3-4801-84b2-46ae3d07c0eb/dqc_reference/reference_markers_gtdb.fasta -out GCF_900142425.1_IMG-taxon_2698536702_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:45,614] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:45,619] [INFO] Selected 9 target genomes.
[2024-01-24 13:58:45,619] [INFO] Target genome list was writen to GCF_900142425.1_IMG-taxon_2698536702_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:45,638] [INFO] Task started: fastANI
[2024-01-24 13:58:45,638] [INFO] Running command: fastANI --query /var/lib/cwl/stgc85f233b-0fc3-4f21-a960-3bb1c4893a78/GCF_900142425.1_IMG-taxon_2698536702_annotated_assembly_genomic.fna.gz --refList GCF_900142425.1_IMG-taxon_2698536702_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900142425.1_IMG-taxon_2698536702_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:52,233] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:52,243] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:52,244] [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_001187845.1	s__Octadecabacter temperatus	99.9976	1086	1086	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_900185015.1	s__Octadecabacter ascidiaceicola	83.5832	772	1086	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018500005.1	s__Octadecabacter sp018500005	83.1904	486	1086	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003533975.1	s__Octadecabacter sp003533975	82.6266	494	1086	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018861045.1	s__Octadecabacter sp018861045	79.7485	501	1086	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018608045.1	s__Octadecabacter sp018608045	78.8137	385	1086	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	98.68	98.68	0.85	0.85	2	-
GCF_000155735.2	s__Octadecabacter arcticus	78.5369	444	1086	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	96.73	96.73	0.93	0.93	2	-
GCA_017886375.1	s__Octadecabacter sp017886375	78.4573	429	1086	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	99.96	99.96	0.97	0.97	2	-
GCF_000155675.2	s__Octadecabacter antarcticus	78.3224	433	1086	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:52,246] [INFO] GTDB search result was written to GCF_900142425.1_IMG-taxon_2698536702_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:52,247] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:52,251] [INFO] DFAST_QC result json was written to GCF_900142425.1_IMG-taxon_2698536702_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:58:52,252] [INFO] DFAST_QC completed!
[2024-01-24 13:58:52,252] [INFO] Total running time: 0h1m8s