[2024-01-24 11:27:19,267] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:27:19,269] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:27:19,269] [INFO] DQC Reference Directory: /var/lib/cwl/stgec9cd14a-61ad-439c-bea9-ade6132e3384/dqc_reference
[2024-01-24 11:27:20,477] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:27:20,478] [INFO] Task started: Prodigal
[2024-01-24 11:27:20,478] [INFO] Running command: gunzip -c /var/lib/cwl/stg71989514-bad5-4e7c-9e32-c8d9c9fe321c/GCF_003002825.1_ASM300282v1_genomic.fna.gz | prodigal -d GCF_003002825.1_ASM300282v1_genomic.fna/cds.fna -a GCF_003002825.1_ASM300282v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:27:50,642] [INFO] Task succeeded: Prodigal
[2024-01-24 11:27:50,643] [INFO] Task started: HMMsearch
[2024-01-24 11:27:50,643] [INFO] Running command: hmmsearch --tblout GCF_003002825.1_ASM300282v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgec9cd14a-61ad-439c-bea9-ade6132e3384/dqc_reference/reference_markers.hmm GCF_003002825.1_ASM300282v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:27:50,941] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:27:50,943] [INFO] Found 6/6 markers.
[2024-01-24 11:27:50,992] [INFO] Query marker FASTA was written to GCF_003002825.1_ASM300282v1_genomic.fna/markers.fasta
[2024-01-24 11:27:50,992] [INFO] Task started: Blastn
[2024-01-24 11:27:50,993] [INFO] Running command: blastn -query GCF_003002825.1_ASM300282v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgec9cd14a-61ad-439c-bea9-ade6132e3384/dqc_reference/reference_markers.fasta -out GCF_003002825.1_ASM300282v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:51,587] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:51,590] [INFO] Selected 17 target genomes.
[2024-01-24 11:27:51,591] [INFO] Target genome list was writen to GCF_003002825.1_ASM300282v1_genomic.fna/target_genomes.txt
[2024-01-24 11:27:51,597] [INFO] Task started: fastANI
[2024-01-24 11:27:51,597] [INFO] Running command: fastANI --query /var/lib/cwl/stg71989514-bad5-4e7c-9e32-c8d9c9fe321c/GCF_003002825.1_ASM300282v1_genomic.fna.gz --refList GCF_003002825.1_ASM300282v1_genomic.fna/target_genomes.txt --output GCF_003002825.1_ASM300282v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:28:09,802] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:09,803] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgec9cd14a-61ad-439c-bea9-ade6132e3384/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:28:09,803] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgec9cd14a-61ad-439c-bea9-ade6132e3384/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:28:09,820] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:28:09,820] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:28:09,821] [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
Spirosoma oryzae	strain=DSM 28354	GCA_003002825.1	1469603	1469603	type	True	100.0	2149	2152	95	conclusive
Spirosoma agri	strain=KCTC 52727	GCA_010747415.1	1987381	1987381	type	True	77.6094	393	2152	95	below_threshold
Spirosoma lacussanchae	strain=CPCC 100624	GCA_005870035.1	1884249	1884249	type	True	77.3056	418	2152	95	below_threshold
Spirosoma rigui	strain=KCTC 12531	GCA_002067135.1	564064	564064	type	True	77.2729	411	2152	95	below_threshold
Spirosoma sordidisoli	strain=TY50	GCA_004138325.1	2502893	2502893	type	True	77.2423	455	2152	95	below_threshold
Spirosoma taeanense	strain=TS118	GCA_013127955.1	2735870	2735870	type	True	77.1883	445	2152	95	below_threshold
Spirosoma montaniterrae	strain=DY10	GCA_001988955.1	1178516	1178516	type	True	77.1276	388	2152	95	below_threshold
Spirosoma fluviale	strain=DSM 29961	GCA_900230225.1	1597977	1597977	type	True	77.092	402	2152	95	below_threshold
Spirosoma aerolatum	strain=KACC 17939	GCA_002056795.1	1211326	1211326	type	True	77.0241	290	2152	95	below_threshold
Spirosoma radiotolerans	strain=DG5A	GCA_000974425.1	1379870	1379870	type	True	77.0153	302	2152	95	below_threshold
Spirosoma panaciterrae	strain=DSM 21099	GCA_000374025.1	496058	496058	type	True	76.8774	322	2152	95	below_threshold
Spirosoma utsteinense	strain=LMG 31447	GCA_014282275.1	2585773	2585773	type	True	76.7531	384	2152	95	below_threshold
Hymenobacter telluris	strain=BT186	GCA_017313265.1	2816474	2816474	type	True	75.7825	53	2152	95	below_threshold
Hymenobacter metallicola	strain=9PBR-1	GCA_004745645.1	2563114	2563114	type	True	75.6723	52	2152	95	below_threshold
