[2024-01-24 13:31:57,745] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:57,747] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:57,747] [INFO] DQC Reference Directory: /var/lib/cwl/stg5bb97d6f-25dc-464c-91a3-7e538d97a9d5/dqc_reference
[2024-01-24 13:31:59,039] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:59,040] [INFO] Task started: Prodigal
[2024-01-24 13:31:59,040] [INFO] Running command: gunzip -c /var/lib/cwl/stg4b81d494-26d9-44c9-9f45-d2448fd474f8/GCF_004761865.1_ASM476186v1_genomic.fna.gz | prodigal -d GCF_004761865.1_ASM476186v1_genomic.fna/cds.fna -a GCF_004761865.1_ASM476186v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:10,650] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:10,651] [INFO] Task started: HMMsearch
[2024-01-24 13:32:10,651] [INFO] Running command: hmmsearch --tblout GCF_004761865.1_ASM476186v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5bb97d6f-25dc-464c-91a3-7e538d97a9d5/dqc_reference/reference_markers.hmm GCF_004761865.1_ASM476186v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:10,883] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:10,886] [INFO] Found 6/6 markers.
[2024-01-24 13:32:10,923] [INFO] Query marker FASTA was written to GCF_004761865.1_ASM476186v1_genomic.fna/markers.fasta
[2024-01-24 13:32:10,924] [INFO] Task started: Blastn
[2024-01-24 13:32:10,924] [INFO] Running command: blastn -query GCF_004761865.1_ASM476186v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5bb97d6f-25dc-464c-91a3-7e538d97a9d5/dqc_reference/reference_markers.fasta -out GCF_004761865.1_ASM476186v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:11,791] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:11,794] [INFO] Selected 20 target genomes.
[2024-01-24 13:32:11,795] [INFO] Target genome list was writen to GCF_004761865.1_ASM476186v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:12,063] [INFO] Task started: fastANI
[2024-01-24 13:32:12,063] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b81d494-26d9-44c9-9f45-d2448fd474f8/GCF_004761865.1_ASM476186v1_genomic.fna.gz --refList GCF_004761865.1_ASM476186v1_genomic.fna/target_genomes.txt --output GCF_004761865.1_ASM476186v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:37,390] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:37,391] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5bb97d6f-25dc-464c-91a3-7e538d97a9d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:37,391] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5bb97d6f-25dc-464c-91a3-7e538d97a9d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:37,407] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:32:37,407] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:32:37,407] [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
Roseomonas alkaliterrae	strain=DSM 25895	GCA_014199195.1	1452450	1452450	type	True	81.2319	848	1421	95	below_threshold
Siccirubricoccus deserti	strain=CGMCC 1.15936	GCA_014644195.1	2013562	2013562	type	True	81.2022	902	1421	95	below_threshold
Siccirubricoccus deserti	strain=SYSU D8009	GCA_014283215.1	2013562	2013562	type	True	81.1749	913	1421	95	below_threshold
Belnapia mucosa	strain=T6	GCA_016775475.1	2804532	2804532	type	True	80.8732	855	1421	95	below_threshold
Belnapia rosea	strain=CGMCC 1.10758	GCA_900104205.1	938405	938405	type	True	80.6784	853	1421	95	below_threshold
Belnapia rosea	strain=CPCC 100156	GCA_900101615.1	938405	938405	type	True	80.6053	882	1421	95	below_threshold
Belnapia arida	strain=T18	GCA_016773205.1	2804533	2804533	type	True	80.4839	864	1421	95	below_threshold
Belnapia moabensis	strain=DSM 16746	GCA_000745835.1	365533	365533	type	True	80.3541	849	1421	95	below_threshold
Roseomonas rhizosphaerae	strain=YW11	GCA_002631185.1	1335062	1335062	type	True	80.1552	746	1421	95	below_threshold
Roseomonas cervicalis	strain=ATCC 49957	GCA_000164635.1	204525	204525	type	True	79.8967	695	1421	95	below_threshold
Roseomonas oryzicola	strain=KCTC 22478	GCA_012163135.1	535904	535904	type	True	79.8816	785	1421	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	79.6034	652	1421	95	below_threshold
Roseomonas coralli	strain=M0104	GCA_009829925.1	2545983	2545983	type	True	79.3916	725	1421	95	below_threshold
Falsiroseomonas selenitidurans	strain=BU-1	GCA_012103215.1	2716335	2716335	type	True	79.3336	806	1421	95	below_threshold
Roseomonas hellenica	strain=LMG 31523	GCA_018129085.1	2687306	2687306	type	True	79.2771	780	1421	95	below_threshold
