[2024-01-24 10:48:09,415] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:48:09,418] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:48:09,418] [INFO] DQC Reference Directory: /var/lib/cwl/stg48211d07-a3d7-402e-9627-094e48d2a05d/dqc_reference
[2024-01-24 10:48:23,956] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:48:23,958] [INFO] Task started: Prodigal
[2024-01-24 10:48:23,959] [INFO] Running command: gunzip -c /var/lib/cwl/stga238c2d7-4179-4ec6-93ce-3b9a527ee13e/GCF_001598515.1_ASM159851v1_genomic.fna.gz | prodigal -d GCF_001598515.1_ASM159851v1_genomic.fna/cds.fna -a GCF_001598515.1_ASM159851v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:48:36,599] [INFO] Task succeeded: Prodigal
[2024-01-24 10:48:36,600] [INFO] Task started: HMMsearch
[2024-01-24 10:48:36,600] [INFO] Running command: hmmsearch --tblout GCF_001598515.1_ASM159851v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg48211d07-a3d7-402e-9627-094e48d2a05d/dqc_reference/reference_markers.hmm GCF_001598515.1_ASM159851v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:48:36,874] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:48:36,876] [INFO] Found 6/6 markers.
[2024-01-24 10:48:36,922] [INFO] Query marker FASTA was written to GCF_001598515.1_ASM159851v1_genomic.fna/markers.fasta
[2024-01-24 10:48:36,923] [INFO] Task started: Blastn
[2024-01-24 10:48:36,923] [INFO] Running command: blastn -query GCF_001598515.1_ASM159851v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg48211d07-a3d7-402e-9627-094e48d2a05d/dqc_reference/reference_markers.fasta -out GCF_001598515.1_ASM159851v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:37,903] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:37,906] [INFO] Selected 13 target genomes.
[2024-01-24 10:48:37,907] [INFO] Target genome list was writen to GCF_001598515.1_ASM159851v1_genomic.fna/target_genomes.txt
[2024-01-24 10:48:37,913] [INFO] Task started: fastANI
[2024-01-24 10:48:37,914] [INFO] Running command: fastANI --query /var/lib/cwl/stga238c2d7-4179-4ec6-93ce-3b9a527ee13e/GCF_001598515.1_ASM159851v1_genomic.fna.gz --refList GCF_001598515.1_ASM159851v1_genomic.fna/target_genomes.txt --output GCF_001598515.1_ASM159851v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:50,171] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:50,171] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg48211d07-a3d7-402e-9627-094e48d2a05d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:50,172] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg48211d07-a3d7-402e-9627-094e48d2a05d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:50,183] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:48:50,183] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:50,183] [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
Sphingobium chlorophenolicum	strain=NBRC 16172	GCA_001598515.1	46429	46429	type	True	100.0	1397	1409	95	conclusive
Sphingobium chlorophenolicum	strain=NBRC 16172	GCA_000722875.1	46429	46429	type	True	99.9816	1393	1409	95	conclusive
Sphingobium indicum	strain=B90A	GCA_000264945.2	332055	332055	type	True	89.4628	799	1409	95	below_threshold
Sphingobium fuliginis	strain=DSM 18781	GCA_004152845.1	336203	336203	type	True	88.211	888	1409	95	below_threshold
Sphingobium fuliginis	strain=CCM 7327	GCA_014636045.1	336203	336203	type	True	88.1294	876	1409	95	below_threshold
Sphingobium chungbukense	strain=DJ77	GCA_001005725.1	56193	56193	type	True	87.3104	837	1409	95	below_threshold
Sphingobium estronivorans	strain=AXB	GCA_008692605.1	1577690	1577690	type	True	86.4227	748	1409	95	below_threshold
Sphingobium quisquiliarum	strain=P25	GCA_000445065.1	538379	538379	type	True	83.774	627	1409	95	below_threshold
Sphingobium terrigena	strain=EO9	GCA_003591655.1	2304063	2304063	type	True	82.1137	636	1409	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	78.4346	331	1409	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	78.4194	336	1409	95	below_threshold
Sphingomonas cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	78.0683	329	1409	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	77.7313	374	1409	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:50,185] [INFO] DFAST Taxonomy check result was written to GCF_001598515.1_ASM159851v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:50,186] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:50,186] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:50,186] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg48211d07-a3d7-402e-9627-094e48d2a05d/dqc_reference/checkm_data
[2024-01-24 10:48:50,187] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:50,232] [INFO] Task started: CheckM
[2024-01-24 10:48:50,232] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001598515.1_ASM159851v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001598515.1_ASM159851v1_genomic.fna/checkm_input GCF_001598515.1_ASM159851v1_genomic.fna/checkm_result
[2024-01-24 10:49:34,461] [INFO] Task succeeded: CheckM
[2024-01-24 10:49:34,463] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:49:34,564] [INFO] ===== Completeness check finished =====
[2024-01-24 10:49:34,564] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:49:34,565] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001598515.1_ASM159851v1_genomic.fna/markers.fasta)
[2024-01-24 10:49:34,565] [INFO] Task started: Blastn
[2024-01-24 10:49:34,565] [INFO] Running command: blastn -query GCF_001598515.1_ASM159851v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg48211d07-a3d7-402e-9627-094e48d2a05d/dqc_reference/reference_markers_gtdb.fasta -out GCF_001598515.1_ASM159851v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:36,574] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:36,577] [INFO] Selected 10 target genomes.
[2024-01-24 10:49:36,577] [INFO] Target genome list was writen to GCF_001598515.1_ASM159851v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:49:36,621] [INFO] Task started: fastANI
[2024-01-24 10:49:36,621] [INFO] Running command: fastANI --query /var/lib/cwl/stga238c2d7-4179-4ec6-93ce-3b9a527ee13e/GCF_001598515.1_ASM159851v1_genomic.fna.gz --refList GCF_001598515.1_ASM159851v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001598515.1_ASM159851v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:49,017] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:49,026] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:49:49,026] [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_000722875.1	s__Sphingobium chlorophenolicum	99.9816	1393	1409	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	97.94	95.89	0.87	0.76	3	conclusive
GCA_000264945.2	s__Sphingobium indicum	89.4758	798	1409	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	98.64	97.75	0.82	0.64	8	-
GCF_013375535.1	s__Sphingobium sp013375535	88.6851	847	1409	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004152845.1	s__Sphingobium fuliginis	88.251	885	1409	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	98.53	97.80	0.87	0.78	14	-
GCF_001005725.1	s__Sphingobium chungbukense	87.3253	836	1409	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	97.77	97.77	0.72	0.72	2	-
GCF_008692605.1	s__Sphingobium estronivorans	86.439	747	1409	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013375555.1	s__Sphingobium sp013375555	85.9631	770	1409	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873695.1	s__Sphingobium sp014873695	85.6267	772	1409	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900218065.1	s__Sphingobium sp900218065	82.8377	597	1409	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	97.42	97.40	0.85	0.85	5	-
GCF_001658005.1	s__Sphingobium sp001658005	82.5248	622	1409	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:49:49,028] [INFO] GTDB search result was written to GCF_001598515.1_ASM159851v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:49,028] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:49,031] [INFO] DFAST_QC result json was written to GCF_001598515.1_ASM159851v1_genomic.fna/dqc_result.json
[2024-01-24 10:49:49,031] [INFO] DFAST_QC completed!
[2024-01-24 10:49:49,032] [INFO] Total running time: 0h1m40s