[2024-01-25 17:34:07,120] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:34:07,124] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:34:07,124] [INFO] DQC Reference Directory: /var/lib/cwl/stga23cb4e0-5c83-4086-aaba-29162e7cdd86/dqc_reference
[2024-01-25 17:34:08,950] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:34:08,951] [INFO] Task started: Prodigal
[2024-01-25 17:34:08,952] [INFO] Running command: gunzip -c /var/lib/cwl/stgb777287b-1267-49f6-aefe-2eab3ed918b6/GCF_000013025.1_ASM1302v1_genomic.fna.gz | prodigal -d GCF_000013025.1_ASM1302v1_genomic.fna/cds.fna -a GCF_000013025.1_ASM1302v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:34:18,994] [INFO] Task succeeded: Prodigal
[2024-01-25 17:34:18,994] [INFO] Task started: HMMsearch
[2024-01-25 17:34:18,994] [INFO] Running command: hmmsearch --tblout GCF_000013025.1_ASM1302v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga23cb4e0-5c83-4086-aaba-29162e7cdd86/dqc_reference/reference_markers.hmm GCF_000013025.1_ASM1302v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:34:19,295] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:34:19,297] [INFO] Found 6/6 markers.
[2024-01-25 17:34:19,330] [INFO] Query marker FASTA was written to GCF_000013025.1_ASM1302v1_genomic.fna/markers.fasta
[2024-01-25 17:34:19,330] [INFO] Task started: Blastn
[2024-01-25 17:34:19,331] [INFO] Running command: blastn -query GCF_000013025.1_ASM1302v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga23cb4e0-5c83-4086-aaba-29162e7cdd86/dqc_reference/reference_markers.fasta -out GCF_000013025.1_ASM1302v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:34:20,165] [INFO] Task succeeded: Blastn
[2024-01-25 17:34:20,168] [INFO] Selected 17 target genomes.
[2024-01-25 17:34:20,168] [INFO] Target genome list was writen to GCF_000013025.1_ASM1302v1_genomic.fna/target_genomes.txt
[2024-01-25 17:34:20,191] [INFO] Task started: fastANI
[2024-01-25 17:34:20,191] [INFO] Running command: fastANI --query /var/lib/cwl/stgb777287b-1267-49f6-aefe-2eab3ed918b6/GCF_000013025.1_ASM1302v1_genomic.fna.gz --refList GCF_000013025.1_ASM1302v1_genomic.fna/target_genomes.txt --output GCF_000013025.1_ASM1302v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:34:34,565] [INFO] Task succeeded: fastANI
[2024-01-25 17:34:34,566] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga23cb4e0-5c83-4086-aaba-29162e7cdd86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:34:34,566] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga23cb4e0-5c83-4086-aaba-29162e7cdd86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:34:34,577] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:34:34,577] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:34:34,577] [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	84.2803	926	1235	95	below_threshold
Hyphomonas sediminis	strain=WL0036	GCA_019679475.1	2866160	2866160	type	True	82.7314	828	1235	95	below_threshold
Hyphomonas chukchiensis	strain=BH-BN04-4	GCA_000682695.1	1280947	1280947	type	True	78.3661	382	1235	95	below_threshold
Hyphomonas jannaschiana	strain=VP2	GCA_000685215.1	86	86	type	True	78.1961	422	1235	95	below_threshold
Hyphomonas oceanitis	strain=SCH89	GCA_000685295.1	81033	81033	type	True	78.1386	365	1235	95	below_threshold
Hyphomonas adhaerens	strain=MHS-3	GCA_000685235.1	81029	81029	type	True	78.0769	394	1235	95	below_threshold
Hyphomonas johnsonii	strain=MHS-2	GCA_000685275.1	81031	81031	type	True	77.9859	376	1235	95	below_threshold
Hyphomonas beringensis	strain=25B14_1	GCA_000682755.1	1280946	1280946	type	True	77.8875	321	1235	95	below_threshold
Henriciella aquimarina	strain=LMG 24711	GCA_002088975.1	545261	545261	type	True	77.399	255	1235	95	below_threshold
Henriciella pelagia	strain=LA220	GCA_002088945.1	1977912	1977912	type	True	77.2786	200	1235	95	below_threshold