Roseomonas deserti	strain=M3	GCA_001982615.1	1817963	1817963	type	True	78.7697	691	1421	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	78.6693	650	1421	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	78.6245	627	1421	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	78.1037	614	1421	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	77.7487	572	1421	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:37,409] [INFO] DFAST Taxonomy check result was written to GCF_004761865.1_ASM476186v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:37,410] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:37,410] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:37,410] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5bb97d6f-25dc-464c-91a3-7e538d97a9d5/dqc_reference/checkm_data
[2024-01-24 13:32:37,412] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:37,459] [INFO] Task started: CheckM
[2024-01-24 13:32:37,460] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004761865.1_ASM476186v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004761865.1_ASM476186v1_genomic.fna/checkm_input GCF_004761865.1_ASM476186v1_genomic.fna/checkm_result
[2024-01-24 13:33:33,639] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:33,640] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:33,659] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:33,659] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:33,659] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004761865.1_ASM476186v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:33,660] [INFO] Task started: Blastn
[2024-01-24 13:33:33,660] [INFO] Running command: blastn -query GCF_004761865.1_ASM476186v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5bb97d6f-25dc-464c-91a3-7e538d97a9d5/dqc_reference/reference_markers_gtdb.fasta -out GCF_004761865.1_ASM476186v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:35,288] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:35,292] [INFO] Selected 12 target genomes.
[2024-01-24 13:33:35,292] [INFO] Target genome list was writen to GCF_004761865.1_ASM476186v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:35,321] [INFO] Task started: fastANI
[2024-01-24 13:33:35,322] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b81d494-26d9-44c9-9f45-d2448fd474f8/GCF_004761865.1_ASM476186v1_genomic.fna.gz --refList GCF_004761865.1_ASM476186v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004761865.1_ASM476186v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:53,004] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:53,014] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:53,014] [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_004761865.1	s__Crenalkalicoccus roseus	100.0	1418	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Crenalkalicoccus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014644455.1	s__Caldovatus sediminis	82.4156	925	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Caldovatus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003258945.1	s__Paracraurococcus frigidaeris	82.024	940	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Paracraurococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004343615.1	s__Paracraurococcus sp004343615	81.8194	964	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Paracraurococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013112485.1	s__Paracraurococcus sp013112485	81.6849	930	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Paracraurococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019084075.1	s__G192 sp019084075	81.6481	961	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__G192	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199195.1	s__Roseomonas_B alkaliterrae	81.2556	844	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	99.89	99.89	0.97	0.97	2	-
GCA_902805545.1	s__Belnapia sp902805545	81.1914	806	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Belnapia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014283215.1	s__Siccirubricoccus deserti	81.1875	910	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Siccirubricoccus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_004353985.1	s__Paracraurococcus ruber	81.1008	905	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Paracraurococcus	95.0	99.87	99.87	0.95	0.95	2	-
GCF_008360935.1	s__Siccirubricoccus phaeus	80.9543	962	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Siccirubricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005222755.1	s__Roseomonas_B sp005222755	79.9182	800	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:53,016] [INFO] GTDB search result was written to GCF_004761865.1_ASM476186v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:53,017] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:53,021] [INFO] DFAST_QC result json was written to GCF_004761865.1_ASM476186v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:53,021] [INFO] DFAST_QC completed!
[2024-01-24 13:33:53,021] [INFO] Total running time: 0h1m55s