[2024-01-24 11:26:03,068] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:03,070] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:03,070] [INFO] DQC Reference Directory: /var/lib/cwl/stg2fc4d5c6-b087-4767-8f17-e561ca5316b6/dqc_reference
[2024-01-24 11:26:04,207] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:04,208] [INFO] Task started: Prodigal
[2024-01-24 11:26:04,208] [INFO] Running command: gunzip -c /var/lib/cwl/stgdb6f4d8f-2815-47aa-a8aa-28252ca7f2a2/GCF_016106015.1_ASM1610601v1_genomic.fna.gz | prodigal -d GCF_016106015.1_ASM1610601v1_genomic.fna/cds.fna -a GCF_016106015.1_ASM1610601v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:16,308] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:16,309] [INFO] Task started: HMMsearch
[2024-01-24 11:26:16,309] [INFO] Running command: hmmsearch --tblout GCF_016106015.1_ASM1610601v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2fc4d5c6-b087-4767-8f17-e561ca5316b6/dqc_reference/reference_markers.hmm GCF_016106015.1_ASM1610601v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:16,559] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:16,560] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgdb6f4d8f-2815-47aa-a8aa-28252ca7f2a2/GCF_016106015.1_ASM1610601v1_genomic.fna.gz]
[2024-01-24 11:26:16,603] [INFO] Query marker FASTA was written to GCF_016106015.1_ASM1610601v1_genomic.fna/markers.fasta
[2024-01-24 11:26:16,603] [INFO] Task started: Blastn
[2024-01-24 11:26:16,603] [INFO] Running command: blastn -query GCF_016106015.1_ASM1610601v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2fc4d5c6-b087-4767-8f17-e561ca5316b6/dqc_reference/reference_markers.fasta -out GCF_016106015.1_ASM1610601v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:17,398] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:17,401] [INFO] Selected 13 target genomes.
[2024-01-24 11:26:17,401] [INFO] Target genome list was writen to GCF_016106015.1_ASM1610601v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:17,411] [INFO] Task started: fastANI
[2024-01-24 11:26:17,411] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb6f4d8f-2815-47aa-a8aa-28252ca7f2a2/GCF_016106015.1_ASM1610601v1_genomic.fna.gz --refList GCF_016106015.1_ASM1610601v1_genomic.fna/target_genomes.txt --output GCF_016106015.1_ASM1610601v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:32,425] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:32,426] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2fc4d5c6-b087-4767-8f17-e561ca5316b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:32,426] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2fc4d5c6-b087-4767-8f17-e561ca5316b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:32,437] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:26:32,437] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:26:32,437] [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 rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	100.0	1289	1302	95	conclusive
Roseomonas alkaliterrae	strain=DSM 25895	GCA_014199195.1	1452450	1452450	type	True	84.3867	906	1302	95	below_threshold
Roseomonas oryzicola	strain=KCTC 22478	GCA_012163135.1	535904	535904	type	True	84.3694	980	1302	95	below_threshold
Roseomonas lacus	strain=CGMCC 1.3617	GCA_014644535.1	287609	287609	type	True	82.1808	939	1302	95	below_threshold
Roseomonas hellenica	strain=LMG 31523	GCA_018129085.1	2687306	2687306	type	True	79.6861	694	1302	95	below_threshold
Falsiroseomonas tokyonensis	strain=K-20	GCA_019024325.1	430521	430521	type	True	79.1941	713	1302	95	below_threshold
Siccirubricoccus deserti	strain=SYSU D8009	GCA_014283215.1	2013562	2013562	type	True	79.0129	616	1302	95	below_threshold
Siccirubricoccus deserti	strain=CGMCC 1.15936	GCA_014644195.1	2013562	2013562	type	True	78.9797	623	1302	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	78.7514	540	1302	95	below_threshold
Rhodovarius lipocyclicus	strain=CCUG 44693	GCA_009900765.1	268410	268410	type	True	78.6876	519	1302	95	below_threshold
Roseomonas deserti	strain=M3	GCA_001982615.1	1817963	1817963	type	True	78.56	556	1302	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	78.4379	464	1302	95	below_threshold
Roseomonas marmotae	strain=1318	GCA_017654485.1	2768161	2768161	type	True	78.3692	447	1302	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:32,447] [INFO] DFAST Taxonomy check result was written to GCF_016106015.1_ASM1610601v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:32,448] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:32,448] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:32,448] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2fc4d5c6-b087-4767-8f17-e561ca5316b6/dqc_reference/checkm_data
[2024-01-24 11:26:32,449] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:32,495] [INFO] Task started: CheckM
[2024-01-24 11:26:32,495] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016106015.1_ASM1610601v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016106015.1_ASM1610601v1_genomic.fna/checkm_input GCF_016106015.1_ASM1610601v1_genomic.fna/checkm_result
[2024-01-24 11:27:13,480] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:13,481] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:13,499] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:13,500] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:13,500] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016106015.1_ASM1610601v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:13,500] [INFO] Task started: Blastn
[2024-01-24 11:27:13,500] [INFO] Running command: blastn -query GCF_016106015.1_ASM1610601v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2fc4d5c6-b087-4767-8f17-e561ca5316b6/dqc_reference/reference_markers_gtdb.fasta -out GCF_016106015.1_ASM1610601v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:14,921] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:14,924] [INFO] Selected 9 target genomes.
[2024-01-24 11:27:14,924] [INFO] Target genome list was writen to GCF_016106015.1_ASM1610601v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:14,934] [INFO] Task started: fastANI
[2024-01-24 11:27:14,934] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb6f4d8f-2815-47aa-a8aa-28252ca7f2a2/GCF_016106015.1_ASM1610601v1_genomic.fna.gz --refList GCF_016106015.1_ASM1610601v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016106015.1_ASM1610601v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:25,809] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:25,820] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:25,821] [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_016106015.1	s__Roseomonas_B sp016106015	100.0	1289	1302	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017813355.1	s__Roseomonas_B sp017813355	91.3973	1135	1302	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016106005.1	s__Roseomonas_B sp016106005	84.667	912	1302	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005222755.1	s__Roseomonas_B sp005222755	84.4176	1006	1302	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199195.1	s__Roseomonas_B alkaliterrae	84.3605	908	1302	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	99.89	99.89	0.97	0.97	2	-
GCF_012163135.1	s__Roseomonas_B oryzicola	84.3455	983	1302	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	99.99	99.99	1.00	1.00	2	-
GCF_018129005.1	s__Roseomonas_B eburnea	84.0383	945	1302	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018129065.1	s__Roseomonas_B soli	83.938	911	1302	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464375.1	s__Roseomonas_B sp001464375	83.5953	881	1302	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 11:27:25,822] [INFO] GTDB search result was written to GCF_016106015.1_ASM1610601v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:25,822] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:25,825] [INFO] DFAST_QC result json was written to GCF_016106015.1_ASM1610601v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:25,825] [INFO] DFAST_QC completed!
[2024-01-24 11:27:25,825] [INFO] Total running time: 0h1m23s