[2024-01-24 14:47:55,937] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:47:55,939] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:47:55,945] [INFO] DQC Reference Directory: /var/lib/cwl/stg77b290ba-645d-4cef-85b4-71cc4d44fe44/dqc_reference
[2024-01-24 14:47:58,533] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:47:58,537] [INFO] Task started: Prodigal
[2024-01-24 14:47:58,537] [INFO] Running command: gunzip -c /var/lib/cwl/stge9f946c3-0936-4a66-9ed8-74f521d0adf7/GCF_900102075.1_IMG-taxon_2615840719_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900102075.1_IMG-taxon_2615840719_annotated_assembly_genomic.fna/cds.fna -a GCF_900102075.1_IMG-taxon_2615840719_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:48:15,774] [INFO] Task succeeded: Prodigal
[2024-01-24 14:48:15,775] [INFO] Task started: HMMsearch
[2024-01-24 14:48:15,775] [INFO] Running command: hmmsearch --tblout GCF_900102075.1_IMG-taxon_2615840719_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg77b290ba-645d-4cef-85b4-71cc4d44fe44/dqc_reference/reference_markers.hmm GCF_900102075.1_IMG-taxon_2615840719_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:48:16,117] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:48:16,119] [INFO] Found 6/6 markers.
[2024-01-24 14:48:16,191] [INFO] Query marker FASTA was written to GCF_900102075.1_IMG-taxon_2615840719_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:48:16,191] [INFO] Task started: Blastn
[2024-01-24 14:48:16,192] [INFO] Running command: blastn -query GCF_900102075.1_IMG-taxon_2615840719_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg77b290ba-645d-4cef-85b4-71cc4d44fe44/dqc_reference/reference_markers.fasta -out GCF_900102075.1_IMG-taxon_2615840719_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:17,200] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:17,204] [INFO] Selected 12 target genomes.
[2024-01-24 14:48:17,205] [INFO] Target genome list was writen to GCF_900102075.1_IMG-taxon_2615840719_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:48:17,222] [INFO] Task started: fastANI
[2024-01-24 14:48:17,222] [INFO] Running command: fastANI --query /var/lib/cwl/stge9f946c3-0936-4a66-9ed8-74f521d0adf7/GCF_900102075.1_IMG-taxon_2615840719_annotated_assembly_genomic.fna.gz --refList GCF_900102075.1_IMG-taxon_2615840719_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900102075.1_IMG-taxon_2615840719_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:48:31,037] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:31,037] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg77b290ba-645d-4cef-85b4-71cc4d44fe44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:48:31,038] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg77b290ba-645d-4cef-85b4-71cc4d44fe44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:48:31,052] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:48:31,053] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:48:31,053] [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
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	100.0	1922	1924	95	conclusive
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	84.6363	1142	1924	95	below_threshold
Salipiger profundus	strain=JLT2016	GCA_001969385.1	1229727	1229727	type	True	84.3392	1115	1924	95	below_threshold
Salipiger profundus	strain=CGMCC 1.12377	GCA_014637265.1	1229727	1229727	type	True	84.2569	1079	1924	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	82.5856	1019	1924	95	below_threshold
Yangia pacifica	strain=CGMCC 1.3455	GCA_900100725.1	311180	311180	suspected-type	True	82.5661	1007	1924	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	82.2476	886	1924	95	below_threshold
Salipiger aestuarii	strain=AD8	GCA_008930655.1	568098	568098	type	True	81.3064	839	1924	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	80.5342	880	1924	95	below_threshold
Mameliella sediminis	strain=DP3N28-2	GCA_019218285.1	2836866	2836866	type	True	78.4482	560	1924	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	78.438	596	1924	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.1534	489	1924	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:48:31,055] [INFO] DFAST Taxonomy check result was written to GCF_900102075.1_IMG-taxon_2615840719_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:48:31,055] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:48:31,055] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:48:31,055] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg77b290ba-645d-4cef-85b4-71cc4d44fe44/dqc_reference/checkm_data
[2024-01-24 14:48:31,056] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:48:31,120] [INFO] Task started: CheckM
[2024-01-24 14:48:31,120] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900102075.1_IMG-taxon_2615840719_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900102075.1_IMG-taxon_2615840719_annotated_assembly_genomic.fna/checkm_input GCF_900102075.1_IMG-taxon_2615840719_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:49:29,048] [INFO] Task succeeded: CheckM
[2024-01-24 14:49:29,050] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:49:29,073] [INFO] ===== Completeness check finished =====
[2024-01-24 14:49:29,073] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:49:29,073] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900102075.1_IMG-taxon_2615840719_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:49:29,074] [INFO] Task started: Blastn
[2024-01-24 14:49:29,074] [INFO] Running command: blastn -query GCF_900102075.1_IMG-taxon_2615840719_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg77b290ba-645d-4cef-85b4-71cc4d44fe44/dqc_reference/reference_markers_gtdb.fasta -out GCF_900102075.1_IMG-taxon_2615840719_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:49:30,834] [INFO] Task succeeded: Blastn
[2024-01-24 14:49:30,838] [INFO] Selected 10 target genomes.
[2024-01-24 14:49:30,838] [INFO] Target genome list was writen to GCF_900102075.1_IMG-taxon_2615840719_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:49:30,846] [INFO] Task started: fastANI
[2024-01-24 14:49:30,846] [INFO] Running command: fastANI --query /var/lib/cwl/stge9f946c3-0936-4a66-9ed8-74f521d0adf7/GCF_900102075.1_IMG-taxon_2615840719_annotated_assembly_genomic.fna.gz --refList GCF_900102075.1_IMG-taxon_2615840719_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900102075.1_IMG-taxon_2615840719_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:49:44,292] [INFO] Task succeeded: fastANI
[2024-01-24 14:49:44,313] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:49:44,315] [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_900102075.1	s__Salipiger thiooxidans	100.0	1922	1924	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	97.34	95.88	0.90	0.85	6	conclusive
GCF_000153725.1	s__Salipiger bermudensis	84.6335	1142	1924	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.06	97.75	0.87	0.75	4	-
GCF_001969385.1	s__Salipiger profundus	84.3135	1119	1924	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	99.85	99.64	0.97	0.94	5	-
GCF_001975705.1	s__Salipiger abyssi	83.5094	1024	1924	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017311415.1	s__Salipiger abyssi_A	83.257	1011	1924	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002300555.1	s__Salipiger sp002300555	82.7154	730	1924	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003111685.1	s__Salipiger pacificus_A	82.3682	974	1924	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	97.69	97.64	0.90	0.89	3	-
GCF_000442255.1	s__Salipiger mucosus	82.254	934	1924	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014643635.1	s__Salipiger pallidus	82.2302	889	1924	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860705.1	s__Salipiger sp018860705	80.8936	902	1924	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:49:44,318] [INFO] GTDB search result was written to GCF_900102075.1_IMG-taxon_2615840719_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:49:44,319] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:49:44,323] [INFO] DFAST_QC result json was written to GCF_900102075.1_IMG-taxon_2615840719_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:49:44,323] [INFO] DFAST_QC completed!
[2024-01-24 14:49:44,323] [INFO] Total running time: 0h1m48s