[2024-01-24 14:06:06,209] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:06,213] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:06,213] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d711329-4b80-4b85-8ede-b24b74d7b608/dqc_reference
[2024-01-24 14:06:07,590] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:07,593] [INFO] Task started: Prodigal
[2024-01-24 14:06:07,594] [INFO] Running command: gunzip -c /var/lib/cwl/stgb3ff1cc2-4475-4d39-8e8c-b6155a87a730/GCF_009068765.1_ASM906876v1_genomic.fna.gz | prodigal -d GCF_009068765.1_ASM906876v1_genomic.fna/cds.fna -a GCF_009068765.1_ASM906876v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:13,718] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:13,719] [INFO] Task started: HMMsearch
[2024-01-24 14:06:13,719] [INFO] Running command: hmmsearch --tblout GCF_009068765.1_ASM906876v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d711329-4b80-4b85-8ede-b24b74d7b608/dqc_reference/reference_markers.hmm GCF_009068765.1_ASM906876v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:14,007] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:14,008] [INFO] Found 6/6 markers.
[2024-01-24 14:06:14,038] [INFO] Query marker FASTA was written to GCF_009068765.1_ASM906876v1_genomic.fna/markers.fasta
[2024-01-24 14:06:14,039] [INFO] Task started: Blastn
[2024-01-24 14:06:14,039] [INFO] Running command: blastn -query GCF_009068765.1_ASM906876v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d711329-4b80-4b85-8ede-b24b74d7b608/dqc_reference/reference_markers.fasta -out GCF_009068765.1_ASM906876v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:14,664] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:14,672] [INFO] Selected 11 target genomes.
[2024-01-24 14:06:14,672] [INFO] Target genome list was writen to GCF_009068765.1_ASM906876v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:14,687] [INFO] Task started: fastANI
[2024-01-24 14:06:14,688] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3ff1cc2-4475-4d39-8e8c-b6155a87a730/GCF_009068765.1_ASM906876v1_genomic.fna.gz --refList GCF_009068765.1_ASM906876v1_genomic.fna/target_genomes.txt --output GCF_009068765.1_ASM906876v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:20,449] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:20,449] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d711329-4b80-4b85-8ede-b24b74d7b608/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:20,449] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d711329-4b80-4b85-8ede-b24b74d7b608/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:20,476] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:20,476] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:20,477] [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
Sulfurimonas hydrogeniphila	strain=NW10	GCA_009068765.1	2509341	2509341	type	True	100.0	778	780	95	conclusive
Sulfurimonas sediminis	strain=S2-6	GCA_014905115.1	2590020	2590020	type	True	92.2056	647	780	95	below_threshold
Sulfurimonas autotrophica	strain=DSM 16294	GCA_000147355.1	202747	202747	type	True	81.9883	499	780	95	below_threshold
Sulfurimonas paralvinellae	strain=GO25	GCA_014905135.1	317658	317658	type	True	78.7318	270	780	95	below_threshold
Sulfurimonas indica	strain=NW8N	GCA_009192995.1	2508707	2508707	type	True	78.6393	250	780	95	below_threshold
Sulfurimonas xiamenensis	strain=1-1N	GCA_009258045.1	2590021	2590021	type	True	78.2126	116	780	95	below_threshold
Sulfurimonas gotlandica	strain=GD 1	GCA_000156095.1	1176482	1176482	type	True	78.1949	142	780	95	below_threshold
Sulfurimonas lithotrophica	strain=GYSZ_1	GCA_009258225.1	2590022	2590022	type	True	78.1333	122	780	95	below_threshold
Candidatus Sulfurimonas marisnigri	strain=SoZ1	GCA_015265475.1	2740405	2740405	type	True	78.1081	119	780	95	below_threshold
Candidatus Sulfurimonas baltica	strain=GD2	GCA_015265455.1	2740404	2740404	type	True	77.9754	130	780	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:20,478] [INFO] DFAST Taxonomy check result was written to GCF_009068765.1_ASM906876v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:20,479] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:20,479] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:20,480] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d711329-4b80-4b85-8ede-b24b74d7b608/dqc_reference/checkm_data
[2024-01-24 14:06:20,481] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:20,527] [INFO] Task started: CheckM
[2024-01-24 14:06:20,528] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009068765.1_ASM906876v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009068765.1_ASM906876v1_genomic.fna/checkm_input GCF_009068765.1_ASM906876v1_genomic.fna/checkm_result
[2024-01-24 14:06:45,199] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:45,200] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:45,220] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:45,220] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:45,221] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009068765.1_ASM906876v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:45,221] [INFO] Task started: Blastn
[2024-01-24 14:06:45,221] [INFO] Running command: blastn -query GCF_009068765.1_ASM906876v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d711329-4b80-4b85-8ede-b24b74d7b608/dqc_reference/reference_markers_gtdb.fasta -out GCF_009068765.1_ASM906876v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:46,087] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:46,090] [INFO] Selected 10 target genomes.
[2024-01-24 14:06:46,090] [INFO] Target genome list was writen to GCF_009068765.1_ASM906876v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:46,098] [INFO] Task started: fastANI
[2024-01-24 14:06:46,099] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3ff1cc2-4475-4d39-8e8c-b6155a87a730/GCF_009068765.1_ASM906876v1_genomic.fna.gz --refList GCF_009068765.1_ASM906876v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009068765.1_ASM906876v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:06:51,080] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:51,093] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:06:51,094] [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_009068765.1	s__Sulfurimonas sp009068765	100.0	778	780	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014905115.1	s__Sulfurimonas sediminis	92.2056	647	780	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000147355.1	s__Sulfurimonas autotrophica	82.0032	498	780	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015662405.1	s__Sulfurimonas autotrophica_A	80.1735	256	780	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014905135.1	s__Sulfurimonas paralvinellae	78.7271	270	780	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009192995.1	s__Sulfurimonas indica	78.6393	250	780	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013607665.1	s__Sulfurimonas sp013607665	78.6129	205	780	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015488615.1	s__Sulfurimonas sp015488615	77.7799	114	780	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.68	99.68	0.82	0.82	2	-
GCA_002733945.2	s__Sulfurimonas sp002733945	77.7079	129	780	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016938175.1	s__Sulfurimonas sp016938175	76.974	126	780	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:06:51,095] [INFO] GTDB search result was written to GCF_009068765.1_ASM906876v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:06:51,096] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:06:51,099] [INFO] DFAST_QC result json was written to GCF_009068765.1_ASM906876v1_genomic.fna/dqc_result.json
[2024-01-24 14:06:51,099] [INFO] DFAST_QC completed!
[2024-01-24 14:06:51,100] [INFO] Total running time: 0h0m45s