Hymenobacter piscis	strain=NST-14	GCA_018760735.1	2839984	2839984	type	True	75.5547	61	2152	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:28:09,822] [INFO] DFAST Taxonomy check result was written to GCF_003002825.1_ASM300282v1_genomic.fna/tc_result.tsv
[2024-01-24 11:28:09,823] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:28:09,823] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:28:09,823] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgec9cd14a-61ad-439c-bea9-ade6132e3384/dqc_reference/checkm_data
[2024-01-24 11:28:09,824] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:28:09,883] [INFO] Task started: CheckM
[2024-01-24 11:28:09,884] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003002825.1_ASM300282v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003002825.1_ASM300282v1_genomic.fna/checkm_input GCF_003002825.1_ASM300282v1_genomic.fna/checkm_result
[2024-01-24 11:29:32,441] [INFO] Task succeeded: CheckM
[2024-01-24 11:29:32,442] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:29:32,461] [INFO] ===== Completeness check finished =====
[2024-01-24 11:29:32,461] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:29:32,462] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003002825.1_ASM300282v1_genomic.fna/markers.fasta)
[2024-01-24 11:29:32,462] [INFO] Task started: Blastn
[2024-01-24 11:29:32,462] [INFO] Running command: blastn -query GCF_003002825.1_ASM300282v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgec9cd14a-61ad-439c-bea9-ade6132e3384/dqc_reference/reference_markers_gtdb.fasta -out GCF_003002825.1_ASM300282v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:29:33,239] [INFO] Task succeeded: Blastn
[2024-01-24 11:29:33,243] [INFO] Selected 14 target genomes.
[2024-01-24 11:29:33,244] [INFO] Target genome list was writen to GCF_003002825.1_ASM300282v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:29:33,254] [INFO] Task started: fastANI
[2024-01-24 11:29:33,254] [INFO] Running command: fastANI --query /var/lib/cwl/stg71989514-bad5-4e7c-9e32-c8d9c9fe321c/GCF_003002825.1_ASM300282v1_genomic.fna.gz --refList GCF_003002825.1_ASM300282v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003002825.1_ASM300282v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:29:50,065] [INFO] Task succeeded: fastANI
[2024-01-24 11:29:50,080] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:29:50,080] [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_003002825.1	s__Spirosoma oryzae	100.0	2149	2152	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_012849055.1	s__Spirosoma sp012849055	81.9917	1353	2152	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013375035.1	s__Spirosoma sp013375035	78.0679	477	2152	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010747415.1	s__Spirosoma agri	77.6094	393	2152	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005870035.1	s__Spirosoma lacussanchae	77.3056	418	2152	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002067135.1	s__Spirosoma rigui	77.2729	411	2152	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004138325.1	s__Spirosoma sordidisoli	77.2421	455	2152	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	98.69	98.69	0.94	0.94	2	-
GCF_013127955.1	s__Spirosoma taeanense	77.1944	444	2152	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001988955.1	s__Spirosoma montaniterrae	77.1288	387	2152	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900230225.1	s__Spirosoma fluviale	77.0993	400	2152	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003583365.1	s__Fibrisoma montanum	77.0685	409	2152	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Fibrisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374025.1	s__Spirosoma panaciterrae	76.8698	323	2152	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003259005.1	s__Spirosoma sp003259005	76.822	280	2152	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014282275.1	s__Spirosoma utsteinense	76.7527	384	2152	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	99.94	99.94	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:29:50,082] [INFO] GTDB search result was written to GCF_003002825.1_ASM300282v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:29:50,082] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:29:50,086] [INFO] DFAST_QC result json was written to GCF_003002825.1_ASM300282v1_genomic.fna/dqc_result.json
[2024-01-24 11:29:50,086] [INFO] DFAST_QC completed!
[2024-01-24 11:29:50,086] [INFO] Total running time: 0h2m31s