[2024-01-24 15:32:05,339] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:32:05,341] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:32:05,341] [INFO] DQC Reference Directory: /var/lib/cwl/stgbdcc1d87-fd9e-441a-b8eb-b1b1d219ec76/dqc_reference
[2024-01-24 15:32:06,629] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:32:06,630] [INFO] Task started: Prodigal
[2024-01-24 15:32:06,630] [INFO] Running command: gunzip -c /var/lib/cwl/stg496fe66e-0913-4368-b489-f690ee18e7e2/GCF_900100175.1_IMG-taxon_2634166324_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900100175.1_IMG-taxon_2634166324_annotated_assembly_genomic.fna/cds.fna -a GCF_900100175.1_IMG-taxon_2634166324_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:32:19,360] [INFO] Task succeeded: Prodigal
[2024-01-24 15:32:19,360] [INFO] Task started: HMMsearch
[2024-01-24 15:32:19,360] [INFO] Running command: hmmsearch --tblout GCF_900100175.1_IMG-taxon_2634166324_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbdcc1d87-fd9e-441a-b8eb-b1b1d219ec76/dqc_reference/reference_markers.hmm GCF_900100175.1_IMG-taxon_2634166324_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:32:19,641] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:32:19,643] [INFO] Found 6/6 markers.
[2024-01-24 15:32:19,686] [INFO] Query marker FASTA was written to GCF_900100175.1_IMG-taxon_2634166324_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 15:32:19,686] [INFO] Task started: Blastn
[2024-01-24 15:32:19,687] [INFO] Running command: blastn -query GCF_900100175.1_IMG-taxon_2634166324_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgbdcc1d87-fd9e-441a-b8eb-b1b1d219ec76/dqc_reference/reference_markers.fasta -out GCF_900100175.1_IMG-taxon_2634166324_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:32:20,577] [INFO] Task succeeded: Blastn
[2024-01-24 15:32:20,582] [INFO] Selected 11 target genomes.
[2024-01-24 15:32:20,582] [INFO] Target genome list was writen to GCF_900100175.1_IMG-taxon_2634166324_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 15:32:20,589] [INFO] Task started: fastANI
[2024-01-24 15:32:20,589] [INFO] Running command: fastANI --query /var/lib/cwl/stg496fe66e-0913-4368-b489-f690ee18e7e2/GCF_900100175.1_IMG-taxon_2634166324_annotated_assembly_genomic.fna.gz --refList GCF_900100175.1_IMG-taxon_2634166324_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900100175.1_IMG-taxon_2634166324_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:32:30,106] [INFO] Task succeeded: fastANI
[2024-01-24 15:32:30,106] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbdcc1d87-fd9e-441a-b8eb-b1b1d219ec76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:32:30,107] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbdcc1d87-fd9e-441a-b8eb-b1b1d219ec76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:32:30,123] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:32:30,123] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:32:30,123] [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
Ferrimonas sediminum	strain=DSM 23317	GCA_900100175.1	718193	718193	type	True	100.0	1436	1437	95	conclusive
Ferrimonas kyonanensis	strain=DSM 18153	GCA_000425405.1	364763	364763	type	True	88.8835	1257	1437	95	below_threshold
Ferrimonas futtsuensis	strain=DSM 18154	GCA_000422645.1	364764	364764	type	True	80.9048	854	1437	95	below_threshold
Ferrimonas sediminicola	strain=IMCC35001	GCA_005116715.1	2569538	2569538	type	True	80.59	829	1437	95	below_threshold
Ferrimonas aestuarii	strain=IMCC35002	GCA_005116665.1	2569539	2569539	type	True	79.0411	478	1437	95	below_threshold
Ferrimonas marina	strain=DSM 16917	GCA_900129905.1	299255	299255	type	True	77.9889	401	1437	95	below_threshold
Shewanella aquimarina	strain=JCM 12193	GCA_023349185.1	260365	260365	type	True	76.4	143	1437	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.0511	93	1437	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	76.023	75	1437	95	below_threshold
Pseudomonas mangiferae	strain=DMKU BBB3-04	GCA_007109405.1	2593654	2593654	type	True	75.9543	78	1437	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	75.6997	87	1437	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:32:30,125] [INFO] DFAST Taxonomy check result was written to GCF_900100175.1_IMG-taxon_2634166324_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 15:32:30,126] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:32:30,126] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:32:30,126] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbdcc1d87-fd9e-441a-b8eb-b1b1d219ec76/dqc_reference/checkm_data
[2024-01-24 15:32:30,127] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:32:30,173] [INFO] Task started: CheckM
[2024-01-24 15:32:30,173] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900100175.1_IMG-taxon_2634166324_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900100175.1_IMG-taxon_2634166324_annotated_assembly_genomic.fna/checkm_input GCF_900100175.1_IMG-taxon_2634166324_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 15:33:10,089] [INFO] Task succeeded: CheckM
[2024-01-24 15:33:10,090] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:33:10,110] [INFO] ===== Completeness check finished =====
[2024-01-24 15:33:10,110] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:33:10,111] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900100175.1_IMG-taxon_2634166324_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 15:33:10,111] [INFO] Task started: Blastn
[2024-01-24 15:33:10,111] [INFO] Running command: blastn -query GCF_900100175.1_IMG-taxon_2634166324_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgbdcc1d87-fd9e-441a-b8eb-b1b1d219ec76/dqc_reference/reference_markers_gtdb.fasta -out GCF_900100175.1_IMG-taxon_2634166324_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:33:11,545] [INFO] Task succeeded: Blastn
[2024-01-24 15:33:11,549] [INFO] Selected 6 target genomes.
[2024-01-24 15:33:11,550] [INFO] Target genome list was writen to GCF_900100175.1_IMG-taxon_2634166324_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:33:11,563] [INFO] Task started: fastANI
[2024-01-24 15:33:11,563] [INFO] Running command: fastANI --query /var/lib/cwl/stg496fe66e-0913-4368-b489-f690ee18e7e2/GCF_900100175.1_IMG-taxon_2634166324_annotated_assembly_genomic.fna.gz --refList GCF_900100175.1_IMG-taxon_2634166324_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900100175.1_IMG-taxon_2634166324_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:33:17,858] [INFO] Task succeeded: fastANI
[2024-01-24 15:33:17,871] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:33:17,871] [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_900100175.1	s__Ferrimonas sediminum	100.0	1436	1437	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000425405.1	s__Ferrimonas kyonanensis	88.8753	1258	1437	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422645.1	s__Ferrimonas futtsuensis	80.8782	858	1437	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005116715.1	s__Ferrimonas sp005116715	80.5901	829	1437	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005116665.1	s__Ferrimonas sp005116665	79.0369	481	1437	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129905.1	s__Ferrimonas marina	77.9951	400	1437	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:33:17,873] [INFO] GTDB search result was written to GCF_900100175.1_IMG-taxon_2634166324_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 15:33:17,874] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:33:17,879] [INFO] DFAST_QC result json was written to GCF_900100175.1_IMG-taxon_2634166324_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 15:33:17,879] [INFO] DFAST_QC completed!
[2024-01-24 15:33:17,879] [INFO] Total running time: 0h1m13s