[2024-01-24 14:12:35,975] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:12:35,979] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:12:35,980] [INFO] DQC Reference Directory: /var/lib/cwl/stgc88e958c-3128-4a55-9b58-2e9c596abe2b/dqc_reference
[2024-01-24 14:12:37,342] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:12:37,343] [INFO] Task started: Prodigal
[2024-01-24 14:12:37,343] [INFO] Running command: gunzip -c /var/lib/cwl/stg553ef21c-de2f-45f9-8e5b-5705f0e75fb2/GCF_000685255.1_SOAPdenovo_v1.05_genomic.fna.gz | prodigal -d GCF_000685255.1_SOAPdenovo_v1.05_genomic.fna/cds.fna -a GCF_000685255.1_SOAPdenovo_v1.05_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:48,257] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:48,258] [INFO] Task started: HMMsearch
[2024-01-24 14:12:48,258] [INFO] Running command: hmmsearch --tblout GCF_000685255.1_SOAPdenovo_v1.05_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc88e958c-3128-4a55-9b58-2e9c596abe2b/dqc_reference/reference_markers.hmm GCF_000685255.1_SOAPdenovo_v1.05_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:48,537] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:48,538] [INFO] Found 6/6 markers.
[2024-01-24 14:12:48,574] [INFO] Query marker FASTA was written to GCF_000685255.1_SOAPdenovo_v1.05_genomic.fna/markers.fasta
[2024-01-24 14:12:48,575] [INFO] Task started: Blastn
[2024-01-24 14:12:48,575] [INFO] Running command: blastn -query GCF_000685255.1_SOAPdenovo_v1.05_genomic.fna/markers.fasta -db /var/lib/cwl/stgc88e958c-3128-4a55-9b58-2e9c596abe2b/dqc_reference/reference_markers.fasta -out GCF_000685255.1_SOAPdenovo_v1.05_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:49,502] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:49,506] [INFO] Selected 17 target genomes.
[2024-01-24 14:12:49,507] [INFO] Target genome list was writen to GCF_000685255.1_SOAPdenovo_v1.05_genomic.fna/target_genomes.txt
[2024-01-24 14:12:49,513] [INFO] Task started: fastANI
[2024-01-24 14:12:49,514] [INFO] Running command: fastANI --query /var/lib/cwl/stg553ef21c-de2f-45f9-8e5b-5705f0e75fb2/GCF_000685255.1_SOAPdenovo_v1.05_genomic.fna.gz --refList GCF_000685255.1_SOAPdenovo_v1.05_genomic.fna/target_genomes.txt --output GCF_000685255.1_SOAPdenovo_v1.05_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:13:02,838] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:02,838] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc88e958c-3128-4a55-9b58-2e9c596abe2b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:13:02,839] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc88e958c-3128-4a55-9b58-2e9c596abe2b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:13:02,852] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:13:02,852] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:13:02,853] [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
Hyphomonas polymorpha	strain=PS728	GCA_000685315.1	74319	74319	type	True	84.1244	917	1215	95	below_threshold
Hyphomonas sediminis	strain=WL0036	GCA_019679475.1	2866160	2866160	type	True	82.6315	837	1215	95	below_threshold
Hyphomonas chukchiensis	strain=BH-BN04-4	GCA_000682695.1	1280947	1280947	type	True	78.332	367	1215	95	below_threshold
Hyphomonas oceanitis	strain=SCH89	GCA_000685295.1	81033	81033	type	True	78.3212	347	1215	95	below_threshold
Hyphomonas jannaschiana	strain=VP2	GCA_000685215.1	86	86	type	True	78.1977	407	1215	95	below_threshold
Hyphomonas johnsonii	strain=MHS-2	GCA_000685275.1	81031	81031	type	True	78.1058	364	1215	95	below_threshold
Hyphomonas adhaerens	strain=MHS-3	GCA_000685235.1	81029	81029	type	True	78.03	383	1215	95	below_threshold
Hyphomonas beringensis	strain=25B14_1	GCA_000682755.1	1280946	1280946	type	True	77.8925	312	1215	95	below_threshold
Henriciella aquimarina	strain=LMG 24711	GCA_002088975.1	545261	545261	type	True	77.5111	242	1215	95	below_threshold
Henriciella pelagia	strain=LA220	GCA_002088945.1	1977912	1977912	type	True	77.3408	185	1215	95	below_threshold
Henriciella pelagia	strain=CGMCC 1.15928	GCA_014644035.1	1977912	1977912	type	True	77.2936	187	1215	95	below_threshold
