[2024-01-24 14:11:51,162] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:11:51,165] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:11:51,165] [INFO] DQC Reference Directory: /var/lib/cwl/stg252fcc22-60d3-4eb8-8184-39c5a9d05ea6/dqc_reference
[2024-01-24 14:11:52,670] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:11:52,671] [INFO] Task started: Prodigal
[2024-01-24 14:11:52,671] [INFO] Running command: gunzip -c /var/lib/cwl/stg090e8653-91c6-4c23-8dc8-c1823f82340d/GCF_000379045.1_ASM37904v1_genomic.fna.gz | prodigal -d GCF_000379045.1_ASM37904v1_genomic.fna/cds.fna -a GCF_000379045.1_ASM37904v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:05,771] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:05,771] [INFO] Task started: HMMsearch
[2024-01-24 14:12:05,772] [INFO] Running command: hmmsearch --tblout GCF_000379045.1_ASM37904v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg252fcc22-60d3-4eb8-8184-39c5a9d05ea6/dqc_reference/reference_markers.hmm GCF_000379045.1_ASM37904v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:06,120] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:06,121] [INFO] Found 6/6 markers.
[2024-01-24 14:12:06,171] [INFO] Query marker FASTA was written to GCF_000379045.1_ASM37904v1_genomic.fna/markers.fasta
[2024-01-24 14:12:06,171] [INFO] Task started: Blastn
[2024-01-24 14:12:06,171] [INFO] Running command: blastn -query GCF_000379045.1_ASM37904v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg252fcc22-60d3-4eb8-8184-39c5a9d05ea6/dqc_reference/reference_markers.fasta -out GCF_000379045.1_ASM37904v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:07,376] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:07,379] [INFO] Selected 14 target genomes.
[2024-01-24 14:12:07,379] [INFO] Target genome list was writen to GCF_000379045.1_ASM37904v1_genomic.fna/target_genomes.txt
[2024-01-24 14:12:07,384] [INFO] Task started: fastANI
[2024-01-24 14:12:07,384] [INFO] Running command: fastANI --query /var/lib/cwl/stg090e8653-91c6-4c23-8dc8-c1823f82340d/GCF_000379045.1_ASM37904v1_genomic.fna.gz --refList GCF_000379045.1_ASM37904v1_genomic.fna/target_genomes.txt --output GCF_000379045.1_ASM37904v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:12:23,663] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:23,664] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg252fcc22-60d3-4eb8-8184-39c5a9d05ea6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:12:23,664] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg252fcc22-60d3-4eb8-8184-39c5a9d05ea6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:12:23,676] [INFO] Found 14 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:12:23,676] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:12:23,676] [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 melonis	strain=DAPP-PG 224	GCA_000379045.1	152682	152682	type	True	100.0	1362	1364	95	inconclusive
Sphingomonas aquatilis	strain=DSM 15581	GCA_014196115.1	93063	93063	type	True	95.916	1108	1364	95	inconclusive
Sphingomonas aquatilis	strain=NBRC 16722	GCA_007990915.1	93063	93063	type	True	95.8122	994	1364	95	inconclusive
Sphingomonas taxi	strain=ATCC 55669	GCA_000764535.1	1549858	1549858	type	True	84.4474	840	1364	95	below_threshold
Sphingomonas insulae	strain=KCTC 12872	GCA_010450875.1	424800	424800	type	True	83.9249	802	1364	95	below_threshold
Sphingomonas metalli	strain=CGMCC 1.15330	GCA_014641735.1	1779358	1779358	type	True	81.5417	668	1364	95	below_threshold
Sphingomonas jinjuensis	strain=YC6723	GCA_014197105.1	535907	535907	type	True	81.4406	708	1364	95	below_threshold
Sphingomonas ginsenosidivorax	strain=KHI67	GCA_007995065.1	862135	862135	type	True	81.0566	684	1364	95	below_threshold
Sphingomonas pseudosanguinis	strain=DSM 19512	GCA_014196255.1	413712	413712	type	True	80.8517	690	1364	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	80.5299	631	1364	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	80.1466	656	1364	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	80.069	646	1364	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	79.8742	634	1364	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	79.7888	576	1364	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:12:23,678] [INFO] DFAST Taxonomy check result was written to GCF_000379045.1_ASM37904v1_genomic.fna/tc_result.tsv
