[2024-01-25 19:48:50,755] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:48:50,757] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:48:50,757] [INFO] DQC Reference Directory: /var/lib/cwl/stga5e26249-5bcf-48c7-ac91-60bebb6e57d2/dqc_reference
[2024-01-25 19:48:51,893] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:48:51,893] [INFO] Task started: Prodigal
[2024-01-25 19:48:51,894] [INFO] Running command: gunzip -c /var/lib/cwl/stg2f5180c8-909c-4ba8-b5c6-4d9d6d072b5b/GCF_003347635.1_ASM334763v1_genomic.fna.gz | prodigal -d GCF_003347635.1_ASM334763v1_genomic.fna/cds.fna -a GCF_003347635.1_ASM334763v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:49:04,061] [INFO] Task succeeded: Prodigal
[2024-01-25 19:49:04,062] [INFO] Task started: HMMsearch
[2024-01-25 19:49:04,062] [INFO] Running command: hmmsearch --tblout GCF_003347635.1_ASM334763v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga5e26249-5bcf-48c7-ac91-60bebb6e57d2/dqc_reference/reference_markers.hmm GCF_003347635.1_ASM334763v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:49:04,373] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:49:04,374] [INFO] Found 6/6 markers.
[2024-01-25 19:49:04,436] [INFO] Query marker FASTA was written to GCF_003347635.1_ASM334763v1_genomic.fna/markers.fasta
[2024-01-25 19:49:04,437] [INFO] Task started: Blastn
[2024-01-25 19:49:04,437] [INFO] Running command: blastn -query GCF_003347635.1_ASM334763v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga5e26249-5bcf-48c7-ac91-60bebb6e57d2/dqc_reference/reference_markers.fasta -out GCF_003347635.1_ASM334763v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:49:05,292] [INFO] Task succeeded: Blastn
[2024-01-25 19:49:05,295] [INFO] Selected 21 target genomes.
[2024-01-25 19:49:05,295] [INFO] Target genome list was writen to GCF_003347635.1_ASM334763v1_genomic.fna/target_genomes.txt
[2024-01-25 19:49:05,313] [INFO] Task started: fastANI
[2024-01-25 19:49:05,313] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f5180c8-909c-4ba8-b5c6-4d9d6d072b5b/GCF_003347635.1_ASM334763v1_genomic.fna.gz --refList GCF_003347635.1_ASM334763v1_genomic.fna/target_genomes.txt --output GCF_003347635.1_ASM334763v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:49:21,047] [INFO] Task succeeded: fastANI
[2024-01-25 19:49:21,047] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga5e26249-5bcf-48c7-ac91-60bebb6e57d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:49:21,048] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga5e26249-5bcf-48c7-ac91-60bebb6e57d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:49:21,062] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:49:21,063] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:49:21,063] [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
Sphingosinicella ginsenosidimutans	strain=BS-11	GCA_007995055.1	1176539	1176539	type	True	80.1474	618	1623	95	below_threshold
Sphingomonas parva	strain=17J27-24	GCA_004564275.1	2555898	2555898	type	True	79.6917	615	1623	95	below_threshold
Sphingosinicella humi	strain=QZX222	GCA_003129465.1	2068657	2068657	type	True	79.474	528	1623	95	below_threshold
Sphingomonas deserti	strain=GL-C-18	GCA_003012735.1	2116704	2116704	type	True	78.9227	635	1623	95	below_threshold
Sphingomonas gilva	strain=ZDH117	GCA_003515075.1	2305907	2305907	type	True	78.2932	469	1623	95	below_threshold
Sphingomonas ginsengisoli An et al. 2013	strain=KACC 16858	GCA_009363895.1	363835	363835	type	True	78.2737	387	1623	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	78.1296	400	1623	95	below_threshold
Sphingomonas ginkgonis	strain=HMF7854	GCA_003970925.1	2315330	2315330	type	True	78.1219	420	1623	95	below_threshold
Sphingomonas oleivorans	strain=FW-11	GCA_003050615.1	1735121	1735121	type	True	77.9277	364	1623	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	77.8586	385	1623	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	77.851	490	1623	95	below_threshold
Sphingomonas formosensis	strain=CC-Nfb-2	GCA_009755815.1	861534	861534	type	True	77.7472	468	1623	95	below_threshold
Sphingomonas baiyangensis	strain=L-1-4 w-11	GCA_005144715.1	2572576	2572576	type	True	77.7146	372	1623	95	below_threshold
Sphingomonas cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	77.7004	380	1623	95	below_threshold
Sphingomonas colocasiae	strain=JCM 31229	GCA_019880585.1	1848973	1848973	type	True	77.6649	480	1623	95	below_threshold
