[2024-01-24 10:47:06,547] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,552] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,552] [INFO] DQC Reference Directory: /var/lib/cwl/stge6d83464-e9d2-476b-984c-28e8ba6b3deb/dqc_reference
[2024-01-24 10:47:12,100] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,102] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,103] [INFO] Running command: gunzip -c /var/lib/cwl/stgf2d4e32d-8fdf-4fad-ad8b-73b6142c575d/GCF_021497585.1_ASM2149758v1_genomic.fna.gz | prodigal -d GCF_021497585.1_ASM2149758v1_genomic.fna/cds.fna -a GCF_021497585.1_ASM2149758v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:19,488] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:19,488] [INFO] Task started: HMMsearch
[2024-01-24 10:47:19,488] [INFO] Running command: hmmsearch --tblout GCF_021497585.1_ASM2149758v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge6d83464-e9d2-476b-984c-28e8ba6b3deb/dqc_reference/reference_markers.hmm GCF_021497585.1_ASM2149758v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:19,738] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:19,739] [INFO] Found 6/6 markers.
[2024-01-24 10:47:19,761] [INFO] Query marker FASTA was written to GCF_021497585.1_ASM2149758v1_genomic.fna/markers.fasta
[2024-01-24 10:47:19,761] [INFO] Task started: Blastn
[2024-01-24 10:47:19,762] [INFO] Running command: blastn -query GCF_021497585.1_ASM2149758v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge6d83464-e9d2-476b-984c-28e8ba6b3deb/dqc_reference/reference_markers.fasta -out GCF_021497585.1_ASM2149758v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:20,729] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:20,732] [INFO] Selected 16 target genomes.
[2024-01-24 10:47:20,733] [INFO] Target genome list was writen to GCF_021497585.1_ASM2149758v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:20,754] [INFO] Task started: fastANI
[2024-01-24 10:47:20,755] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2d4e32d-8fdf-4fad-ad8b-73b6142c575d/GCF_021497585.1_ASM2149758v1_genomic.fna.gz --refList GCF_021497585.1_ASM2149758v1_genomic.fna/target_genomes.txt --output GCF_021497585.1_ASM2149758v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:29,996] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:29,996] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge6d83464-e9d2-476b-984c-28e8ba6b3deb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:29,997] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge6d83464-e9d2-476b-984c-28e8ba6b3deb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:30,009] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:47:30,010] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:30,010] [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 lutea	strain=KCTC 23642	GCA_021497585.1	1045317	1045317	type	True	100.0	805	805	95	conclusive
Sphingomonas lutea	strain=KCTC 23642	GCA_014396785.1	1045317	1045317	type	True	99.9905	804	805	95	conclusive
Sphingomonas segetis	strain=YJ09	GCA_009720245.1	1104779	1104779	type	True	80.0472	401	805	95	below_threshold
Sphingomonas sinipercae	strain=HDW15C	GCA_011302055.1	2714944	2714944	type	True	79.7651	367	805	95	below_threshold
Sphingomonas sabuli	strain=sand1-3	GCA_014352855.1	2764186	2764186	type	True	79.7629	414	805	95	below_threshold
Sphingomonas mesophila	strain=SYSUP0001	GCA_003499275.1	2303576	2303576	type	True	79.758	406	805	95	below_threshold
Sphingomonas jaspsi	strain=DSM 18422	GCA_000585415.1	392409	392409	type	True	79.6032	353	805	95	below_threshold
Sphingomonas ginsengisoli An et al. 2013	strain=KACC 16858	GCA_009363895.1	363835	363835	type	True	79.4892	387	805	95	below_threshold
Sphingomonas rhizophila	strain=KACC 19189	GCA_014396585.1	2071607	2071607	type	True	79.309	342	805	95	below_threshold
Sphingomonas kaistensis	strain=DSM 16846	GCA_011927725.1	298708	298708	type	True	79.3017	375	805	95	below_threshold
Sphingomonas ginkgonis	strain=HMF7854	GCA_003970925.1	2315330	2315330	type	True	79.2975	372	805	95	below_threshold
Sphingomonas xanthus	strain=AE3	GCA_007998985.1	2594473	2594473	type	True	78.6101	288	805	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	78.1042	260	805	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	78.0682	279	805	95	below_threshold
Sphingomonas aurantiaca	strain=MA101b	GCA_003050705.1	185949	185949	type	True	77.7622	238	805	95	below_threshold
Qipengyuania thermophila	strain=CFH 74456	GCA_004153605.1	2509361	2509361	type	True	77.5529	132	805	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:30,012] [INFO] DFAST Taxonomy check result was written to GCF_021497585.1_ASM2149758v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:30,012] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:30,012] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:30,012] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge6d83464-e9d2-476b-984c-28e8ba6b3deb/dqc_reference/checkm_data
