[2024-01-24 14:28:18,022] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:18,029] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:18,029] [INFO] DQC Reference Directory: /var/lib/cwl/stgd740fede-1eba-4034-b7f0-1467fb114e0a/dqc_reference
[2024-01-24 14:28:20,488] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:20,491] [INFO] Task started: Prodigal
[2024-01-24 14:28:20,491] [INFO] Running command: gunzip -c /var/lib/cwl/stg54465b19-386c-4d19-acd4-1ea9a5493cbd/GCF_002078015.1_ASM207801v1_genomic.fna.gz | prodigal -d GCF_002078015.1_ASM207801v1_genomic.fna/cds.fna -a GCF_002078015.1_ASM207801v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:29:04,021] [INFO] Task succeeded: Prodigal
[2024-01-24 14:29:04,022] [INFO] Task started: HMMsearch
[2024-01-24 14:29:04,022] [INFO] Running command: hmmsearch --tblout GCF_002078015.1_ASM207801v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd740fede-1eba-4034-b7f0-1467fb114e0a/dqc_reference/reference_markers.hmm GCF_002078015.1_ASM207801v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:29:04,401] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:29:04,403] [INFO] Found 6/6 markers.
[2024-01-24 14:29:04,469] [INFO] Query marker FASTA was written to GCF_002078015.1_ASM207801v1_genomic.fna/markers.fasta
[2024-01-24 14:29:04,470] [INFO] Task started: Blastn
[2024-01-24 14:29:04,470] [INFO] Running command: blastn -query GCF_002078015.1_ASM207801v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd740fede-1eba-4034-b7f0-1467fb114e0a/dqc_reference/reference_markers.fasta -out GCF_002078015.1_ASM207801v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:29:05,071] [INFO] Task succeeded: Blastn
[2024-01-24 14:29:05,075] [INFO] Selected 13 target genomes.
[2024-01-24 14:29:05,075] [INFO] Target genome list was writen to GCF_002078015.1_ASM207801v1_genomic.fna/target_genomes.txt
[2024-01-24 14:29:05,086] [INFO] Task started: fastANI
[2024-01-24 14:29:05,086] [INFO] Running command: fastANI --query /var/lib/cwl/stg54465b19-386c-4d19-acd4-1ea9a5493cbd/GCF_002078015.1_ASM207801v1_genomic.fna.gz --refList GCF_002078015.1_ASM207801v1_genomic.fna/target_genomes.txt --output GCF_002078015.1_ASM207801v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:29:24,601] [INFO] Task succeeded: fastANI
[2024-01-24 14:29:24,602] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd740fede-1eba-4034-b7f0-1467fb114e0a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:29:24,602] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd740fede-1eba-4034-b7f0-1467fb114e0a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:29:24,615] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:29:24,615] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:29:24,616] [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
Niastella populi	strain=CCTCC AB 208238	GCA_002078015.1	550983	550983	type	True	100.0	2761	2768	95	conclusive
Niastella vici	strain=DJ57	GCA_002077945.1	1703345	1703345	type	True	81.33	1516	2768	95	below_threshold
Niastella caeni	strain=HX-16-21	GCA_004834005.1	2569763	2569763	type	True	81.1234	1416	2768	95	below_threshold
Niastella yeongjuensis	strain=DSM 17621	GCA_002077935.1	354355	354355	type	True	80.4854	1290	2768	95	below_threshold
Niastella yeongjuensis	strain=DSM 17621	GCA_900110245.1	354355	354355	type	True	80.4727	1290	2768	95	below_threshold
Niastella koreensis	strain=GR20-10	GCA_000246855.1	354356	354356	type	True	80.3175	1384	2768	95	below_threshold
Niastella koreensis	strain=DSM 17620	GCA_002077985.1	354356	354356	type	True	80.2818	1383	2768	95	below_threshold
Niastella soli	strain=MAH-29	GCA_017742245.1	2821487	2821487	type	True	80.1986	1313	2768	95	below_threshold
Pinibacter aurantiacus	strain=MAH-26	GCA_019130065.1	2851599	2851599	type	True	76.3179	109	2768	95	below_threshold
Filimonas effusa	strain=TTM-71	GCA_004118675.1	2508721	2508721	type	True	75.9372	102	2768	95	below_threshold
Panacibacter microcysteis	strain=DH6	GCA_015831355.1	2793269	2793269	type	True	75.6021	76	2768	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:29:24,617] [INFO] DFAST Taxonomy check result was written to GCF_002078015.1_ASM207801v1_genomic.fna/tc_result.tsv
[2024-01-24 14:29:24,618] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:29:24,618] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:29:24,618] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd740fede-1eba-4034-b7f0-1467fb114e0a/dqc_reference/checkm_data
[2024-01-24 14:29:24,619] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:29:24,700] [INFO] Task started: CheckM
[2024-01-24 14:29:24,700] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002078015.1_ASM207801v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002078015.1_ASM207801v1_genomic.fna/checkm_input GCF_002078015.1_ASM207801v1_genomic.fna/checkm_result
[2024-01-24 14:31:19,170] [INFO] Task succeeded: CheckM
[2024-01-24 14:31:19,172] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:31:19,194] [INFO] ===== Completeness check finished =====
[2024-01-24 14:31:19,195] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:31:19,195] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002078015.1_ASM207801v1_genomic.fna/markers.fasta)
[2024-01-24 14:31:19,196] [INFO] Task started: Blastn
[2024-01-24 14:31:19,196] [INFO] Running command: blastn -query GCF_002078015.1_ASM207801v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd740fede-1eba-4034-b7f0-1467fb114e0a/dqc_reference/reference_markers_gtdb.fasta -out GCF_002078015.1_ASM207801v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:20,106] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:20,109] [INFO] Selected 9 target genomes.
[2024-01-24 14:31:20,109] [INFO] Target genome list was writen to GCF_002078015.1_ASM207801v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:31:20,116] [INFO] Task started: fastANI
[2024-01-24 14:31:20,116] [INFO] Running command: fastANI --query /var/lib/cwl/stg54465b19-386c-4d19-acd4-1ea9a5493cbd/GCF_002078015.1_ASM207801v1_genomic.fna.gz --refList GCF_002078015.1_ASM207801v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002078015.1_ASM207801v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:31:39,646] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:39,656] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:31:39,656] [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_002078015.1	s__Niastella populi	100.0	2761	2768	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004341975.1	s__Niastella sp004341975	82.8518	1792	2768	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002077945.1	s__Niastella vici	81.3386	1514	2768	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004834005.1	s__Niastella caeni	81.1167	1418	2768	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017356035.1	s__Niastella sp017356035	80.7398	1363	2768	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110245.1	s__Niastella yeongjuensis	80.4727	1290	2768	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000246855.1	s__Niastella koreensis	80.3116	1385	2768	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017742245.1	s__Niastella sp017742245	80.2092	1310	2768	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017306865.1	s__JAFKHH01 sp017306865	75.8847	89	2768	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JAFKHH01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:31:39,660] [INFO] GTDB search result was written to GCF_002078015.1_ASM207801v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:31:39,661] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:31:39,664] [INFO] DFAST_QC result json was written to GCF_002078015.1_ASM207801v1_genomic.fna/dqc_result.json
[2024-01-24 14:31:39,665] [INFO] DFAST_QC completed!
[2024-01-24 14:31:39,665] [INFO] Total running time: 0h3m22s