[2024-01-24 12:52:26,683] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:52:26,691] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:52:26,692] [INFO] DQC Reference Directory: /var/lib/cwl/stg34da202e-8bcf-4a2b-80c9-73d51a06bd19/dqc_reference
[2024-01-24 12:52:27,956] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:52:27,957] [INFO] Task started: Prodigal
[2024-01-24 12:52:27,957] [INFO] Running command: gunzip -c /var/lib/cwl/stgc4786fb9-594e-4a27-b965-e297b4b425e6/GCF_021044425.1_ASM2104442v1_genomic.fna.gz | prodigal -d GCF_021044425.1_ASM2104442v1_genomic.fna/cds.fna -a GCF_021044425.1_ASM2104442v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:53:00,754] [INFO] Task succeeded: Prodigal
[2024-01-24 12:53:00,754] [INFO] Task started: HMMsearch
[2024-01-24 12:53:00,755] [INFO] Running command: hmmsearch --tblout GCF_021044425.1_ASM2104442v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg34da202e-8bcf-4a2b-80c9-73d51a06bd19/dqc_reference/reference_markers.hmm GCF_021044425.1_ASM2104442v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:53:01,069] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:53:01,071] [INFO] Found 6/6 markers.
[2024-01-24 12:53:01,124] [INFO] Query marker FASTA was written to GCF_021044425.1_ASM2104442v1_genomic.fna/markers.fasta
[2024-01-24 12:53:01,124] [INFO] Task started: Blastn
[2024-01-24 12:53:01,125] [INFO] Running command: blastn -query GCF_021044425.1_ASM2104442v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34da202e-8bcf-4a2b-80c9-73d51a06bd19/dqc_reference/reference_markers.fasta -out GCF_021044425.1_ASM2104442v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:53:01,787] [INFO] Task succeeded: Blastn
[2024-01-24 12:53:01,801] [INFO] Selected 12 target genomes.
[2024-01-24 12:53:01,802] [INFO] Target genome list was writen to GCF_021044425.1_ASM2104442v1_genomic.fna/target_genomes.txt
[2024-01-24 12:53:01,826] [INFO] Task started: fastANI
[2024-01-24 12:53:01,827] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4786fb9-594e-4a27-b965-e297b4b425e6/GCF_021044425.1_ASM2104442v1_genomic.fna.gz --refList GCF_021044425.1_ASM2104442v1_genomic.fna/target_genomes.txt --output GCF_021044425.1_ASM2104442v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:53:14,713] [INFO] Task succeeded: fastANI
[2024-01-24 12:53:14,714] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg34da202e-8bcf-4a2b-80c9-73d51a06bd19/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:53:14,715] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg34da202e-8bcf-4a2b-80c9-73d51a06bd19/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:53:14,729] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:53:14,729] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:53:14,729] [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
Niabella pedocola	strain=JCM 31011	GCA_021044425.1	1752077	1752077	type	True	100.0	2154	2154	95	conclusive
Niabella drilacis	strain=DSM 25811	GCA_900101395.1	1285928	1285928	type	True	81.1472	1065	2154	95	below_threshold
Niabella aurantiaca	strain=DSM 17617	GCA_000374125.1	379900	379900	type	True	80.2653	1037	2154	95	below_threshold
Niabella beijingensis	strain=3A5MI-3	GCA_020034665.1	2872700	2872700	type	True	80.028	983	2154	95	below_threshold
Niabella ginsenosidivorans	strain=BS26	GCA_001654455.1	1176587	1176587	type	True	77.7582	493	2154	95	below_threshold
Niabella soli	strain=JS13-8; DSM 19437	GCA_000243115.3	446683	446683	type	True	77.6831	474	2154	95	below_threshold
Flavisolibacter nicotianae	strain=X7X	GCA_003628535.1	2364882	2364882	type	True	76.2644	72	2154	95	below_threshold
Niabella ginsengisoli	strain=GR10-1	GCA_022513635.1	522298	522298	type	True	76.2546	98	2154	95	below_threshold
Flavisolibacter ginsengisoli	strain=DSM 18119	GCA_900129295.1	462367	462367	type	True	76.2288	54	2154	95	below_threshold
Flavihumibacter rivuli	strain=IMCC34838	GCA_018595685.2	2838156	2838156	type	True	76.1845	68	2154	95	below_threshold
Niastella caeni	strain=HX-16-21	GCA_004834005.1	2569763	2569763	type	True	75.944	84	2154	95	below_threshold
Chitinophaga chungangae	strain=MAH-28	GCA_017742215.1	2821488	2821488	type	True	75.48	55	2154	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:53:14,732] [INFO] DFAST Taxonomy check result was written to GCF_021044425.1_ASM2104442v1_genomic.fna/tc_result.tsv
