[2024-01-24 14:28:15,540] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:15,542] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:15,542] [INFO] DQC Reference Directory: /var/lib/cwl/stg7da8f527-2b0b-4b4e-ac27-673e302c8827/dqc_reference
[2024-01-24 14:28:17,936] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:17,938] [INFO] Task started: Prodigal
[2024-01-24 14:28:17,938] [INFO] Running command: gunzip -c /var/lib/cwl/stg567c8415-d57e-40a4-85de-b11a3b2b6132/GCF_009607675.1_ASM960767v1_genomic.fna.gz | prodigal -d GCF_009607675.1_ASM960767v1_genomic.fna/cds.fna -a GCF_009607675.1_ASM960767v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:29,148] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:29,148] [INFO] Task started: HMMsearch
[2024-01-24 14:28:29,148] [INFO] Running command: hmmsearch --tblout GCF_009607675.1_ASM960767v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7da8f527-2b0b-4b4e-ac27-673e302c8827/dqc_reference/reference_markers.hmm GCF_009607675.1_ASM960767v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:29,427] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:29,429] [INFO] Found 6/6 markers.
[2024-01-24 14:28:29,470] [INFO] Query marker FASTA was written to GCF_009607675.1_ASM960767v1_genomic.fna/markers.fasta
[2024-01-24 14:28:29,470] [INFO] Task started: Blastn
[2024-01-24 14:28:29,470] [INFO] Running command: blastn -query GCF_009607675.1_ASM960767v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7da8f527-2b0b-4b4e-ac27-673e302c8827/dqc_reference/reference_markers.fasta -out GCF_009607675.1_ASM960767v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:30,386] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:30,390] [INFO] Selected 15 target genomes.
[2024-01-24 14:28:30,390] [INFO] Target genome list was writen to GCF_009607675.1_ASM960767v1_genomic.fna/target_genomes.txt
[2024-01-24 14:28:30,484] [INFO] Task started: fastANI
[2024-01-24 14:28:30,484] [INFO] Running command: fastANI --query /var/lib/cwl/stg567c8415-d57e-40a4-85de-b11a3b2b6132/GCF_009607675.1_ASM960767v1_genomic.fna.gz --refList GCF_009607675.1_ASM960767v1_genomic.fna/target_genomes.txt --output GCF_009607675.1_ASM960767v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:28:40,652] [INFO] Task succeeded: fastANI
[2024-01-24 14:28:40,653] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7da8f527-2b0b-4b4e-ac27-673e302c8827/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:28:40,653] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7da8f527-2b0b-4b4e-ac27-673e302c8827/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:28:40,665] [INFO] Found 15 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:28:40,666] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:28:40,666] [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
Polymorphobacter fuscus	strain=D40P	GCA_009607675.1	1439888	1439888	type	True	100.0	1118	1118	95	conclusive
Polymorphobacter fuscus	strain=D40P	GCA_009372075.1	1439888	1439888	type	True	100.0	1118	1118	95	conclusive
Polymorphobacter fuscus	strain=DSM 105347	GCA_011927825.1	1439888	1439888	type	True	99.9842	1116	1118	95	conclusive
Polymorphobacter glacialis	strain=CGMCC 1.15519	GCA_014643455.1	1614636	1614636	type	True	80.7164	580	1118	95	below_threshold
Polymorphobacter multimanifer	strain=JCM 18140	GCA_014647295.1	1070431	1070431	type	True	79.2671	443	1118	95	below_threshold
Polymorphobacter multimanifer	strain=DSM 102189	GCA_014205635.1	1070431	1070431	type	True	79.2603	491	1118	95	below_threshold
Sandarakinorhabdus rubra	strain=MO-4	GCA_010994245.1	2672568	2672568	type	True	78.9941	357	1118	95	below_threshold
Sandarakinorhabdus oryzae	strain=NM-18	GCA_009733735.1	2675220	2675220	type	True	78.937	399	1118	95	below_threshold
Sandarakinorhabdus limnophila	strain=DSM 17366	GCA_000420765.1	210512	210512	type	True	78.5658	376	1118	95	below_threshold
Sphingomonas lutea	strain=KCTC 23642	GCA_021497585.1	1045317	1045317	type	True	77.4137	158	1118	95	below_threshold
Tardibacter chloracetimidivorans	strain=JJ-A5	GCA_001890385.1	1921510	1921510	type	True	77.2855	177	1118	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	77.205	319	1118	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	77.0395	314	1118	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	76.9862	282	1118	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	76.7704	330	1118	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:28:40,668] [INFO] DFAST Taxonomy check result was written to GCF_009607675.1_ASM960767v1_genomic.fna/tc_result.tsv
