[2024-01-24 14:20:00,947] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:20:00,949] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:20:00,949] [INFO] DQC Reference Directory: /var/lib/cwl/stgec00aa81-b721-475d-b3e6-cef0ae70d4d9/dqc_reference
[2024-01-24 14:20:02,156] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:20:02,157] [INFO] Task started: Prodigal
[2024-01-24 14:20:02,157] [INFO] Running command: gunzip -c /var/lib/cwl/stg5d6044e7-a50b-4e8e-be0d-981223893000/GCF_004337505.1_ASM433750v1_genomic.fna.gz | prodigal -d GCF_004337505.1_ASM433750v1_genomic.fna/cds.fna -a GCF_004337505.1_ASM433750v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:20:25,198] [INFO] Task succeeded: Prodigal
[2024-01-24 14:20:25,199] [INFO] Task started: HMMsearch
[2024-01-24 14:20:25,199] [INFO] Running command: hmmsearch --tblout GCF_004337505.1_ASM433750v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgec00aa81-b721-475d-b3e6-cef0ae70d4d9/dqc_reference/reference_markers.hmm GCF_004337505.1_ASM433750v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:20:25,453] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:20:25,455] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5d6044e7-a50b-4e8e-be0d-981223893000/GCF_004337505.1_ASM433750v1_genomic.fna.gz]
[2024-01-24 14:20:25,495] [INFO] Query marker FASTA was written to GCF_004337505.1_ASM433750v1_genomic.fna/markers.fasta
[2024-01-24 14:20:25,496] [INFO] Task started: Blastn
[2024-01-24 14:20:25,496] [INFO] Running command: blastn -query GCF_004337505.1_ASM433750v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgec00aa81-b721-475d-b3e6-cef0ae70d4d9/dqc_reference/reference_markers.fasta -out GCF_004337505.1_ASM433750v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:26,086] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:26,091] [INFO] Selected 12 target genomes.
[2024-01-24 14:20:26,091] [INFO] Target genome list was writen to GCF_004337505.1_ASM433750v1_genomic.fna/target_genomes.txt
[2024-01-24 14:20:26,098] [INFO] Task started: fastANI
[2024-01-24 14:20:26,098] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d6044e7-a50b-4e8e-be0d-981223893000/GCF_004337505.1_ASM433750v1_genomic.fna.gz --refList GCF_004337505.1_ASM433750v1_genomic.fna/target_genomes.txt --output GCF_004337505.1_ASM433750v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:36,431] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:36,431] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgec00aa81-b721-475d-b3e6-cef0ae70d4d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:36,432] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgec00aa81-b721-475d-b3e6-cef0ae70d4d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:36,442] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:20:36,442] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:20:36,442] [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
Flaviaesturariibacter flavus	strain=17J68-12	GCA_004337505.1	2502780	2502780	type	True	100.0	1292	1296	95	conclusive
Flaviaesturariibacter aridisoli	strain=17J68-15	GCA_004343705.1	2545761	2545761	type	True	80.7985	724	1296	95	below_threshold
Cnuella takakiae	strain=RG1-1	GCA_001953305.1	1302690	1302690	type	True	77.2874	204	1296	95	below_threshold
Cnuella takakiae	strain=DSM 26897	GCA_900129015.1	1302690	1302690	type	True	77.2454	203	1296	95	below_threshold
Flavisolibacter nicotianae	strain=X7X	GCA_003628535.1	2364882	2364882	type	True	76.7919	157	1296	95	below_threshold
Niastella koreensis	strain=GR20-10	GCA_000246855.1	354356	354356	type	True	76.2573	54	1296	95	below_threshold
Chitinophaga parva	strain=LY-1	GCA_003071345.1	2169414	2169414	type	True	76.1885	90	1296	95	below_threshold
Puia dinghuensis	strain=CGMCC 1.15448	GCA_014642875.1	1792502	1792502	type	True	76.0227	69	1296	95	below_threshold
Niastella koreensis	strain=DSM 17620	GCA_002077985.1	354356	354356	type	True	75.6956	53	1296	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:36,444] [INFO] DFAST Taxonomy check result was written to GCF_004337505.1_ASM433750v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:36,444] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:36,444] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:36,445] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgec00aa81-b721-475d-b3e6-cef0ae70d4d9/dqc_reference/checkm_data
[2024-01-24 14:20:36,445] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:36,482] [INFO] Task started: CheckM
[2024-01-24 14:20:36,483] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004337505.1_ASM433750v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004337505.1_ASM433750v1_genomic.fna/checkm_input GCF_004337505.1_ASM433750v1_genomic.fna/checkm_result
[2024-01-24 14:21:38,281] [INFO] Task succeeded: CheckM
[2024-01-24 14:21:38,283] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:21:38,301] [INFO] ===== Completeness check finished =====
[2024-01-24 14:21:38,301] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:21:38,302] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004337505.1_ASM433750v1_genomic.fna/markers.fasta)
[2024-01-24 14:21:38,302] [INFO] Task started: Blastn
[2024-01-24 14:21:38,302] [INFO] Running command: blastn -query GCF_004337505.1_ASM433750v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgec00aa81-b721-475d-b3e6-cef0ae70d4d9/dqc_reference/reference_markers_gtdb.fasta -out GCF_004337505.1_ASM433750v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:39,073] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:39,077] [INFO] Selected 12 target genomes.
[2024-01-24 14:21:39,077] [INFO] Target genome list was writen to GCF_004337505.1_ASM433750v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:21:39,086] [INFO] Task started: fastANI
[2024-01-24 14:21:39,086] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d6044e7-a50b-4e8e-be0d-981223893000/GCF_004337505.1_ASM433750v1_genomic.fna.gz --refList GCF_004337505.1_ASM433750v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004337505.1_ASM433750v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:49,989] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:50,003] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:21:50,003] [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_004337505.1	s__Flaviaesturariibacter flavus	100.0	1293	1296	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flaviaesturariibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004343705.1	s__Flaviaesturariibacter aridisoli	80.7777	726	1296	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flaviaesturariibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004173235.1	s__Flaviaesturariibacter sp004173235	79.1882	581	1296	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flaviaesturariibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001953305.1	s__Cnuella takakiae	77.2874	204	1296	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Cnuella	95.0	99.98	99.98	1.00	1.00	2	-
GCF_003628535.1	s__Flavisolibacter nicotianae	76.7919	157	1296	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003332885.2	s__Paracnuella aquatica	76.6313	164	1296	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Paracnuella	95.0	95.63	95.63	0.92	0.92	2	-
GCA_014163555.1	s__Flavisolibacter sp014163555	76.5805	103	1296	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007970805.1	s__Flavisolibacter ginsenosidimutans	76.303	110	1296	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003243445.1	s__46-32 sp003243445	76.1213	58	1296	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__46-32	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014642875.1	s__Puia dinghuensis	76.0227	69	1296	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Puia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016219985.1	s__JJ008 sp016219985	75.7614	75	1296	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:21:50,004] [INFO] GTDB search result was written to GCF_004337505.1_ASM433750v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:50,005] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:50,008] [INFO] DFAST_QC result json was written to GCF_004337505.1_ASM433750v1_genomic.fna/dqc_result.json
[2024-01-24 14:21:50,008] [INFO] DFAST_QC completed!
[2024-01-24 14:21:50,008] [INFO] Total running time: 0h1m49s