[2024-01-25 19:53:20,385] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:53:20,386] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:53:20,386] [INFO] DQC Reference Directory: /var/lib/cwl/stg52b7ee6f-5039-48ac-b414-3ac976a97c83/dqc_reference
[2024-01-25 19:53:21,509] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:53:21,510] [INFO] Task started: Prodigal
[2024-01-25 19:53:21,510] [INFO] Running command: gunzip -c /var/lib/cwl/stg59c875d7-121e-4d02-a4c8-11b203919aa0/GCF_028550415.1_ASM2855041v1_genomic.fna.gz | prodigal -d GCF_028550415.1_ASM2855041v1_genomic.fna/cds.fna -a GCF_028550415.1_ASM2855041v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:53:30,869] [INFO] Task succeeded: Prodigal
[2024-01-25 19:53:30,870] [INFO] Task started: HMMsearch
[2024-01-25 19:53:30,870] [INFO] Running command: hmmsearch --tblout GCF_028550415.1_ASM2855041v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg52b7ee6f-5039-48ac-b414-3ac976a97c83/dqc_reference/reference_markers.hmm GCF_028550415.1_ASM2855041v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:53:31,071] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:53:31,072] [INFO] Found 6/6 markers.
[2024-01-25 19:53:31,102] [INFO] Query marker FASTA was written to GCF_028550415.1_ASM2855041v1_genomic.fna/markers.fasta
[2024-01-25 19:53:31,102] [INFO] Task started: Blastn
[2024-01-25 19:53:31,102] [INFO] Running command: blastn -query GCF_028550415.1_ASM2855041v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg52b7ee6f-5039-48ac-b414-3ac976a97c83/dqc_reference/reference_markers.fasta -out GCF_028550415.1_ASM2855041v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:53:31,961] [INFO] Task succeeded: Blastn
[2024-01-25 19:53:31,964] [INFO] Selected 12 target genomes.
[2024-01-25 19:53:31,964] [INFO] Target genome list was writen to GCF_028550415.1_ASM2855041v1_genomic.fna/target_genomes.txt
[2024-01-25 19:53:31,983] [INFO] Task started: fastANI
[2024-01-25 19:53:31,983] [INFO] Running command: fastANI --query /var/lib/cwl/stg59c875d7-121e-4d02-a4c8-11b203919aa0/GCF_028550415.1_ASM2855041v1_genomic.fna.gz --refList GCF_028550415.1_ASM2855041v1_genomic.fna/target_genomes.txt --output GCF_028550415.1_ASM2855041v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:53:41,139] [INFO] Task succeeded: fastANI
[2024-01-25 19:53:41,139] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg52b7ee6f-5039-48ac-b414-3ac976a97c83/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:53:41,140] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg52b7ee6f-5039-48ac-b414-3ac976a97c83/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:53:41,148] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:53:41,148] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:53:41,148] [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
Asticcacaulis excentricus	strain=CB 48	GCA_000175215.2	78587	78587	type	True	80.8067	749	1316	95	below_threshold
Asticcacaulis taihuensis	strain=CGMCC 1.3431	GCA_900100255.1	260084	260084	type	True	78.8479	463	1316	95	below_threshold
Asticcacaulis benevestitus	strain=DSM 16100	GCA_000376105.1	347481	347481	type	True	78.7808	461	1316	95	below_threshold
Asticcacaulis benevestitus	strain=DSM 16100	GCA_000495775.1	347481	347481	type	True	78.6333	469	1316	95	below_threshold
Asticcacaulis biprosthecium	strain=C19	GCA_000204015.1	76891	76891	type	True	78.5158	448	1316	95	below_threshold
Asticcacaulis tiandongensis	strain=3.1105	GCA_006475605.1	2565365	2565365	type	True	78.3482	426	1316	95	below_threshold
Asticcacaulis endophyticus	strain=KCTC 32296	GCA_014652575.1	1395890	1395890	type	True	78.3051	449	1316	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	77.8659	212	1316	95	below_threshold
Devosia oryziradicis	strain=G19	GCA_016698645.1	2801335	2801335	type	True	76.2807	84	1316	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	76.2307	128	1316	95	below_threshold
Microvirga splendida	strain=BT325	GCA_016427565.1	2795727	2795727	type	True	76.0608	85	1316	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	75.7025	95	1316	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:53:41,149] [INFO] DFAST Taxonomy check result was written to GCF_028550415.1_ASM2855041v1_genomic.fna/tc_result.tsv
[2024-01-25 19:53:41,150] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:53:41,150] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:53:41,150] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg52b7ee6f-5039-48ac-b414-3ac976a97c83/dqc_reference/checkm_data
