[2024-01-24 14:47:08,349] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:47:08,352] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:47:08,352] [INFO] DQC Reference Directory: /var/lib/cwl/stgfc8dd031-01c0-4b3c-a3a0-df3bb099d0ea/dqc_reference
[2024-01-24 14:47:09,770] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:47:09,771] [INFO] Task started: Prodigal
[2024-01-24 14:47:09,771] [INFO] Running command: gunzip -c /var/lib/cwl/stg472ee375-1f91-4dc7-9703-588a6f3af5d1/GCF_019898765.1_ASM1989876v1_genomic.fna.gz | prodigal -d GCF_019898765.1_ASM1989876v1_genomic.fna/cds.fna -a GCF_019898765.1_ASM1989876v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:22,154] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:22,154] [INFO] Task started: HMMsearch
[2024-01-24 14:47:22,154] [INFO] Running command: hmmsearch --tblout GCF_019898765.1_ASM1989876v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfc8dd031-01c0-4b3c-a3a0-df3bb099d0ea/dqc_reference/reference_markers.hmm GCF_019898765.1_ASM1989876v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:22,467] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:22,468] [INFO] Found 6/6 markers.
[2024-01-24 14:47:22,531] [INFO] Query marker FASTA was written to GCF_019898765.1_ASM1989876v1_genomic.fna/markers.fasta
[2024-01-24 14:47:22,532] [INFO] Task started: Blastn
[2024-01-24 14:47:22,532] [INFO] Running command: blastn -query GCF_019898765.1_ASM1989876v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc8dd031-01c0-4b3c-a3a0-df3bb099d0ea/dqc_reference/reference_markers.fasta -out GCF_019898765.1_ASM1989876v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:23,637] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:23,646] [INFO] Selected 10 target genomes.
[2024-01-24 14:47:23,647] [INFO] Target genome list was writen to GCF_019898765.1_ASM1989876v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:23,657] [INFO] Task started: fastANI
[2024-01-24 14:47:23,657] [INFO] Running command: fastANI --query /var/lib/cwl/stg472ee375-1f91-4dc7-9703-588a6f3af5d1/GCF_019898765.1_ASM1989876v1_genomic.fna.gz --refList GCF_019898765.1_ASM1989876v1_genomic.fna/target_genomes.txt --output GCF_019898765.1_ASM1989876v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:35,022] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:35,022] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfc8dd031-01c0-4b3c-a3a0-df3bb099d0ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:35,022] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfc8dd031-01c0-4b3c-a3a0-df3bb099d0ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:35,035] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:47:35,035] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:35,035] [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
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	100.0	1471	1471	95	conclusive
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	91.6535	1168	1471	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	91.2389	1155	1471	95	below_threshold
Sphingomonas endophytica	strain=DSM 101535	GCA_014199415.1	869719	869719	type	True	82.9968	835	1471	95	below_threshold
Sphingomonas adhaesiva	strain=NBRC 15099	GCA_001592345.1	28212	28212	type	True	82.443	578	1471	95	below_threshold
Sphingomonas phyllosphaerae	strain=FA2	GCA_000427645.1	257003	257003	type	True	82.3666	828	1471	95	below_threshold
Sphingomonas adhaesiva	strain=DSM 7418	GCA_002374855.1	28212	28212	type	True	82.1607	716	1471	95	below_threshold
Sphingomonas ginsenosidimutans	strain=KACC 14949	GCA_002374835.1	862134	862134	type	True	82.001	715	1471	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	81.5992	753	1471	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	79.687	572	1471	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:35,037] [INFO] DFAST Taxonomy check result was written to GCF_019898765.1_ASM1989876v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:35,038] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:35,038] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:35,039] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfc8dd031-01c0-4b3c-a3a0-df3bb099d0ea/dqc_reference/checkm_data
[2024-01-24 14:47:35,041] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:35,101] [INFO] Task started: CheckM
[2024-01-24 14:47:35,101] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019898765.1_ASM1989876v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019898765.1_ASM1989876v1_genomic.fna/checkm_input GCF_019898765.1_ASM1989876v1_genomic.fna/checkm_result
[2024-01-24 14:48:15,012] [INFO] Task succeeded: CheckM
[2024-01-24 14:48:15,013] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:48:15,032] [INFO] ===== Completeness check finished =====
[2024-01-24 14:48:15,032] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:48:15,033] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019898765.1_ASM1989876v1_genomic.fna/markers.fasta)
[2024-01-24 14:48:15,033] [INFO] Task started: Blastn
[2024-01-24 14:48:15,034] [INFO] Running command: blastn -query GCF_019898765.1_ASM1989876v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc8dd031-01c0-4b3c-a3a0-df3bb099d0ea/dqc_reference/reference_markers_gtdb.fasta -out GCF_019898765.1_ASM1989876v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:17,152] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:17,156] [INFO] Selected 11 target genomes.
[2024-01-24 14:48:17,156] [INFO] Target genome list was writen to GCF_019898765.1_ASM1989876v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:48:17,163] [INFO] Task started: fastANI
[2024-01-24 14:48:17,163] [INFO] Running command: fastANI --query /var/lib/cwl/stg472ee375-1f91-4dc7-9703-588a6f3af5d1/GCF_019898765.1_ASM1989876v1_genomic.fna.gz --refList GCF_019898765.1_ASM1989876v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019898765.1_ASM1989876v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:48:30,065] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:30,080] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:48:30,080] [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_014194975.1	s__Sphingomonas sp014194975	91.6625	1192	1471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014193845.1	s__Sphingomonas sp014193845	91.6125	1173	1471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.90	98.90	0.87	0.87	2	-
GCF_004345855.1	s__Sphingomonas sp004345855	89.4764	1066	1471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199415.1	s__Sphingomonas endophytica	82.989	835	1471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.00	98.00	0.92	0.92	2	-
GCF_902506455.1	s__Sphingomonas sp902506455	82.4168	828	1471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000427645.1	s__Sphingomonas phyllosphaerae	82.3872	826	1471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002374855.1	s__Sphingomonas adhaesiva	82.1462	718	1471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.76	99.56	0.89	0.87	3	-
GCF_002374835.1	s__Sphingomonas ginsenosidimutans	81.9831	717	1471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.62	98.43	0.85	0.81	6	-
GCF_000419605.1	s__Sphingomonas phyllosphaerae_B	81.6926	829	1471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001421995.1	s__Sphingomonas sp001421995	81.3095	772	1471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204695.1	s__Sphingomonas sp001897045	80.2242	677	1471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.82	96.97	0.94	0.83	6	-
--------------------------------------------------------------------------------
[2024-01-24 14:48:30,082] [INFO] GTDB search result was written to GCF_019898765.1_ASM1989876v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:48:30,083] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:48:30,086] [INFO] DFAST_QC result json was written to GCF_019898765.1_ASM1989876v1_genomic.fna/dqc_result.json
[2024-01-24 14:48:30,087] [INFO] DFAST_QC completed!
[2024-01-24 14:48:30,087] [INFO] Total running time: 0h1m22s