[2024-01-24 14:19:45,313] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:45,314] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:45,314] [INFO] DQC Reference Directory: /var/lib/cwl/stg133c4296-285d-4d08-b936-a80aabc4ead7/dqc_reference
[2024-01-24 14:19:47,128] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:47,129] [INFO] Task started: Prodigal
[2024-01-24 14:19:47,129] [INFO] Running command: gunzip -c /var/lib/cwl/stg5d59cd45-4261-4bfd-ad10-e23e40cd77c4/GCF_900116195.1_IMG-taxon_2619618962_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900116195.1_IMG-taxon_2619618962_annotated_assembly_genomic.fna/cds.fna -a GCF_900116195.1_IMG-taxon_2619618962_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:20:03,400] [INFO] Task succeeded: Prodigal
[2024-01-24 14:20:03,400] [INFO] Task started: HMMsearch
[2024-01-24 14:20:03,400] [INFO] Running command: hmmsearch --tblout GCF_900116195.1_IMG-taxon_2619618962_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg133c4296-285d-4d08-b936-a80aabc4ead7/dqc_reference/reference_markers.hmm GCF_900116195.1_IMG-taxon_2619618962_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:20:03,757] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:20:03,758] [INFO] Found 6/6 markers.
[2024-01-24 14:20:03,806] [INFO] Query marker FASTA was written to GCF_900116195.1_IMG-taxon_2619618962_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:20:03,807] [INFO] Task started: Blastn
[2024-01-24 14:20:03,807] [INFO] Running command: blastn -query GCF_900116195.1_IMG-taxon_2619618962_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg133c4296-285d-4d08-b936-a80aabc4ead7/dqc_reference/reference_markers.fasta -out GCF_900116195.1_IMG-taxon_2619618962_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:04,836] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:04,839] [INFO] Selected 12 target genomes.
[2024-01-24 14:20:04,839] [INFO] Target genome list was writen to GCF_900116195.1_IMG-taxon_2619618962_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:20:04,842] [INFO] Task started: fastANI
[2024-01-24 14:20:04,842] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d59cd45-4261-4bfd-ad10-e23e40cd77c4/GCF_900116195.1_IMG-taxon_2619618962_annotated_assembly_genomic.fna.gz --refList GCF_900116195.1_IMG-taxon_2619618962_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900116195.1_IMG-taxon_2619618962_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:18,229] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:18,230] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg133c4296-285d-4d08-b936-a80aabc4ead7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:18,230] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg133c4296-285d-4d08-b936-a80aabc4ead7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:18,240] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:20:18,240] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:20:18,240] [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
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	100.0	2029	2029	95	conclusive
Yangia pacifica	strain=CGMCC 1.3455	GCA_900100725.1	311180	311180	suspected-type	True	99.9912	2016	2029	95	conclusive
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	82.5533	1017	2029	95	below_threshold
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	82.3911	1003	2029	95	below_threshold
Salipiger profundus	strain=CGMCC 1.12377	GCA_014637265.1	1229727	1229727	type	True	81.9417	869	2029	95	below_threshold
Salipiger profundus	strain=JLT2016	GCA_001969385.1	1229727	1229727	type	True	81.88	927	2029	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	80.7855	918	2029	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	80.3794	752	2029	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	79.4664	721	2029	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.7245	425	2029	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	77.7114	348	2029	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	77.539	411	2029	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:18,245] [INFO] DFAST Taxonomy check result was written to GCF_900116195.1_IMG-taxon_2619618962_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:20:18,245] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:18,245] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:18,246] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg133c4296-285d-4d08-b936-a80aabc4ead7/dqc_reference/checkm_data
[2024-01-24 14:20:18,247] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:18,302] [INFO] Task started: CheckM
[2024-01-24 14:20:18,302] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900116195.1_IMG-taxon_2619618962_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900116195.1_IMG-taxon_2619618962_annotated_assembly_genomic.fna/checkm_input GCF_900116195.1_IMG-taxon_2619618962_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:21:13,028] [INFO] Task succeeded: CheckM
[2024-01-24 14:21:13,029] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:21:13,043] [INFO] ===== Completeness check finished =====
[2024-01-24 14:21:13,043] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:21:13,043] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900116195.1_IMG-taxon_2619618962_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:21:13,043] [INFO] Task started: Blastn
[2024-01-24 14:21:13,043] [INFO] Running command: blastn -query GCF_900116195.1_IMG-taxon_2619618962_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg133c4296-285d-4d08-b936-a80aabc4ead7/dqc_reference/reference_markers_gtdb.fasta -out GCF_900116195.1_IMG-taxon_2619618962_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:14,774] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:14,776] [INFO] Selected 5 target genomes.
[2024-01-24 14:21:14,776] [INFO] Target genome list was writen to GCF_900116195.1_IMG-taxon_2619618962_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:21:14,780] [INFO] Task started: fastANI
[2024-01-24 14:21:14,780] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d59cd45-4261-4bfd-ad10-e23e40cd77c4/GCF_900116195.1_IMG-taxon_2619618962_annotated_assembly_genomic.fna.gz --refList GCF_900116195.1_IMG-taxon_2619618962_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900116195.1_IMG-taxon_2619618962_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:22,185] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:22,190] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:21:22,190] [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_900116195.1	s__Salipiger pacificus	100.0	2029	2029	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_015223355.1	s__Salipiger pacificus_B	89.4815	1535	2029	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	89.0907	988	2029	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	88.4299	1334	2029	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	97.69	97.64	0.90	0.89	3	-
GCF_001687105.1	s__Salipiger sp001687105	86.5861	1309	2029	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	96.47	96.47	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:21:22,191] [INFO] GTDB search result was written to GCF_900116195.1_IMG-taxon_2619618962_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:22,192] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:22,194] [INFO] DFAST_QC result json was written to GCF_900116195.1_IMG-taxon_2619618962_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:21:22,194] [INFO] DFAST_QC completed!
[2024-01-24 14:21:22,194] [INFO] Total running time: 0h1m37s