Henriciella marina	strain=DSM 19595	GCA_000376805.1	453851	453851	type	True	77.0	182	1215	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	76.4188	104	1215	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	76.2931	88	1215	95	below_threshold
Methylobacterium tardum	strain=DSM 19566	GCA_023546765.1	374432	374432	type	True	76.1542	93	1215	95	below_threshold
Methylobacterium tardum	strain=NBRC 103632	GCA_022179585.1	374432	374432	type	True	76.007	88	1215	95	below_threshold
Lichenibacterium minor	strain=RmlP026	GCA_004137685.1	2316528	2316528	type	True	75.5472	89	1215	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:13:02,854] [INFO] DFAST Taxonomy check result was written to GCF_000685255.1_SOAPdenovo_v1.05_genomic.fna/tc_result.tsv
[2024-01-24 14:13:02,855] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:13:02,855] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:13:02,855] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc88e958c-3128-4a55-9b58-2e9c596abe2b/dqc_reference/checkm_data
[2024-01-24 14:13:02,856] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:13:02,893] [INFO] Task started: CheckM
[2024-01-24 14:13:02,893] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000685255.1_SOAPdenovo_v1.05_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000685255.1_SOAPdenovo_v1.05_genomic.fna/checkm_input GCF_000685255.1_SOAPdenovo_v1.05_genomic.fna/checkm_result
[2024-01-24 14:13:37,602] [INFO] Task succeeded: CheckM
[2024-01-24 14:13:37,603] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:13:37,625] [INFO] ===== Completeness check finished =====
[2024-01-24 14:13:37,625] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:13:37,626] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000685255.1_SOAPdenovo_v1.05_genomic.fna/markers.fasta)
[2024-01-24 14:13:37,626] [INFO] Task started: Blastn
[2024-01-24 14:13:37,626] [INFO] Running command: blastn -query GCF_000685255.1_SOAPdenovo_v1.05_genomic.fna/markers.fasta -db /var/lib/cwl/stgc88e958c-3128-4a55-9b58-2e9c596abe2b/dqc_reference/reference_markers_gtdb.fasta -out GCF_000685255.1_SOAPdenovo_v1.05_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:39,214] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:39,218] [INFO] Selected 6 target genomes.
[2024-01-24 14:13:39,219] [INFO] Target genome list was writen to GCF_000685255.1_SOAPdenovo_v1.05_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:13:39,241] [INFO] Task started: fastANI
[2024-01-24 14:13:39,241] [INFO] Running command: fastANI --query /var/lib/cwl/stg553ef21c-de2f-45f9-8e5b-5705f0e75fb2/GCF_000685255.1_SOAPdenovo_v1.05_genomic.fna.gz --refList GCF_000685255.1_SOAPdenovo_v1.05_genomic.fna/target_genomes_gtdb.txt --output GCF_000685255.1_SOAPdenovo_v1.05_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:13:44,740] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:44,752] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:13:44,752] [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_000013025.1	s__Hyphomonas neptunium	99.9992	1214	1215	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_002841155.1	s__Hyphomonas sp002841155	86.0941	932	1215	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402285.1	s__Hyphomonas sp018402285	85.0342	779	1215	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013823385.1	s__Hyphomonas sp013823385	84.9308	874	1215	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002282565.1	s__Hyphomonas sp002282565	84.2746	655	1215	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000685315.1	s__Hyphomonas polymorpha	84.1198	919	1215	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	98.45	98.45	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:13:44,754] [INFO] GTDB search result was written to GCF_000685255.1_SOAPdenovo_v1.05_genomic.fna/result_gtdb.tsv
[2024-01-24 14:13:44,755] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:13:44,758] [INFO] DFAST_QC result json was written to GCF_000685255.1_SOAPdenovo_v1.05_genomic.fna/dqc_result.json
[2024-01-24 14:13:44,758] [INFO] DFAST_QC completed!
[2024-01-24 14:13:44,758] [INFO] Total running time: 0h1m9s