[2024-01-24 14:12:23,679] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:12:23,679] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:12:23,679] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg252fcc22-60d3-4eb8-8184-39c5a9d05ea6/dqc_reference/checkm_data
[2024-01-24 14:12:23,680] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:12:23,723] [INFO] Task started: CheckM
[2024-01-24 14:12:23,723] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000379045.1_ASM37904v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000379045.1_ASM37904v1_genomic.fna/checkm_input GCF_000379045.1_ASM37904v1_genomic.fna/checkm_result
[2024-01-24 14:13:04,763] [INFO] Task succeeded: CheckM
[2024-01-24 14:13:04,764] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:13:04,787] [INFO] ===== Completeness check finished =====
[2024-01-24 14:13:04,788] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:13:04,788] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000379045.1_ASM37904v1_genomic.fna/markers.fasta)
[2024-01-24 14:13:04,789] [INFO] Task started: Blastn
[2024-01-24 14:13:04,789] [INFO] Running command: blastn -query GCF_000379045.1_ASM37904v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg252fcc22-60d3-4eb8-8184-39c5a9d05ea6/dqc_reference/reference_markers_gtdb.fasta -out GCF_000379045.1_ASM37904v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:06,900] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:06,904] [INFO] Selected 14 target genomes.
[2024-01-24 14:13:06,905] [INFO] Target genome list was writen to GCF_000379045.1_ASM37904v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:13:06,915] [INFO] Task started: fastANI
[2024-01-24 14:13:06,916] [INFO] Running command: fastANI --query /var/lib/cwl/stg090e8653-91c6-4c23-8dc8-c1823f82340d/GCF_000379045.1_ASM37904v1_genomic.fna.gz --refList GCF_000379045.1_ASM37904v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000379045.1_ASM37904v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:13:20,955] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:20,966] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:13:20,967] [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_014196115.1	s__Sphingomonas aquatilis	95.916	1108	1364	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.36	95.86	0.87	0.82	11	conclusive
GCA_003075315.1	s__Sphingomonas sp003075315	93.3795	1090	1364	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.84	96.53	0.96	0.89	4	-
GCA_002292295.1	s__Sphingomonas sp002292295	85.0313	804	1364	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000764535.1	s__Sphingomonas taxi	84.4778	837	1364	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.55	97.55	0.88	0.88	2	-
GCF_013409985.1	s__Sphingomonas melonis_A	84.2346	839	1364	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000632225.1	s__Sphingomonas sp000632225	84.0514	815	1364	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003355005.1	s__Sphingomonas sp003355005	83.959	826	1364	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010450875.1	s__Sphingomonas insulae	83.897	802	1364	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_016107325.1	s__Sphingomonas sp016107325	83.0326	827	1364	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197105.1	s__Sphingomonas jinjuensis	81.4342	708	1364	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007995065.1	s__Sphingomonas ginsenosidivorax	81.0536	684	1364	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001476905.1	s__Sphingomonas sanguinis_B	81.0517	634	1364	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.13	96.11	0.83	0.82	3	-
GCF_014196255.1	s__Sphingomonas pseudosanguinis	80.8182	695	1364	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004340945.1	s__Sphingomonas sp004340945	79.7926	652	1364	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	95.25	95.25	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:13:20,969] [INFO] GTDB search result was written to GCF_000379045.1_ASM37904v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:13:20,970] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:13:20,976] [INFO] DFAST_QC result json was written to GCF_000379045.1_ASM37904v1_genomic.fna/dqc_result.json
[2024-01-24 14:13:20,976] [INFO] DFAST_QC completed!
[2024-01-24 14:13:20,976] [INFO] Total running time: 0h1m30s