[2024-01-24 13:26:11,442] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:26:11,443] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:26:11,444] [INFO] DQC Reference Directory: /var/lib/cwl/stgadeb56c5-7d56-4ad6-acc7-d1f3137c8ea5/dqc_reference
[2024-01-24 13:26:12,802] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:26:12,803] [INFO] Task started: Prodigal
[2024-01-24 13:26:12,803] [INFO] Running command: gunzip -c /var/lib/cwl/stg615af76d-148e-47bb-8136-dff3dcebe32c/GCF_004118155.1_ASM411815v1_genomic.fna.gz | prodigal -d GCF_004118155.1_ASM411815v1_genomic.fna/cds.fna -a GCF_004118155.1_ASM411815v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:26:28,674] [INFO] Task succeeded: Prodigal
[2024-01-24 13:26:28,674] [INFO] Task started: HMMsearch
[2024-01-24 13:26:28,675] [INFO] Running command: hmmsearch --tblout GCF_004118155.1_ASM411815v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgadeb56c5-7d56-4ad6-acc7-d1f3137c8ea5/dqc_reference/reference_markers.hmm GCF_004118155.1_ASM411815v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:26:28,954] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:26:28,956] [INFO] Found 6/6 markers.
[2024-01-24 13:26:28,985] [INFO] Query marker FASTA was written to GCF_004118155.1_ASM411815v1_genomic.fna/markers.fasta
[2024-01-24 13:26:28,985] [INFO] Task started: Blastn
[2024-01-24 13:26:28,985] [INFO] Running command: blastn -query GCF_004118155.1_ASM411815v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgadeb56c5-7d56-4ad6-acc7-d1f3137c8ea5/dqc_reference/reference_markers.fasta -out GCF_004118155.1_ASM411815v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:29,592] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:29,596] [INFO] Selected 18 target genomes.
[2024-01-24 13:26:29,597] [INFO] Target genome list was writen to GCF_004118155.1_ASM411815v1_genomic.fna/target_genomes.txt
[2024-01-24 13:26:29,609] [INFO] Task started: fastANI
[2024-01-24 13:26:29,609] [INFO] Running command: fastANI --query /var/lib/cwl/stg615af76d-148e-47bb-8136-dff3dcebe32c/GCF_004118155.1_ASM411815v1_genomic.fna.gz --refList GCF_004118155.1_ASM411815v1_genomic.fna/target_genomes.txt --output GCF_004118155.1_ASM411815v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:46,469] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:46,469] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgadeb56c5-7d56-4ad6-acc7-d1f3137c8ea5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:46,470] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgadeb56c5-7d56-4ad6-acc7-d1f3137c8ea5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:46,483] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:26:46,483] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:26:46,483] [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 flava	strain=HME-24	GCA_004118155.1	2499629	2499629	type	True	100.0	1174	1175	95	conclusive
Edaphocola aurantiacus	strain=H2	GCA_019797745.1	2601682	2601682	type	True	94.8089	1080	1175	95	below_threshold
Taibaiella chishuiensis	strain=CGMCC 1.12700	GCA_003014535.1	1434707	1434707	type	True	77.033	94	1175	95	below_threshold
Taibaiella lutea	strain=KVB11	GCA_008629695.1	2608001	2608001	type	True	76.7485	76	1175	95	below_threshold
Taibaiella koreensis	strain=THG-DT86	GCA_003545715.1	1268548	1268548	type	True	76.3224	77	1175	95	below_threshold
Chitinophaga arvensicola	strain=DSM 3695	GCA_900110835.1	29529	29529	type	True	76.1136	52	1175	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:26:46,485] [INFO] DFAST Taxonomy check result was written to GCF_004118155.1_ASM411815v1_genomic.fna/tc_result.tsv
[2024-01-24 13:26:46,486] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:46,486] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:46,487] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgadeb56c5-7d56-4ad6-acc7-d1f3137c8ea5/dqc_reference/checkm_data
[2024-01-24 13:26:46,488] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:46,524] [INFO] Task started: CheckM
[2024-01-24 13:26:46,524] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004118155.1_ASM411815v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004118155.1_ASM411815v1_genomic.fna/checkm_input GCF_004118155.1_ASM411815v1_genomic.fna/checkm_result
[2024-01-24 13:27:34,330] [INFO] Task succeeded: CheckM
[2024-01-24 13:27:34,331] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:27:34,353] [INFO] ===== Completeness check finished =====
[2024-01-24 13:27:34,354] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:27:34,354] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004118155.1_ASM411815v1_genomic.fna/markers.fasta)
[2024-01-24 13:27:34,355] [INFO] Task started: Blastn
[2024-01-24 13:27:34,355] [INFO] Running command: blastn -query GCF_004118155.1_ASM411815v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgadeb56c5-7d56-4ad6-acc7-d1f3137c8ea5/dqc_reference/reference_markers_gtdb.fasta -out GCF_004118155.1_ASM411815v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:35,168] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:35,173] [INFO] Selected 19 target genomes.
[2024-01-24 13:27:35,173] [INFO] Target genome list was writen to GCF_004118155.1_ASM411815v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:27:35,192] [INFO] Task started: fastANI
[2024-01-24 13:27:35,192] [INFO] Running command: fastANI --query /var/lib/cwl/stg615af76d-148e-47bb-8136-dff3dcebe32c/GCF_004118155.1_ASM411815v1_genomic.fna.gz --refList GCF_004118155.1_ASM411815v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004118155.1_ASM411815v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:27:51,239] [INFO] Task succeeded: fastANI
[2024-01-24 13:27:51,253] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:27:51,253] [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	100.0	1174	1175	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Edaphocola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003852495.1	s__Edaphocola sp003852495	78.5654	373	1175	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	77.6391	222	1175	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	77.4757	215	1175	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	77.0379	93	1175	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Edaphocola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003236175.1	s__Flavipsychrobacter soli	76.5886	70	1175	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavipsychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001897155.1	s__Edaphocola sp001897155	76.4787	57	1175	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	76.3458	76	1175	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 13:27:51,255] [INFO] GTDB search result was written to GCF_004118155.1_ASM411815v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:27:51,256] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:27:51,259] [INFO] DFAST_QC result json was written to GCF_004118155.1_ASM411815v1_genomic.fna/dqc_result.json
[2024-01-24 13:27:51,259] [INFO] DFAST_QC completed!
[2024-01-24 13:27:51,259] [INFO] Total running time: 0h1m40s