[2024-01-24 12:53:14,733] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:53:14,733] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:53:14,733] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg34da202e-8bcf-4a2b-80c9-73d51a06bd19/dqc_reference/checkm_data
[2024-01-24 12:53:14,735] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:53:14,801] [INFO] Task started: CheckM
[2024-01-24 12:53:14,801] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021044425.1_ASM2104442v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021044425.1_ASM2104442v1_genomic.fna/checkm_input GCF_021044425.1_ASM2104442v1_genomic.fna/checkm_result
[2024-01-24 12:54:39,410] [INFO] Task succeeded: CheckM
[2024-01-24 12:54:39,411] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:54:39,445] [INFO] ===== Completeness check finished =====
[2024-01-24 12:54:39,445] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:54:39,446] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021044425.1_ASM2104442v1_genomic.fna/markers.fasta)
[2024-01-24 12:54:39,446] [INFO] Task started: Blastn
[2024-01-24 12:54:39,447] [INFO] Running command: blastn -query GCF_021044425.1_ASM2104442v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34da202e-8bcf-4a2b-80c9-73d51a06bd19/dqc_reference/reference_markers_gtdb.fasta -out GCF_021044425.1_ASM2104442v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:40,317] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:40,325] [INFO] Selected 11 target genomes.
[2024-01-24 12:54:40,325] [INFO] Target genome list was writen to GCF_021044425.1_ASM2104442v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:54:40,364] [INFO] Task started: fastANI
[2024-01-24 12:54:40,364] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4786fb9-594e-4a27-b965-e297b4b425e6/GCF_021044425.1_ASM2104442v1_genomic.fna.gz --refList GCF_021044425.1_ASM2104442v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021044425.1_ASM2104442v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:54:52,481] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:52,491] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:54:52,491] [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
GCA_017744715.1	s__Niabella sp017744715	88.9443	1735	2154	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niabella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101395.1	s__Niabella drilacis	81.141	1066	2154	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niabella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374125.1	s__Niabella aurantiaca	80.2654	1037	2154	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niabella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001654455.1	s__Niabella ginsenosidivorans	77.7631	493	2154	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niabella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000243115.2	s__Niabella soli	77.6833	474	2154	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niabella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744795.1	s__Niabella sp017744795	77.476	426	2154	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niabella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002399735.1	s__Terrimonas sp002399735	76.136	86	2154	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Terrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018595685.1	s__Flavihumibacter sp018595685	76.0863	72	2154	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavihumibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014879565.1	s__JJ008 sp014879565	76.0185	95	2154	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004834005.1	s__Niastella caeni	75.9551	85	2154	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016708765.1	s__JJ008 sp016708765	75.8845	53	2154	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	99.32	99.14	0.92	0.90	6	-
--------------------------------------------------------------------------------
[2024-01-24 12:54:52,493] [INFO] GTDB search result was written to GCF_021044425.1_ASM2104442v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:54:52,494] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:54:52,497] [INFO] DFAST_QC result json was written to GCF_021044425.1_ASM2104442v1_genomic.fna/dqc_result.json
[2024-01-24 12:54:52,497] [INFO] DFAST_QC completed!
[2024-01-24 12:54:52,497] [INFO] Total running time: 0h2m26s