[2024-01-24 13:22:15,919] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:15,921] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:15,921] [INFO] DQC Reference Directory: /var/lib/cwl/stg9c06aef1-ac92-476c-b550-7f8cb3b743e1/dqc_reference
[2024-01-24 13:22:17,239] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:17,240] [INFO] Task started: Prodigal
[2024-01-24 13:22:17,240] [INFO] Running command: gunzip -c /var/lib/cwl/stg93bf7017-b6f1-4f85-87b1-a981bb7ba810/GCF_004310335.1_ASM431033v1_genomic.fna.gz | prodigal -d GCF_004310335.1_ASM431033v1_genomic.fna/cds.fna -a GCF_004310335.1_ASM431033v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:30,588] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:30,589] [INFO] Task started: HMMsearch
[2024-01-24 13:22:30,589] [INFO] Running command: hmmsearch --tblout GCF_004310335.1_ASM431033v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9c06aef1-ac92-476c-b550-7f8cb3b743e1/dqc_reference/reference_markers.hmm GCF_004310335.1_ASM431033v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:30,946] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:30,948] [INFO] Found 6/6 markers.
[2024-01-24 13:22:30,985] [INFO] Query marker FASTA was written to GCF_004310335.1_ASM431033v1_genomic.fna/markers.fasta
[2024-01-24 13:22:30,985] [INFO] Task started: Blastn
[2024-01-24 13:22:30,985] [INFO] Running command: blastn -query GCF_004310335.1_ASM431033v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c06aef1-ac92-476c-b550-7f8cb3b743e1/dqc_reference/reference_markers.fasta -out GCF_004310335.1_ASM431033v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:31,707] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:31,710] [INFO] Selected 12 target genomes.
[2024-01-24 13:22:31,710] [INFO] Target genome list was writen to GCF_004310335.1_ASM431033v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:31,716] [INFO] Task started: fastANI
[2024-01-24 13:22:31,716] [INFO] Running command: fastANI --query /var/lib/cwl/stg93bf7017-b6f1-4f85-87b1-a981bb7ba810/GCF_004310335.1_ASM431033v1_genomic.fna.gz --refList GCF_004310335.1_ASM431033v1_genomic.fna/target_genomes.txt --output GCF_004310335.1_ASM431033v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:41,397] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:41,398] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9c06aef1-ac92-476c-b550-7f8cb3b743e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:41,398] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9c06aef1-ac92-476c-b550-7f8cb3b743e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:41,408] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:22:41,409] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:41,409] [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=SW033	GCA_004310335.1	1080224	1080224	type	True	100.0	1367	1367	95	conclusive
Hyunsoonleella pacifica	strain=CGMCC 1.11009	GCA_014636335.1	1080224	1080224	type	True	99.9971	1363	1367	95	conclusive
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	87.3395	1031	1367	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	80.7588	743	1367	95	below_threshold
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	78.6134	492	1367	95	below_threshold
Hyunsoonleella aquatilis	strain=SJ7	GCA_014270105.1	2762758	2762758	type	True	78.3767	385	1367	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	78.0439	418	1367	95	below_threshold
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	77.8946	410	1367	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	77.7486	317	1367	95	below_threshold
Aestuariivivens insulae	strain=AH-MY3	GCA_022662195.1	1621988	1621988	type	True	77.4361	243	1367	95	below_threshold
Aurantibacter aestuarii	strain=KCTC 32269	GCA_003008425.1	1266046	1266046	type	True	77.3283	165	1367	95	below_threshold
Winogradskyella thalassocola	strain=DSM 15363	GCA_900099995.1	262004	262004	type	True	77.0512	198	1367	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:41,411] [INFO] DFAST Taxonomy check result was written to GCF_004310335.1_ASM431033v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:41,411] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:41,411] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:41,411] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9c06aef1-ac92-476c-b550-7f8cb3b743e1/dqc_reference/checkm_data
[2024-01-24 13:22:41,412] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:41,455] [INFO] Task started: CheckM
[2024-01-24 13:22:41,455] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004310335.1_ASM431033v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004310335.1_ASM431033v1_genomic.fna/checkm_input GCF_004310335.1_ASM431033v1_genomic.fna/checkm_result
[2024-01-24 13:23:23,411] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:23,412] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:23,434] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:23,434] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:23,435] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004310335.1_ASM431033v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:23,435] [INFO] Task started: Blastn
[2024-01-24 13:23:23,435] [INFO] Running command: blastn -query GCF_004310335.1_ASM431033v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c06aef1-ac92-476c-b550-7f8cb3b743e1/dqc_reference/reference_markers_gtdb.fasta -out GCF_004310335.1_ASM431033v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:24,422] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:24,434] [INFO] Selected 8 target genomes.
[2024-01-24 13:23:24,434] [INFO] Target genome list was writen to GCF_004310335.1_ASM431033v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:24,453] [INFO] Task started: fastANI
[2024-01-24 13:23:24,453] [INFO] Running command: fastANI --query /var/lib/cwl/stg93bf7017-b6f1-4f85-87b1-a981bb7ba810/GCF_004310335.1_ASM431033v1_genomic.fna.gz --refList GCF_004310335.1_ASM431033v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004310335.1_ASM431033v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:31,481] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:31,494] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:31,494] [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	100.0	1367	1367	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	87.3395	1031	1367	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	80.7621	743	1367	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	79.4931	584	1367	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	79.3682	588	1367	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	79.1496	543	1367	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	78.6385	489	1367	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	77.7099	346	1367	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:31,496] [INFO] GTDB search result was written to GCF_004310335.1_ASM431033v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:31,497] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:31,502] [INFO] DFAST_QC result json was written to GCF_004310335.1_ASM431033v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:31,503] [INFO] DFAST_QC completed!
[2024-01-24 13:23:31,503] [INFO] Total running time: 0h1m16s