Henriciella pelagia	strain=CGMCC 1.15928	GCA_014644035.1	1977912	1977912	type	True	77.2643	197	1235	95	below_threshold
Henriciella marina	strain=DSM 19595	GCA_000376805.1	453851	453851	type	True	76.9159	197	1235	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	76.2084	94	1235	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	76.0633	113	1235	95	below_threshold
Methylobacterium tardum	strain=DSM 19566	GCA_023546765.1	374432	374432	type	True	75.9931	105	1235	95	below_threshold
Methylobacterium tardum	strain=NBRC 103632	GCA_022179585.1	374432	374432	type	True	75.8315	100	1235	95	below_threshold
Lichenibacterium minor	strain=RmlP026	GCA_004137685.1	2316528	2316528	type	True	75.5955	91	1235	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:34:34,578] [INFO] DFAST Taxonomy check result was written to GCF_000013025.1_ASM1302v1_genomic.fna/tc_result.tsv
[2024-01-25 17:34:34,579] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:34:34,579] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:34:34,579] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga23cb4e0-5c83-4086-aaba-29162e7cdd86/dqc_reference/checkm_data
[2024-01-25 17:34:34,580] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:34:34,624] [INFO] Task started: CheckM
[2024-01-25 17:34:34,624] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000013025.1_ASM1302v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000013025.1_ASM1302v1_genomic.fna/checkm_input GCF_000013025.1_ASM1302v1_genomic.fna/checkm_result
[2024-01-25 17:35:06,697] [INFO] Task succeeded: CheckM
[2024-01-25 17:35:06,698] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:35:06,738] [INFO] ===== Completeness check finished =====
[2024-01-25 17:35:06,738] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:35:06,738] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000013025.1_ASM1302v1_genomic.fna/markers.fasta)
[2024-01-25 17:35:06,739] [INFO] Task started: Blastn
[2024-01-25 17:35:06,739] [INFO] Running command: blastn -query GCF_000013025.1_ASM1302v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga23cb4e0-5c83-4086-aaba-29162e7cdd86/dqc_reference/reference_markers_gtdb.fasta -out GCF_000013025.1_ASM1302v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:35:08,391] [INFO] Task succeeded: Blastn
[2024-01-25 17:35:08,395] [INFO] Selected 6 target genomes.
[2024-01-25 17:35:08,395] [INFO] Target genome list was writen to GCF_000013025.1_ASM1302v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:35:08,399] [INFO] Task started: fastANI
[2024-01-25 17:35:08,399] [INFO] Running command: fastANI --query /var/lib/cwl/stgb777287b-1267-49f6-aefe-2eab3ed918b6/GCF_000013025.1_ASM1302v1_genomic.fna.gz --refList GCF_000013025.1_ASM1302v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000013025.1_ASM1302v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:35:14,026] [INFO] Task succeeded: fastANI
[2024-01-25 17:35:14,032] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:35:14,032] [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	100.0	1235	1235	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	86.1289	945	1235	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	84.8897	798	1235	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	84.8764	901	1235	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	84.2898	662	1235	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	84.2697	927	1235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	98.45	98.45	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:35:14,034] [INFO] GTDB search result was written to GCF_000013025.1_ASM1302v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:35:14,034] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:35:14,037] [INFO] DFAST_QC result json was written to GCF_000013025.1_ASM1302v1_genomic.fna/dqc_result.json
[2024-01-25 17:35:14,037] [INFO] DFAST_QC completed!
[2024-01-25 17:35:14,038] [INFO] Total running time: 0h1m7s