[2024-01-24 13:24:47,864] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:24:47,873] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:24:47,874] [INFO] DQC Reference Directory: /var/lib/cwl/stge7a32730-5a17-45b4-94f8-dd0a754a206c/dqc_reference
[2024-01-24 13:24:49,262] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:24:49,263] [INFO] Task started: Prodigal
[2024-01-24 13:24:49,264] [INFO] Running command: gunzip -c /var/lib/cwl/stg858e5aa6-4535-45a1-a31b-4e8e87c773f5/GCF_000764535.1_ASM76453v1_genomic.fna.gz | prodigal -d GCF_000764535.1_ASM76453v1_genomic.fna/cds.fna -a GCF_000764535.1_ASM76453v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:01,495] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:01,495] [INFO] Task started: HMMsearch
[2024-01-24 13:25:01,495] [INFO] Running command: hmmsearch --tblout GCF_000764535.1_ASM76453v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge7a32730-5a17-45b4-94f8-dd0a754a206c/dqc_reference/reference_markers.hmm GCF_000764535.1_ASM76453v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:01,799] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:01,800] [INFO] Found 6/6 markers.
[2024-01-24 13:25:01,837] [INFO] Query marker FASTA was written to GCF_000764535.1_ASM76453v1_genomic.fna/markers.fasta
[2024-01-24 13:25:01,838] [INFO] Task started: Blastn
[2024-01-24 13:25:01,838] [INFO] Running command: blastn -query GCF_000764535.1_ASM76453v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge7a32730-5a17-45b4-94f8-dd0a754a206c/dqc_reference/reference_markers.fasta -out GCF_000764535.1_ASM76453v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:02,914] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:02,917] [INFO] Selected 17 target genomes.
[2024-01-24 13:25:02,917] [INFO] Target genome list was writen to GCF_000764535.1_ASM76453v1_genomic.fna/target_genomes.txt
[2024-01-24 13:25:02,927] [INFO] Task started: fastANI
[2024-01-24 13:25:02,927] [INFO] Running command: fastANI --query /var/lib/cwl/stg858e5aa6-4535-45a1-a31b-4e8e87c773f5/GCF_000764535.1_ASM76453v1_genomic.fna.gz --refList GCF_000764535.1_ASM76453v1_genomic.fna/target_genomes.txt --output GCF_000764535.1_ASM76453v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:25:19,203] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:19,204] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge7a32730-5a17-45b4-94f8-dd0a754a206c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:25:19,204] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge7a32730-5a17-45b4-94f8-dd0a754a206c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:25:19,217] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:25:19,218] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:25:19,218] [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 taxi	strain=ATCC 55669	GCA_000764535.1	1549858	1549858	type	True	100.0	1353	1353	95	conclusive
Sphingomonas insulae	strain=KCTC 12872	GCA_010450875.1	424800	424800	type	True	84.9053	856	1353	95	below_threshold
Sphingomonas insulae	strain=DSM 21792	GCA_011762035.1	424800	424800	type	True	84.8278	845	1353	95	below_threshold
Sphingomonas aquatilis	strain=DSM 15581	GCA_014196115.1	93063	93063	type	True	84.6464	828	1353	95	below_threshold
Sphingomonas aquatilis	strain=NBRC 16722	GCA_007990915.1	93063	93063	type	True	84.6397	742	1353	95	below_threshold
Sphingomonas melonis	strain=DAPP-PG 224	GCA_000379045.1	152682	152682	type	True	84.5281	842	1353	95	below_threshold
Sphingomonas metalli	strain=CGMCC 1.15330	GCA_014641735.1	1779358	1779358	type	True	81.5614	722	1353	95	below_threshold
Sphingomonas rubra	strain=CGMCC 1.9113	GCA_900115745.1	634430	634430	type	True	81.5073	671	1353	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	81.0892	763	1353	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	81.0507	786	1353	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	81.0426	769	1353	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	80.3631	661	1353	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	80.0337	609	1353	95	below_threshold
Sphingomonas kyeonggiensis	strain=DSM 101806	GCA_014196745.1	1268553	1268553	type	True	79.5498	654	1353	95	below_threshold