[2024-01-24 14:28:40,668] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:28:40,668] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:28:40,668] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7da8f527-2b0b-4b4e-ac27-673e302c8827/dqc_reference/checkm_data
[2024-01-24 14:28:40,670] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:28:40,705] [INFO] Task started: CheckM
[2024-01-24 14:28:40,705] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009607675.1_ASM960767v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009607675.1_ASM960767v1_genomic.fna/checkm_input GCF_009607675.1_ASM960767v1_genomic.fna/checkm_result
[2024-01-24 14:29:18,386] [INFO] Task succeeded: CheckM
[2024-01-24 14:29:18,387] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:29:18,410] [INFO] ===== Completeness check finished =====
[2024-01-24 14:29:18,411] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:29:18,411] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009607675.1_ASM960767v1_genomic.fna/markers.fasta)
[2024-01-24 14:29:18,411] [INFO] Task started: Blastn
[2024-01-24 14:29:18,411] [INFO] Running command: blastn -query GCF_009607675.1_ASM960767v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7da8f527-2b0b-4b4e-ac27-673e302c8827/dqc_reference/reference_markers_gtdb.fasta -out GCF_009607675.1_ASM960767v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:29:20,113] [INFO] Task succeeded: Blastn
[2024-01-24 14:29:20,117] [INFO] Selected 11 target genomes.
[2024-01-24 14:29:20,117] [INFO] Target genome list was writen to GCF_009607675.1_ASM960767v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:29:20,147] [INFO] Task started: fastANI
[2024-01-24 14:29:20,147] [INFO] Running command: fastANI --query /var/lib/cwl/stg567c8415-d57e-40a4-85de-b11a3b2b6132/GCF_009607675.1_ASM960767v1_genomic.fna.gz --refList GCF_009607675.1_ASM960767v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009607675.1_ASM960767v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:29:29,213] [INFO] Task succeeded: fastANI
[2024-01-24 14:29:29,225] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:29:29,226] [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_011927825.1	s__Polymorphobacter fuscus	99.9842	1116	1118	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Polymorphobacter	95.0	99.98	99.98	1.00	1.00	3	conclusive
GCA_003241875.1	s__Polymorphobacter sp003241875	82.1984	667	1118	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Polymorphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002256005.1	s__Polymorphobacter sp002256005	81.6823	613	1118	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Polymorphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013298745.1	s__Polymorphobacter sp013298745	81.4037	467	1118	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Polymorphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903939555.1	s__Polymorphobacter sp903939555	80.9849	433	1118	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Polymorphobacter	95.0	98.54	98.06	0.84	0.82	4	-
GCF_014643455.1	s__Polymorphobacter glacialis	80.7332	579	1118	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Polymorphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001295935.1	s__Polymorphobacter sp001295935	80.1897	563	1118	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Polymorphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002423025.1	s__Polymorphobacter sp002423025	79.3151	468	1118	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Polymorphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205635.1	s__Polymorphobacter multimanifer	79.26	491	1118	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Polymorphobacter	95.0	99.78	99.78	0.99	0.99	2	-
GCF_004681125.1	s__Polymorphobacter_A arshaanensis	78.8481	417	1118	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Polymorphobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014377915.1	s__Tardiphaga sp014377915	75.3073	122	1118	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Tardiphaga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:29:29,227] [INFO] GTDB search result was written to GCF_009607675.1_ASM960767v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:29:29,228] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:29:29,232] [INFO] DFAST_QC result json was written to GCF_009607675.1_ASM960767v1_genomic.fna/dqc_result.json
[2024-01-24 14:29:29,233] [INFO] DFAST_QC completed!
[2024-01-24 14:29:29,233] [INFO] Total running time: 0h1m14s