[2024-01-24 13:13:51,388] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:51,391] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:51,391] [INFO] DQC Reference Directory: /var/lib/cwl/stgfc44c2ed-3c07-4689-aa1a-3139ed86a50b/dqc_reference
[2024-01-24 13:13:52,690] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:52,691] [INFO] Task started: Prodigal
[2024-01-24 13:13:52,692] [INFO] Running command: gunzip -c /var/lib/cwl/stg7fa438b3-6f56-4676-a3ac-4c8795e8bbea/GCF_009830105.1_ASM983010v1_genomic.fna.gz | prodigal -d GCF_009830105.1_ASM983010v1_genomic.fna/cds.fna -a GCF_009830105.1_ASM983010v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:14:08,721] [INFO] Task succeeded: Prodigal
[2024-01-24 13:14:08,722] [INFO] Task started: HMMsearch
[2024-01-24 13:14:08,722] [INFO] Running command: hmmsearch --tblout GCF_009830105.1_ASM983010v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfc44c2ed-3c07-4689-aa1a-3139ed86a50b/dqc_reference/reference_markers.hmm GCF_009830105.1_ASM983010v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:14:09,298] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:14:09,300] [INFO] Found 6/6 markers.
[2024-01-24 13:14:09,356] [INFO] Query marker FASTA was written to GCF_009830105.1_ASM983010v1_genomic.fna/markers.fasta
[2024-01-24 13:14:09,357] [INFO] Task started: Blastn
[2024-01-24 13:14:09,357] [INFO] Running command: blastn -query GCF_009830105.1_ASM983010v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc44c2ed-3c07-4689-aa1a-3139ed86a50b/dqc_reference/reference_markers.fasta -out GCF_009830105.1_ASM983010v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:10,298] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:10,302] [INFO] Selected 15 target genomes.
[2024-01-24 13:14:10,302] [INFO] Target genome list was writen to GCF_009830105.1_ASM983010v1_genomic.fna/target_genomes.txt
[2024-01-24 13:14:10,310] [INFO] Task started: fastANI
[2024-01-24 13:14:10,310] [INFO] Running command: fastANI --query /var/lib/cwl/stg7fa438b3-6f56-4676-a3ac-4c8795e8bbea/GCF_009830105.1_ASM983010v1_genomic.fna.gz --refList GCF_009830105.1_ASM983010v1_genomic.fna/target_genomes.txt --output GCF_009830105.1_ASM983010v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:14:28,673] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:28,673] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfc44c2ed-3c07-4689-aa1a-3139ed86a50b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:14:28,674] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfc44c2ed-3c07-4689-aa1a-3139ed86a50b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:14:28,687] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:14:28,687] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:14:28,687] [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
Microvirga makkahensis	strain=KCTC 23863	GCA_009830105.1	1128670	1128670	type	True	100.0	1812	1815	95	conclusive
Microvirga pakistanensis	strain=NCCP-1258	GCA_004458765.1	1682650	1682650	type	True	86.0622	1159	1815	95	below_threshold
Microvirga vignae	strain=BR3299	GCA_001017175.1	1225564	1225564	type	True	83.7107	1012	1815	95	below_threshold
Microvirga guangxiensis	strain=CGMCC 1.7666	GCA_900102135.1	549386	549386	type	True	83.5062	965	1815	95	below_threshold
Microvirga flocculans	strain=ATCC BAA-817	GCA_000518665.1	217168	217168	type	True	82.6453	799	1815	95	below_threshold
Microvirga splendida	strain=BT325	GCA_016427565.1	2795727	2795727	type	True	82.3478	899	1815	95	below_threshold
Microvirga mediterraneensis	strain=Marseille-Q2068	GCA_013520865.1	2754695	2754695	type	True	82.2252	866	1815	95	below_threshold
Microvirga lotononidis	strain=WSM3557	GCA_000262405.1	864069	864069	type	True	82.1078	887	1815	95	below_threshold
Microvirga zambiensis	strain=WSM3693	GCA_016735695.1	1402137	1402137	type	True	81.8702	898	1815	95	below_threshold
Microvirga roseola	strain=SM2	GCA_020866965.1	2883126	2883126	type	True	81.8657	851	1815	95	below_threshold
Microvirga soli	strain=R491	GCA_016734765.1	1854496	1854496	type	True	81.7955	915	1815	95	below_threshold
Microvirga lenta	strain=SM9	GCA_020532555.1	2881337	2881337	type	True	81.6829	791	1815	95	below_threshold