[2024-01-24 10:47:30,013] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:30,038] [INFO] Task started: CheckM
[2024-01-24 10:47:30,038] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021497585.1_ASM2149758v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021497585.1_ASM2149758v1_genomic.fna/checkm_input GCF_021497585.1_ASM2149758v1_genomic.fna/checkm_result
[2024-01-24 10:47:57,017] [INFO] Task succeeded: CheckM
[2024-01-24 10:47:57,018] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:47:57,046] [INFO] ===== Completeness check finished =====
[2024-01-24 10:47:57,047] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:47:57,047] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021497585.1_ASM2149758v1_genomic.fna/markers.fasta)
[2024-01-24 10:47:57,047] [INFO] Task started: Blastn
[2024-01-24 10:47:57,047] [INFO] Running command: blastn -query GCF_021497585.1_ASM2149758v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge6d83464-e9d2-476b-984c-28e8ba6b3deb/dqc_reference/reference_markers_gtdb.fasta -out GCF_021497585.1_ASM2149758v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:59,083] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:59,088] [INFO] Selected 20 target genomes.
[2024-01-24 10:47:59,088] [INFO] Target genome list was writen to GCF_021497585.1_ASM2149758v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:47:59,119] [INFO] Task started: fastANI
[2024-01-24 10:47:59,119] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2d4e32d-8fdf-4fad-ad8b-73b6142c575d/GCF_021497585.1_ASM2149758v1_genomic.fna.gz --refList GCF_021497585.1_ASM2149758v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021497585.1_ASM2149758v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:09,269] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:09,285] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:09,285] [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_014396785.1	s__Sphingomicrobium lutea	99.9905	804	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003097155.1	s__Sphingomicrobium sp003097155	80.2032	459	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620665.1	s__Sphingomicrobium sp000620665	80.1375	463	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009720245.1	s__Sphingomicrobium sp009720245	80.056	400	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011053295.1	s__Sphingomicrobium sp011053295	79.8899	326	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014352855.1	s__Sphingomicrobium sp014352855	79.7757	413	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003499275.1	s__Sphingomicrobium mesophila	79.7587	406	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873795.1	s__Sphingomicrobium sp014873795	79.713	395	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019242355.1	s__Sphingomicrobium sp019242355	79.6408	310	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806275.1	s__Sphingomicrobium sp902806275	79.6322	301	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000585415.1	s__Sphingomicrobium jaspsi	79.6002	354	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019247755.1	s__Sphingomicrobium sp019247755	79.4337	266	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014396585.1	s__Sphingomicrobium rhizophilum	79.3232	341	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003970925.1	s__Sphingomicrobium sp003970925	79.2712	374	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873475.1	s__Sphingomicrobium sp014873475	79.1553	384	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013361785.1	s__Sphingomicrobium sp013361785	79.1239	329	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007998985.1	s__Sphingomicrobium xanthus	78.582	290	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001421805.1	s__Sphingomonas sp001421805	77.8259	224	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.24	98.24	0.93	0.93	2	-
GCA_004331795.1	s__CFH-75059 sp004331795	77.5744	131	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__CFH-75059	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001421355.1	s__Sphingomonas sp001421355	77.4847	246	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.29	96.58	0.97	0.94	3	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:09,287] [INFO] GTDB search result was written to GCF_021497585.1_ASM2149758v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:09,289] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:09,293] [INFO] DFAST_QC result json was written to GCF_021497585.1_ASM2149758v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:09,293] [INFO] DFAST_QC completed!
[2024-01-24 10:48:09,294] [INFO] Total running time: 0h1m3s