[2024-01-24 11:51:11,553] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:11,555] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:11,555] [INFO] DQC Reference Directory: /var/lib/cwl/stgd956e3d8-b224-42fc-b8ce-22f172b5bc15/dqc_reference
[2024-01-24 11:51:12,820] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:12,821] [INFO] Task started: Prodigal
[2024-01-24 11:51:12,821] [INFO] Running command: gunzip -c /var/lib/cwl/stg4a8fd044-13f3-4433-b38a-5195ed9b4616/GCF_019797745.1_ASM1979774v1_genomic.fna.gz | prodigal -d GCF_019797745.1_ASM1979774v1_genomic.fna/cds.fna -a GCF_019797745.1_ASM1979774v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:29,041] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:29,042] [INFO] Task started: HMMsearch
[2024-01-24 11:51:29,042] [INFO] Running command: hmmsearch --tblout GCF_019797745.1_ASM1979774v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd956e3d8-b224-42fc-b8ce-22f172b5bc15/dqc_reference/reference_markers.hmm GCF_019797745.1_ASM1979774v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:29,355] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:29,356] [INFO] Found 6/6 markers.
[2024-01-24 11:51:29,405] [INFO] Query marker FASTA was written to GCF_019797745.1_ASM1979774v1_genomic.fna/markers.fasta
[2024-01-24 11:51:29,406] [INFO] Task started: Blastn
[2024-01-24 11:51:29,406] [INFO] Running command: blastn -query GCF_019797745.1_ASM1979774v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd956e3d8-b224-42fc-b8ce-22f172b5bc15/dqc_reference/reference_markers.fasta -out GCF_019797745.1_ASM1979774v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:29,987] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:29,992] [INFO] Selected 20 target genomes.
[2024-01-24 11:51:29,992] [INFO] Target genome list was writen to GCF_019797745.1_ASM1979774v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:29,999] [INFO] Task started: fastANI
[2024-01-24 11:51:30,000] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a8fd044-13f3-4433-b38a-5195ed9b4616/GCF_019797745.1_ASM1979774v1_genomic.fna.gz --refList GCF_019797745.1_ASM1979774v1_genomic.fna/target_genomes.txt --output GCF_019797745.1_ASM1979774v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:48,904] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:48,905] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd956e3d8-b224-42fc-b8ce-22f172b5bc15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:48,905] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd956e3d8-b224-42fc-b8ce-22f172b5bc15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:48,912] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:51:48,912] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:48,912] [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
Edaphocola aurantiacus	strain=H2	GCA_019797745.1	2601682	2601682	type	True	100.0	1227	1227	95	conclusive
Edaphocola flava	strain=HME-24	GCA_004118155.1	2499629	2499629	type	True	94.856	1080	1227	95	below_threshold
Taibaiella chishuiensis	strain=CGMCC 1.12700	GCA_003014535.1	1434707	1434707	type	True	76.7521	107	1227	95	below_threshold
Taibaiella koreensis	strain=THG-DT86	GCA_003545715.1	1268548	1268548	type	True	76.4066	72	1227	95	below_threshold
Taibaiella lutea	strain=KVB11	GCA_008629695.1	2608001	2608001	type	True	76.3559	83	1227	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:48,914] [INFO] DFAST Taxonomy check result was written to GCF_019797745.1_ASM1979774v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:48,915] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:48,915] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:48,916] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd956e3d8-b224-42fc-b8ce-22f172b5bc15/dqc_reference/checkm_data
[2024-01-24 11:51:48,917] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:48,955] [INFO] Task started: CheckM
[2024-01-24 11:51:48,955] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019797745.1_ASM1979774v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019797745.1_ASM1979774v1_genomic.fna/checkm_input GCF_019797745.1_ASM1979774v1_genomic.fna/checkm_result
[2024-01-24 11:52:36,482] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:36,483] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:36,504] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:36,504] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:36,504] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019797745.1_ASM1979774v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:36,505] [INFO] Task started: Blastn
[2024-01-24 11:52:36,505] [INFO] Running command: blastn -query GCF_019797745.1_ASM1979774v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd956e3d8-b224-42fc-b8ce-22f172b5bc15/dqc_reference/reference_markers_gtdb.fasta -out GCF_019797745.1_ASM1979774v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:37,317] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:37,321] [INFO] Selected 17 target genomes.
[2024-01-24 11:52:37,321] [INFO] Target genome list was writen to GCF_019797745.1_ASM1979774v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:37,341] [INFO] Task started: fastANI
[2024-01-24 11:52:37,341] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a8fd044-13f3-4433-b38a-5195ed9b4616/GCF_019797745.1_ASM1979774v1_genomic.fna.gz --refList GCF_019797745.1_ASM1979774v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019797745.1_ASM1979774v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:50,539] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:50,546] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:52:50,546] [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_004118155.1	s__Edaphocola flava	94.856	1080	1227	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Edaphocola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003852495.1	s__Edaphocola sp003852495	78.4016	395	1227	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Edaphocola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001897525.1	s__Edaphocola sp001897525	77.5408	224	1227	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Edaphocola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016786705.1	s__Edaphocola sp016786705	77.5372	217	1227	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Edaphocola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003014535.1	s__Edaphocola chishuiensis	76.7299	109	1227	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Edaphocola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001897155.1	s__Edaphocola sp001897155	76.7182	50	1227	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Edaphocola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003545715.1	s__Edaphocola koreensis	76.3814	73	1227	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Edaphocola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:50,548] [INFO] GTDB search result was written to GCF_019797745.1_ASM1979774v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:50,549] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:50,552] [INFO] DFAST_QC result json was written to GCF_019797745.1_ASM1979774v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:50,552] [INFO] DFAST_QC completed!
[2024-01-24 11:52:50,552] [INFO] Total running time: 0h1m39s