[2024-01-25 19:53:41,151] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:53:41,192] [INFO] Task started: CheckM
[2024-01-25 19:53:41,193] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028550415.1_ASM2855041v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028550415.1_ASM2855041v1_genomic.fna/checkm_input GCF_028550415.1_ASM2855041v1_genomic.fna/checkm_result
[2024-01-25 19:54:11,135] [INFO] Task succeeded: CheckM
[2024-01-25 19:54:11,136] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:54:11,152] [INFO] ===== Completeness check finished =====
[2024-01-25 19:54:11,152] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:54:11,153] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028550415.1_ASM2855041v1_genomic.fna/markers.fasta)
[2024-01-25 19:54:11,153] [INFO] Task started: Blastn
[2024-01-25 19:54:11,153] [INFO] Running command: blastn -query GCF_028550415.1_ASM2855041v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg52b7ee6f-5039-48ac-b414-3ac976a97c83/dqc_reference/reference_markers_gtdb.fasta -out GCF_028550415.1_ASM2855041v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:54:12,836] [INFO] Task succeeded: Blastn
[2024-01-25 19:54:12,839] [INFO] Selected 12 target genomes.
[2024-01-25 19:54:12,839] [INFO] Target genome list was writen to GCF_028550415.1_ASM2855041v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:54:12,852] [INFO] Task started: fastANI
[2024-01-25 19:54:12,852] [INFO] Running command: fastANI --query /var/lib/cwl/stg59c875d7-121e-4d02-a4c8-11b203919aa0/GCF_028550415.1_ASM2855041v1_genomic.fna.gz --refList GCF_028550415.1_ASM2855041v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028550415.1_ASM2855041v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:54:23,662] [INFO] Task succeeded: fastANI
[2024-01-25 19:54:23,671] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:54:23,671] [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_000495855.1	s__Asticcacaulis sp000495855	88.7952	1050	1316	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Asticcacaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003053985.1	s__Asticcacaulis sp003053985	82.8005	898	1316	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Asticcacaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003966695.1	s__Asticcacaulis excentricus_A	81.8518	762	1316	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Asticcacaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000175215.2	s__Asticcacaulis excentricus	80.808	750	1316	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Asticcacaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017875235.1	s__Asticcacaulis solisilvae	79.2681	523	1316	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Asticcacaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873225.1	s__Asticcacaulis sp014873225	78.9828	489	1316	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Asticcacaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000376105.1	s__Asticcacaulis benevestitus	78.7572	464	1316	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Asticcacaulis	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000495795.1	s__Asticcacaulis sp000495795	78.7368	495	1316	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Asticcacaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006475605.1	s__Asticcacaulis tiandongensis	78.369	423	1316	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Asticcacaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002342035.1	s__Asticcacaulis sp002342035	78.3626	424	1316	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Asticcacaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652575.1	s__Asticcacaulis endophyticus	78.3229	447	1316	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Asticcacaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000495815.1	s__Asticcacaulis sp000495815	78.2911	382	1316	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Asticcacaulis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:54:23,673] [INFO] GTDB search result was written to GCF_028550415.1_ASM2855041v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:54:23,673] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:54:23,676] [INFO] DFAST_QC result json was written to GCF_028550415.1_ASM2855041v1_genomic.fna/dqc_result.json
[2024-01-25 19:54:23,676] [INFO] DFAST_QC completed!
[2024-01-25 19:54:23,676] [INFO] Total running time: 0h1m3s