[2024-01-24 11:12:27,725] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:27,727] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:27,727] [INFO] DQC Reference Directory: /var/lib/cwl/stg3f7f9016-ce3c-4cfb-a12d-3a7651c2335f/dqc_reference
[2024-01-24 11:12:29,014] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:29,015] [INFO] Task started: Prodigal
[2024-01-24 11:12:29,015] [INFO] Running command: gunzip -c /var/lib/cwl/stg4795a03b-0992-4fb9-8654-4b7e8aed6a57/GCF_016653355.1_ASM1665335v1_genomic.fna.gz | prodigal -d GCF_016653355.1_ASM1665335v1_genomic.fna/cds.fna -a GCF_016653355.1_ASM1665335v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:45,419] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:45,419] [INFO] Task started: HMMsearch
[2024-01-24 11:12:45,420] [INFO] Running command: hmmsearch --tblout GCF_016653355.1_ASM1665335v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3f7f9016-ce3c-4cfb-a12d-3a7651c2335f/dqc_reference/reference_markers.hmm GCF_016653355.1_ASM1665335v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:45,833] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:45,834] [INFO] Found 6/6 markers.
[2024-01-24 11:12:45,888] [INFO] Query marker FASTA was written to GCF_016653355.1_ASM1665335v1_genomic.fna/markers.fasta
[2024-01-24 11:12:45,888] [INFO] Task started: Blastn
[2024-01-24 11:12:45,888] [INFO] Running command: blastn -query GCF_016653355.1_ASM1665335v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f7f9016-ce3c-4cfb-a12d-3a7651c2335f/dqc_reference/reference_markers.fasta -out GCF_016653355.1_ASM1665335v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:47,117] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:47,121] [INFO] Selected 13 target genomes.
[2024-01-24 11:12:47,121] [INFO] Target genome list was writen to GCF_016653355.1_ASM1665335v1_genomic.fna/target_genomes.txt
[2024-01-24 11:12:47,127] [INFO] Task started: fastANI
[2024-01-24 11:12:47,127] [INFO] Running command: fastANI --query /var/lib/cwl/stg4795a03b-0992-4fb9-8654-4b7e8aed6a57/GCF_016653355.1_ASM1665335v1_genomic.fna.gz --refList GCF_016653355.1_ASM1665335v1_genomic.fna/target_genomes.txt --output GCF_016653355.1_ASM1665335v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:08,859] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:08,859] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3f7f9016-ce3c-4cfb-a12d-3a7651c2335f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:08,860] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3f7f9016-ce3c-4cfb-a12d-3a7651c2335f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:08,870] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:13:08,871] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:08,871] [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
Rhodoplanes elegans	strain=DSM 11907	GCA_016653355.1	29408	29408	type	True	100.0	1990	2020	95	conclusive
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	99.6291	1577	2020	95	conclusive
Rhodoplanes roseus	strain=DSM 5909	GCA_003258865.1	29409	29409	type	True	86.7725	1343	2020	95	below_threshold
Rhodoplanes piscinae	strain=DSM 19946	GCA_003258855.1	444923	444923	type	True	84.8842	1078	2020	95	below_threshold
Rhodopseudomonas pentothenatexigens	strain=JA575	GCA_900218015.1	999699	999699	type	True	78.4233	663	2020	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	78.1387	628	2020	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	78.1349	597	2020	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	78.0924	580	2020	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	78.0811	625	2020	95	below_threshold
Bradyrhizobium quebecense	strain=66S1MB, /ecotype=symbiovar septentrionalis	GCA_013373795.3	2748629	2748629	type	True	78.0186	632	2020	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_023278185.1	29448	29448	type	True	77.9716	662	2020	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	77.406	656	2020	95	below_threshold
Bosea thiooxidans	strain=DSM 9653	GCA_900168195.1	53254	53254	type	True	77.4036	525	2020	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:08,872] [INFO] DFAST Taxonomy check result was written to GCF_016653355.1_ASM1665335v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:08,873] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:08,873] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:08,873] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3f7f9016-ce3c-4cfb-a12d-3a7651c2335f/dqc_reference/checkm_data
[2024-01-24 11:13:08,874] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:08,941] [INFO] Task started: CheckM
[2024-01-24 11:13:08,941] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016653355.1_ASM1665335v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016653355.1_ASM1665335v1_genomic.fna/checkm_input GCF_016653355.1_ASM1665335v1_genomic.fna/checkm_result
[2024-01-24 11:14:02,084] [INFO] Task succeeded: CheckM
[2024-01-24 11:14:02,086] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:14:02,125] [INFO] ===== Completeness check finished =====
[2024-01-24 11:14:02,125] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:14:02,126] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016653355.1_ASM1665335v1_genomic.fna/markers.fasta)
[2024-01-24 11:14:02,126] [INFO] Task started: Blastn
[2024-01-24 11:14:02,126] [INFO] Running command: blastn -query GCF_016653355.1_ASM1665335v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f7f9016-ce3c-4cfb-a12d-3a7651c2335f/dqc_reference/reference_markers_gtdb.fasta -out GCF_016653355.1_ASM1665335v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:14:04,447] [INFO] Task succeeded: Blastn
[2024-01-24 11:14:04,452] [INFO] Selected 5 target genomes.
[2024-01-24 11:14:04,452] [INFO] Target genome list was writen to GCF_016653355.1_ASM1665335v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:14:04,457] [INFO] Task started: fastANI
[2024-01-24 11:14:04,457] [INFO] Running command: fastANI --query /var/lib/cwl/stg4795a03b-0992-4fb9-8654-4b7e8aed6a57/GCF_016653355.1_ASM1665335v1_genomic.fna.gz --refList GCF_016653355.1_ASM1665335v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016653355.1_ASM1665335v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:14:15,459] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:15,465] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:14:15,465] [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_016653355.1	s__Rhodoplanes elegans	100.0	1993	2020	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	99.89	99.89	0.96	0.96	2	conclusive
GCF_003258865.1	s__Rhodoplanes roseus	86.7176	1350	2020	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013377085.1	s__Rhodoplanes sp013377085	85.8876	1370	2020	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009720755.1	s__Rhodoplanes serenus	85.3228	1272	2020	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	97.72	97.48	0.91	0.88	4	-
GCF_000293785.1	s__Rhodoplanes sp000293785	82.7992	1007	2020	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:14:15,467] [INFO] GTDB search result was written to GCF_016653355.1_ASM1665335v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:14:15,467] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:14:15,470] [INFO] DFAST_QC result json was written to GCF_016653355.1_ASM1665335v1_genomic.fna/dqc_result.json
[2024-01-24 11:14:15,470] [INFO] DFAST_QC completed!
[2024-01-24 11:14:15,470] [INFO] Total running time: 0h1m48s