Sphingobium yanoikuyae	strain=ATCC 51230	GCA_000315525.1	13690	13690	suspected-type	True	77.3564	383	1623	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:49:21,065] [INFO] DFAST Taxonomy check result was written to GCF_003347635.1_ASM334763v1_genomic.fna/tc_result.tsv
[2024-01-25 19:49:21,065] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:49:21,066] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:49:21,066] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga5e26249-5bcf-48c7-ac91-60bebb6e57d2/dqc_reference/checkm_data
[2024-01-25 19:49:21,067] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:49:21,114] [INFO] Task started: CheckM
[2024-01-25 19:49:21,114] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003347635.1_ASM334763v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003347635.1_ASM334763v1_genomic.fna/checkm_input GCF_003347635.1_ASM334763v1_genomic.fna/checkm_result
[2024-01-25 19:49:57,375] [INFO] Task succeeded: CheckM
[2024-01-25 19:49:57,376] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:49:57,393] [INFO] ===== Completeness check finished =====
[2024-01-25 19:49:57,393] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:49:57,393] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003347635.1_ASM334763v1_genomic.fna/markers.fasta)
[2024-01-25 19:49:57,394] [INFO] Task started: Blastn
[2024-01-25 19:49:57,394] [INFO] Running command: blastn -query GCF_003347635.1_ASM334763v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga5e26249-5bcf-48c7-ac91-60bebb6e57d2/dqc_reference/reference_markers_gtdb.fasta -out GCF_003347635.1_ASM334763v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:49:58,762] [INFO] Task succeeded: Blastn
[2024-01-25 19:49:58,765] [INFO] Selected 17 target genomes.
[2024-01-25 19:49:58,765] [INFO] Target genome list was writen to GCF_003347635.1_ASM334763v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:49:58,776] [INFO] Task started: fastANI
[2024-01-25 19:49:58,776] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f5180c8-909c-4ba8-b5c6-4d9d6d072b5b/GCF_003347635.1_ASM334763v1_genomic.fna.gz --refList GCF_003347635.1_ASM334763v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003347635.1_ASM334763v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:50:11,629] [INFO] Task succeeded: fastANI
[2024-01-25 19:50:11,638] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:50:11,639] [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
GCA_003347635.1	s__Allosphingosinicella sp003347635	100.0	1622	1623	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004151485.1	s__Allosphingosinicella sp004151485	81.4271	876	1623	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019239785.1	s__Allosphingosinicella sp019239785	80.184	564	1623	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005883305.1	s__Allosphingosinicella sp005883305	80.1738	582	1623	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011320075.1	s__Allosphingosinicella sp011320075	80.1584	569	1623	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007995055.1	s__Allosphingosinicella ginsenosidimutans	80.124	621	1623	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004564275.1	s__Allosphingosinicella parva	79.683	616	1623	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019239415.1	s__Allosphingosinicella sp019239415	79.5203	554	1623	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003129465.1	s__Allosphingosinicella humi	79.4453	531	1623	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019232625.1	s__Allosphingosinicella sp019232625	79.4266	618	1623	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	99.90	99.89	0.98	0.97	3	-
GCA_005882415.1	s__Allosphingosinicella sp005882415	79.3932	451	1623	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135585.1	s__Allosphingosinicella sp004135585	78.9993	615	1623	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009755815.1	s__Sphingomonas_M formosensis	77.7681	465	1623	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_M	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:50:11,640] [INFO] GTDB search result was written to GCF_003347635.1_ASM334763v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:50:11,641] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:50:11,644] [INFO] DFAST_QC result json was written to GCF_003347635.1_ASM334763v1_genomic.fna/dqc_result.json
[2024-01-25 19:50:11,644] [INFO] DFAST_QC completed!
[2024-01-25 19:50:11,644] [INFO] Total running time: 0h1m21s