Microvirga rosea	strain=CGMCC1.16488	GCA_020595095.1	2715425	2715425	type	True	79.6179	600	1815	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	78.0713	449	1815	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	77.8667	449	1815	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:14:28,750] [INFO] DFAST Taxonomy check result was written to GCF_009830105.1_ASM983010v1_genomic.fna/tc_result.tsv
[2024-01-24 13:14:28,784] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:14:28,784] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:14:28,785] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfc44c2ed-3c07-4689-aa1a-3139ed86a50b/dqc_reference/checkm_data
[2024-01-24 13:14:28,786] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:14:28,924] [INFO] Task started: CheckM
[2024-01-24 13:14:28,925] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009830105.1_ASM983010v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009830105.1_ASM983010v1_genomic.fna/checkm_input GCF_009830105.1_ASM983010v1_genomic.fna/checkm_result
[2024-01-24 13:15:18,176] [INFO] Task succeeded: CheckM
[2024-01-24 13:15:18,178] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:15:18,199] [INFO] ===== Completeness check finished =====
[2024-01-24 13:15:18,199] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:15:18,200] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009830105.1_ASM983010v1_genomic.fna/markers.fasta)
[2024-01-24 13:15:18,200] [INFO] Task started: Blastn
[2024-01-24 13:15:18,200] [INFO] Running command: blastn -query GCF_009830105.1_ASM983010v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc44c2ed-3c07-4689-aa1a-3139ed86a50b/dqc_reference/reference_markers_gtdb.fasta -out GCF_009830105.1_ASM983010v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:15:20,162] [INFO] Task succeeded: Blastn
[2024-01-24 13:15:20,167] [INFO] Selected 11 target genomes.
[2024-01-24 13:15:20,168] [INFO] Target genome list was writen to GCF_009830105.1_ASM983010v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:15:20,176] [INFO] Task started: fastANI
[2024-01-24 13:15:20,176] [INFO] Running command: fastANI --query /var/lib/cwl/stg7fa438b3-6f56-4676-a3ac-4c8795e8bbea/GCF_009830105.1_ASM983010v1_genomic.fna.gz --refList GCF_009830105.1_ASM983010v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009830105.1_ASM983010v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:15:35,387] [INFO] Task succeeded: fastANI
[2024-01-24 13:15:35,397] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:15:35,398] [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_009830105.1	s__Microvirga makkahensis	100.0	1812	1815	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004458765.1	s__Microvirga pakistanensis	86.0622	1159	1815	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003075415.1	s__Microvirga sp003075415	83.9653	1011	1815	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001017175.1	s__Microvirga vignae	83.7213	1010	1815	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102135.1	s__Microvirga guangxiensis	83.5307	962	1815	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009910705.1	s__Microvirga sp009910705	82.8846	871	1815	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016811235.1	s__Microvirga arabica	82.3212	999	1815	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013520865.1	s__Microvirga mediterraneensis	82.2184	867	1815	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000262405.1	s__Microvirga lotononidis	82.0752	892	1815	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003347665.1	s__Microvirga calopogonii	81.9863	890	1815	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016864375.1	s__Microvirga sp016864375	81.561	966	1815	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:15:35,400] [INFO] GTDB search result was written to GCF_009830105.1_ASM983010v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:15:35,401] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:15:35,406] [INFO] DFAST_QC result json was written to GCF_009830105.1_ASM983010v1_genomic.fna/dqc_result.json
[2024-01-24 13:15:35,406] [INFO] DFAST_QC completed!
[2024-01-24 13:15:35,406] [INFO] Total running time: 0h1m44s