[2024-01-24 14:23:05,253] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:23:05,254] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:23:05,254] [INFO] DQC Reference Directory: /var/lib/cwl/stgf6bf988c-70e0-475c-bc0e-6891809e9af8/dqc_reference
[2024-01-24 14:23:06,621] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:23:06,622] [INFO] Task started: Prodigal
[2024-01-24 14:23:06,622] [INFO] Running command: gunzip -c /var/lib/cwl/stg51ca43db-de5a-403d-a751-fe6a80ac9581/GCF_019218265.1_ASM1921826v1_genomic.fna.gz | prodigal -d GCF_019218265.1_ASM1921826v1_genomic.fna/cds.fna -a GCF_019218265.1_ASM1921826v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:23:19,031] [INFO] Task succeeded: Prodigal
[2024-01-24 14:23:19,031] [INFO] Task started: HMMsearch
[2024-01-24 14:23:19,031] [INFO] Running command: hmmsearch --tblout GCF_019218265.1_ASM1921826v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf6bf988c-70e0-475c-bc0e-6891809e9af8/dqc_reference/reference_markers.hmm GCF_019218265.1_ASM1921826v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:23:19,317] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:23:19,319] [INFO] Found 6/6 markers.
[2024-01-24 14:23:19,355] [INFO] Query marker FASTA was written to GCF_019218265.1_ASM1921826v1_genomic.fna/markers.fasta
[2024-01-24 14:23:19,355] [INFO] Task started: Blastn
[2024-01-24 14:23:19,356] [INFO] Running command: blastn -query GCF_019218265.1_ASM1921826v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf6bf988c-70e0-475c-bc0e-6891809e9af8/dqc_reference/reference_markers.fasta -out GCF_019218265.1_ASM1921826v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:20,271] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:20,279] [INFO] Selected 14 target genomes.
[2024-01-24 14:23:20,279] [INFO] Target genome list was writen to GCF_019218265.1_ASM1921826v1_genomic.fna/target_genomes.txt
[2024-01-24 14:23:20,285] [INFO] Task started: fastANI
[2024-01-24 14:23:20,285] [INFO] Running command: fastANI --query /var/lib/cwl/stg51ca43db-de5a-403d-a751-fe6a80ac9581/GCF_019218265.1_ASM1921826v1_genomic.fna.gz --refList GCF_019218265.1_ASM1921826v1_genomic.fna/target_genomes.txt --output GCF_019218265.1_ASM1921826v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:32,140] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:32,141] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf6bf988c-70e0-475c-bc0e-6891809e9af8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:32,141] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf6bf988c-70e0-475c-bc0e-6891809e9af8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:32,154] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:23:32,154] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:23:32,155] [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
Maritimibacter alexandrii	strain=LZ-17	GCA_005871115.1	2570355	2570355	type	True	81.4902	786	1311	95	below_threshold
Maritimibacter alkaliphilus	strain=HTCC2654	GCA_000152805.1	404236	404236	type	True	81.2898	787	1311	95	below_threshold
Maritimibacter alkaliphilus	strain=HTCC2654	GCA_008124775.1	404236	404236	type	True	81.2705	784	1311	95	below_threshold
Maritimibacter harenae	strain=DP07	GCA_009882975.1	2606218	2606218	type	True	80.3034	685	1311	95	below_threshold
Salipiger profundus	strain=CGMCC 1.12377	GCA_014637265.1	1229727	1229727	type	True	78.9553	402	1311	95	below_threshold
Celeribacter indicus	strain=P73	GCA_000819565.1	1208324	1208324	type	True	78.8246	360	1311	95	below_threshold
Maribius salinus	strain=DSM 26892	GCA_900141995.1	313368	313368	type	True	78.0783	309	1311	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.8051	306	1311	95	below_threshold
Halovulum dunhuangense	strain=YYQ-30	GCA_013093415.1	1505036	1505036	type	True	77.7084	223	1311	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	77.6736	302	1311	95	below_threshold
Actibacterium atlanticum	strain=22II-S11-z10	GCA_000671395.1	1461693	1461693	type	True	77.6216	185	1311	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	77.5977	300	1311	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	77.4174	297	1311	95	below_threshold
Rubellimicrobium roseum	strain=YIM 48858	GCA_006152145.1	687525	687525	type	True	77.143	204	1311	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:32,156] [INFO] DFAST Taxonomy check result was written to GCF_019218265.1_ASM1921826v1_genomic.fna/tc_result.tsv
[2024-01-24 14:23:32,157] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:32,157] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:32,157] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf6bf988c-70e0-475c-bc0e-6891809e9af8/dqc_reference/checkm_data
[2024-01-24 14:23:32,159] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:32,201] [INFO] Task started: CheckM
[2024-01-24 14:23:32,202] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019218265.1_ASM1921826v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019218265.1_ASM1921826v1_genomic.fna/checkm_input GCF_019218265.1_ASM1921826v1_genomic.fna/checkm_result
[2024-01-24 14:24:12,622] [INFO] Task succeeded: CheckM
[2024-01-24 14:24:12,624] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:24:12,642] [INFO] ===== Completeness check finished =====
[2024-01-24 14:24:12,642] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:24:12,643] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019218265.1_ASM1921826v1_genomic.fna/markers.fasta)
[2024-01-24 14:24:12,643] [INFO] Task started: Blastn
[2024-01-24 14:24:12,644] [INFO] Running command: blastn -query GCF_019218265.1_ASM1921826v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf6bf988c-70e0-475c-bc0e-6891809e9af8/dqc_reference/reference_markers_gtdb.fasta -out GCF_019218265.1_ASM1921826v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:24:14,158] [INFO] Task succeeded: Blastn
[2024-01-24 14:24:14,161] [INFO] Selected 8 target genomes.
[2024-01-24 14:24:14,162] [INFO] Target genome list was writen to GCF_019218265.1_ASM1921826v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:24:14,169] [INFO] Task started: fastANI
[2024-01-24 14:24:14,170] [INFO] Running command: fastANI --query /var/lib/cwl/stg51ca43db-de5a-403d-a751-fe6a80ac9581/GCF_019218265.1_ASM1921826v1_genomic.fna.gz --refList GCF_019218265.1_ASM1921826v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019218265.1_ASM1921826v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:24:21,207] [INFO] Task succeeded: fastANI
[2024-01-24 14:24:21,219] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:24:21,219] [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_019218265.1	s__Maritimibacter sp019218265	100.0	1311	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000152805.1	s__Maritimibacter alkaliphilus	81.307	785	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	97.94	96.90	0.93	0.88	4	-
GCA_001626765.1	s__Maritimibacter sp001626765	80.8902	592	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	99.88	99.88	0.89	0.89	2	-
GCA_003520545.1	s__Maritimibacter sp003520545	80.5644	540	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009882975.1	s__Maritimibacter harenae	80.3082	684	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011389895.1	s__Maritimibacter sp011389895	80.2326	637	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002695005.1	s__Maritimibacter sp002695005	80.1991	685	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_014640115.1	s__Muriiphilus lacisalsi	78.5357	432	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Muriiphilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:24:21,221] [INFO] GTDB search result was written to GCF_019218265.1_ASM1921826v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:24:21,222] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:24:21,225] [INFO] DFAST_QC result json was written to GCF_019218265.1_ASM1921826v1_genomic.fna/dqc_result.json
[2024-01-24 14:24:21,226] [INFO] DFAST_QC completed!
[2024-01-24 14:24:21,226] [INFO] Total running time: 0h1m16s