Sphingomonas leidyi	strain=DSM 4733	GCA_011761945.1	68569	68569	type	True	79.4484	626	1353	95	below_threshold
Sphingosinithalassobacter tenebrarum	strain=zrk23	GCA_011057975.1	2711215	2711215	type	True	79.0461	485	1353	95	below_threshold
Sphingosinithalassobacter portus	strain=FM6	GCA_003171655.1	2676234	2676234	type	True	78.5036	461	1353	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:25:19,220] [INFO] DFAST Taxonomy check result was written to GCF_000764535.1_ASM76453v1_genomic.fna/tc_result.tsv
[2024-01-24 13:25:19,220] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:25:19,220] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:25:19,221] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge7a32730-5a17-45b4-94f8-dd0a754a206c/dqc_reference/checkm_data
[2024-01-24 13:25:19,222] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:25:19,263] [INFO] Task started: CheckM
[2024-01-24 13:25:19,263] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000764535.1_ASM76453v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000764535.1_ASM76453v1_genomic.fna/checkm_input GCF_000764535.1_ASM76453v1_genomic.fna/checkm_result
[2024-01-24 13:25:56,931] [INFO] Task succeeded: CheckM
[2024-01-24 13:25:56,933] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:25:56,959] [INFO] ===== Completeness check finished =====
[2024-01-24 13:25:56,959] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:25:56,960] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000764535.1_ASM76453v1_genomic.fna/markers.fasta)
[2024-01-24 13:25:56,960] [INFO] Task started: Blastn
[2024-01-24 13:25:56,960] [INFO] Running command: blastn -query GCF_000764535.1_ASM76453v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge7a32730-5a17-45b4-94f8-dd0a754a206c/dqc_reference/reference_markers_gtdb.fasta -out GCF_000764535.1_ASM76453v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:59,050] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:59,054] [INFO] Selected 10 target genomes.
[2024-01-24 13:25:59,055] [INFO] Target genome list was writen to GCF_000764535.1_ASM76453v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:25:59,074] [INFO] Task started: fastANI
[2024-01-24 13:25:59,074] [INFO] Running command: fastANI --query /var/lib/cwl/stg858e5aa6-4535-45a1-a31b-4e8e87c773f5/GCF_000764535.1_ASM76453v1_genomic.fna.gz --refList GCF_000764535.1_ASM76453v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000764535.1_ASM76453v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:26:09,980] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:09,990] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:26:09,990] [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_000764535.1	s__Sphingomonas taxi	100.0	1353	1353	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.55	97.55	0.88	0.88	2	conclusive
GCF_013409985.1	s__Sphingomonas melonis_A	90.3324	1076	1353	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	87.8561	1017	1353	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002292295.1	s__Sphingomonas sp002292295	86.6297	859	1353	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	84.922	854	1353	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_014196115.1	s__Sphingomonas aquatilis	84.616	832	1353	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.36	95.86	0.87	0.82	11	-
GCA_003075315.1	s__Sphingomonas sp003075315	84.4016	809	1353	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.84	96.53	0.96	0.89	4	-
GCA_017744835.1	s__Sphingomonas sp017744835	80.0299	616	1353	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204495.1	s__Sphingomonas kyeonggiensis_A	79.5954	632	1353	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002127225.1	s__Sphingomonas sp002127225	79.484	625	1353	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:26:09,992] [INFO] GTDB search result was written to GCF_000764535.1_ASM76453v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:26:09,992] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:26:09,995] [INFO] DFAST_QC result json was written to GCF_000764535.1_ASM76453v1_genomic.fna/dqc_result.json
[2024-01-24 13:26:09,995] [INFO] DFAST_QC completed!
[2024-01-24 13:26:09,996] [INFO] Total running time: 0h1m22s