[2024-01-24 13:18:46,422] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:46,424] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:46,424] [INFO] DQC Reference Directory: /var/lib/cwl/stg4fbddf77-089e-43d8-9bfc-5130433c5918/dqc_reference
[2024-01-24 13:18:47,754] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:47,755] [INFO] Task started: Prodigal
[2024-01-24 13:18:47,755] [INFO] Running command: gunzip -c /var/lib/cwl/stg54e36953-5074-40b8-b2e0-a53254b7ae0f/GCF_009720245.1_ASM972024v1_genomic.fna.gz | prodigal -d GCF_009720245.1_ASM972024v1_genomic.fna/cds.fna -a GCF_009720245.1_ASM972024v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:54,983] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:54,984] [INFO] Task started: HMMsearch
[2024-01-24 13:18:54,984] [INFO] Running command: hmmsearch --tblout GCF_009720245.1_ASM972024v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4fbddf77-089e-43d8-9bfc-5130433c5918/dqc_reference/reference_markers.hmm GCF_009720245.1_ASM972024v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:55,258] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:55,260] [INFO] Found 6/6 markers.
[2024-01-24 13:18:55,286] [INFO] Query marker FASTA was written to GCF_009720245.1_ASM972024v1_genomic.fna/markers.fasta
[2024-01-24 13:18:55,287] [INFO] Task started: Blastn
[2024-01-24 13:18:55,287] [INFO] Running command: blastn -query GCF_009720245.1_ASM972024v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4fbddf77-089e-43d8-9bfc-5130433c5918/dqc_reference/reference_markers.fasta -out GCF_009720245.1_ASM972024v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:56,222] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:56,225] [INFO] Selected 14 target genomes.
[2024-01-24 13:18:56,225] [INFO] Target genome list was writen to GCF_009720245.1_ASM972024v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:56,237] [INFO] Task started: fastANI
[2024-01-24 13:18:56,237] [INFO] Running command: fastANI --query /var/lib/cwl/stg54e36953-5074-40b8-b2e0-a53254b7ae0f/GCF_009720245.1_ASM972024v1_genomic.fna.gz --refList GCF_009720245.1_ASM972024v1_genomic.fna/target_genomes.txt --output GCF_009720245.1_ASM972024v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:05,714] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:05,714] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4fbddf77-089e-43d8-9bfc-5130433c5918/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:05,715] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4fbddf77-089e-43d8-9bfc-5130433c5918/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:05,726] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:19:05,726] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:05,726] [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 segetis	strain=YJ09	GCA_009720245.1	1104779	1104779	type	True	100.0	788	799	95	conclusive
Sphingomonas lutea	strain=KCTC 23642	GCA_021497585.1	1045317	1045317	type	True	79.9031	404	799	95	below_threshold
Sphingomonas lutea	strain=KCTC 23642	GCA_014396785.1	1045317	1045317	type	True	79.868	405	799	95	below_threshold
Sphingomonas mesophila	strain=SYSUP0001	GCA_003499275.1	2303576	2303576	type	True	79.4084	328	799	95	below_threshold
Sphingomonas sinipercae	strain=HDW15C	GCA_011302055.1	2714944	2714944	type	True	79.3082	318	799	95	below_threshold
Sphingomonas ginkgonis	strain=HMF7854	GCA_003970925.1	2315330	2315330	type	True	79.295	364	799	95	below_threshold
Sphingomonas ginsengisoli An et al. 2013	strain=KACC 16858	GCA_009363895.1	363835	363835	type	True	79.2687	331	799	95	below_threshold
Sphingomonas sabuli	strain=sand1-3	GCA_014352855.1	2764186	2764186	type	True	79.0774	350	799	95	below_threshold
Sphingomonas jaspsi	strain=DSM 18422	GCA_000585415.1	392409	392409	type	True	78.5335	286	799	95	below_threshold
Sphingosinicella humi	strain=QZX222	GCA_003129465.1	2068657	2068657	type	True	78.3509	251	799	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	77.9984	232	799	95	below_threshold
Sphingosinithalassobacter tenebrarum	strain=zrk23	GCA_011057975.1	2711215	2711215	type	True	77.7891	193	799	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	77.7485	299	799	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:05,733] [INFO] DFAST Taxonomy check result was written to GCF_009720245.1_ASM972024v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:05,734] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:05,734] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:05,734] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4fbddf77-089e-43d8-9bfc-5130433c5918/dqc_reference/checkm_data
[2024-01-24 13:19:05,736] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:05,770] [INFO] Task started: CheckM
[2024-01-24 13:19:05,771] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009720245.1_ASM972024v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009720245.1_ASM972024v1_genomic.fna/checkm_input GCF_009720245.1_ASM972024v1_genomic.fna/checkm_result
[2024-01-24 13:19:32,153] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:32,154] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:32,172] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:32,173] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:32,173] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009720245.1_ASM972024v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:32,173] [INFO] Task started: Blastn
[2024-01-24 13:19:32,174] [INFO] Running command: blastn -query GCF_009720245.1_ASM972024v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4fbddf77-089e-43d8-9bfc-5130433c5918/dqc_reference/reference_markers_gtdb.fasta -out GCF_009720245.1_ASM972024v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:34,006] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:34,011] [INFO] Selected 16 target genomes.
[2024-01-24 13:19:34,011] [INFO] Target genome list was writen to GCF_009720245.1_ASM972024v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:34,031] [INFO] Task started: fastANI
[2024-01-24 13:19:34,031] [INFO] Running command: fastANI --query /var/lib/cwl/stg54e36953-5074-40b8-b2e0-a53254b7ae0f/GCF_009720245.1_ASM972024v1_genomic.fna.gz --refList GCF_009720245.1_ASM972024v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009720245.1_ASM972024v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:42,283] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:42,296] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:42,296] [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_009720245.1	s__Sphingomicrobium sp009720245	100.0	788	799	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013361785.1	s__Sphingomicrobium sp013361785	81.4042	381	799	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003097155.1	s__Sphingomicrobium sp003097155	81.0692	483	799	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	80.7726	436	799	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	80.0065	393	799	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	79.9698	282	799	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	79.9039	327	799	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014396785.1	s__Sphingomicrobium lutea	79.868	405	799	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	79.3971	242	799	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011302055.1	s__Sphingomicrobium sinipercae	79.3161	317	799	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	79.0804	356	799	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013816595.1	s__Sphingomicrobium sp013816595	78.6793	259	799	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011057975.1	s__Sphingomonas sp011057975	77.806	192	799	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003432385.1	s__Breoghania sp003432385	76.6561	84	799	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Breoghania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002423025.1	s__Polymorphobacter sp002423025	76.2615	82	799	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Polymorphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002701395.1	s__Rhodobacter_B sp002701395	75.8908	63	799	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:42,297] [INFO] GTDB search result was written to GCF_009720245.1_ASM972024v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:42,298] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:42,302] [INFO] DFAST_QC result json was written to GCF_009720245.1_ASM972024v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:42,302] [INFO] DFAST_QC completed!
[2024-01-24 13:19:42,302] [INFO] Total running time: 0h0m56s