[2024-01-25 19:51:20,708] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:51:20,710] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:51:20,710] [INFO] DQC Reference Directory: /var/lib/cwl/stgfad0d377-742c-4fde-8b33-54850d2874a7/dqc_reference
[2024-01-25 19:51:21,943] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:51:21,943] [INFO] Task started: Prodigal
[2024-01-25 19:51:21,943] [INFO] Running command: gunzip -c /var/lib/cwl/stg1228dd7b-10e6-4561-b810-e277cd338671/GCF_014636335.1_ASM1463633v1_genomic.fna.gz | prodigal -d GCF_014636335.1_ASM1463633v1_genomic.fna/cds.fna -a GCF_014636335.1_ASM1463633v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:51:32,528] [INFO] Task succeeded: Prodigal
[2024-01-25 19:51:32,529] [INFO] Task started: HMMsearch
[2024-01-25 19:51:32,529] [INFO] Running command: hmmsearch --tblout GCF_014636335.1_ASM1463633v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfad0d377-742c-4fde-8b33-54850d2874a7/dqc_reference/reference_markers.hmm GCF_014636335.1_ASM1463633v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:51:32,745] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:51:32,746] [INFO] Found 6/6 markers.
[2024-01-25 19:51:32,780] [INFO] Query marker FASTA was written to GCF_014636335.1_ASM1463633v1_genomic.fna/markers.fasta
[2024-01-25 19:51:32,781] [INFO] Task started: Blastn
[2024-01-25 19:51:32,781] [INFO] Running command: blastn -query GCF_014636335.1_ASM1463633v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfad0d377-742c-4fde-8b33-54850d2874a7/dqc_reference/reference_markers.fasta -out GCF_014636335.1_ASM1463633v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:51:33,441] [INFO] Task succeeded: Blastn
[2024-01-25 19:51:33,444] [INFO] Selected 12 target genomes.
[2024-01-25 19:51:33,444] [INFO] Target genome list was writen to GCF_014636335.1_ASM1463633v1_genomic.fna/target_genomes.txt
[2024-01-25 19:51:33,458] [INFO] Task started: fastANI
[2024-01-25 19:51:33,458] [INFO] Running command: fastANI --query /var/lib/cwl/stg1228dd7b-10e6-4561-b810-e277cd338671/GCF_014636335.1_ASM1463633v1_genomic.fna.gz --refList GCF_014636335.1_ASM1463633v1_genomic.fna/target_genomes.txt --output GCF_014636335.1_ASM1463633v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:51:43,681] [INFO] Task succeeded: fastANI
[2024-01-25 19:51:43,681] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfad0d377-742c-4fde-8b33-54850d2874a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:51:43,681] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfad0d377-742c-4fde-8b33-54850d2874a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:51:43,692] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:51:43,692] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:51:43,692] [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
Hyunsoonleella pacifica	strain=CGMCC 1.11009	GCA_014636335.1	1080224	1080224	type	True	100.0	1368	1368	95	conclusive
Hyunsoonleella pacifica	strain=SW033	GCA_004310335.1	1080224	1080224	type	True	99.9954	1363	1368	95	conclusive
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	87.2651	1043	1368	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	80.7137	754	1368	95	below_threshold
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	78.6585	503	1368	95	below_threshold
Hyunsoonleella aquatilis	strain=SJ7	GCA_014270105.1	2762758	2762758	type	True	78.5229	383	1368	95	below_threshold
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	78.2108	387	1368	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	78.0408	407	1368	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	77.6664	335	1368	95	below_threshold
Aestuariivivens insulae	strain=AH-MY3	GCA_022662195.1	1621988	1621988	type	True	77.4057	249	1368	95	below_threshold
Aurantibacter aestuarii	strain=KCTC 32269	GCA_003008425.1	1266046	1266046	type	True	77.1462	174	1368	95	below_threshold
Winogradskyella thalassocola	strain=DSM 15363	GCA_900099995.1	262004	262004	type	True	77.0701	194	1368	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:51:43,694] [INFO] DFAST Taxonomy check result was written to GCF_014636335.1_ASM1463633v1_genomic.fna/tc_result.tsv
[2024-01-25 19:51:43,695] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:51:43,695] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:51:43,695] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfad0d377-742c-4fde-8b33-54850d2874a7/dqc_reference/checkm_data
[2024-01-25 19:51:43,696] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:51:43,743] [INFO] Task started: CheckM
[2024-01-25 19:51:43,743] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014636335.1_ASM1463633v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014636335.1_ASM1463633v1_genomic.fna/checkm_input GCF_014636335.1_ASM1463633v1_genomic.fna/checkm_result
[2024-01-25 19:52:16,461] [INFO] Task succeeded: CheckM
[2024-01-25 19:52:16,462] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:52:16,491] [INFO] ===== Completeness check finished =====
[2024-01-25 19:52:16,491] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:52:16,492] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014636335.1_ASM1463633v1_genomic.fna/markers.fasta)
[2024-01-25 19:52:16,493] [INFO] Task started: Blastn
[2024-01-25 19:52:16,493] [INFO] Running command: blastn -query GCF_014636335.1_ASM1463633v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfad0d377-742c-4fde-8b33-54850d2874a7/dqc_reference/reference_markers_gtdb.fasta -out GCF_014636335.1_ASM1463633v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:52:17,478] [INFO] Task succeeded: Blastn
[2024-01-25 19:52:17,481] [INFO] Selected 8 target genomes.
[2024-01-25 19:52:17,481] [INFO] Target genome list was writen to GCF_014636335.1_ASM1463633v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:52:17,497] [INFO] Task started: fastANI
[2024-01-25 19:52:17,497] [INFO] Running command: fastANI --query /var/lib/cwl/stg1228dd7b-10e6-4561-b810-e277cd338671/GCF_014636335.1_ASM1463633v1_genomic.fna.gz --refList GCF_014636335.1_ASM1463633v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014636335.1_ASM1463633v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:52:24,774] [INFO] Task succeeded: fastANI
[2024-01-25 19:52:24,780] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:52:24,781] [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_004310335.1	s__Jejuia pacifica	99.9954	1363	1368	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_016827605.1	s__Jejuia sp016827605	87.2651	1043	1368	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004310325.1	s__Jejuia sp004310325	80.7025	756	1368	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111025.1	s__Jejuia jejuensis	79.5391	584	1368	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002973595.1	s__Jejuia pallidilutea	79.4291	595	1368	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	98.03	97.97	0.83	0.83	4	-
GCA_002428965.1	s__Jejuia sp002428965	79.1108	555	1368	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143755.1	s__Algibacter_B sp003143755	78.667	502	1368	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004791695.1	s__Flavivirga rizhaonensis	77.7259	354	1368	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:52:24,782] [INFO] GTDB search result was written to GCF_014636335.1_ASM1463633v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:52:24,783] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:52:24,785] [INFO] DFAST_QC result json was written to GCF_014636335.1_ASM1463633v1_genomic.fna/dqc_result.json
[2024-01-25 19:52:24,785] [INFO] DFAST_QC completed!
[2024-01-25 19:52:24,786] [INFO] Total running time: 0h1m4s