[2024-01-24 12:51:05,413] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:51:05,414] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:51:05,414] [INFO] DQC Reference Directory: /var/lib/cwl/stg70cab832-ab7d-4e4a-ab92-677396e2f911/dqc_reference
[2024-01-24 12:51:06,595] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:51:06,596] [INFO] Task started: Prodigal
[2024-01-24 12:51:06,596] [INFO] Running command: gunzip -c /var/lib/cwl/stgfaddc5d1-a40d-4444-9560-259417ab0d75/GCF_012641475.1_ASM1264147v1_genomic.fna.gz | prodigal -d GCF_012641475.1_ASM1264147v1_genomic.fna/cds.fna -a GCF_012641475.1_ASM1264147v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:51:30,697] [INFO] Task succeeded: Prodigal
[2024-01-24 12:51:30,698] [INFO] Task started: HMMsearch
[2024-01-24 12:51:30,698] [INFO] Running command: hmmsearch --tblout GCF_012641475.1_ASM1264147v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg70cab832-ab7d-4e4a-ab92-677396e2f911/dqc_reference/reference_markers.hmm GCF_012641475.1_ASM1264147v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:51:31,038] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:51:31,040] [INFO] Found 6/6 markers.
[2024-01-24 12:51:31,097] [INFO] Query marker FASTA was written to GCF_012641475.1_ASM1264147v1_genomic.fna/markers.fasta
[2024-01-24 12:51:31,097] [INFO] Task started: Blastn
[2024-01-24 12:51:31,097] [INFO] Running command: blastn -query GCF_012641475.1_ASM1264147v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg70cab832-ab7d-4e4a-ab92-677396e2f911/dqc_reference/reference_markers.fasta -out GCF_012641475.1_ASM1264147v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:51:31,674] [INFO] Task succeeded: Blastn
[2024-01-24 12:51:31,677] [INFO] Selected 10 target genomes.
[2024-01-24 12:51:31,677] [INFO] Target genome list was writen to GCF_012641475.1_ASM1264147v1_genomic.fna/target_genomes.txt
[2024-01-24 12:51:31,697] [INFO] Task started: fastANI
[2024-01-24 12:51:31,697] [INFO] Running command: fastANI --query /var/lib/cwl/stgfaddc5d1-a40d-4444-9560-259417ab0d75/GCF_012641475.1_ASM1264147v1_genomic.fna.gz --refList GCF_012641475.1_ASM1264147v1_genomic.fna/target_genomes.txt --output GCF_012641475.1_ASM1264147v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:51:41,450] [INFO] Task succeeded: fastANI
[2024-01-24 12:51:41,451] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg70cab832-ab7d-4e4a-ab92-677396e2f911/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:51:41,452] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg70cab832-ab7d-4e4a-ab92-677396e2f911/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:51:41,460] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:51:41,460] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:51:41,460] [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
Flammeovirga agarivorans	strain=SR4	GCA_012641475.1	2726742	2726742	type	True	100.0	2410	2413	95	conclusive
Flammeovirga yaeyamensis	strain=NBRC:100898	GCA_018736045.1	367791	367791	type	True	79.307	721	2413	95	below_threshold
Flammeovirga yaeyamensis	strain=DSM 25626	GCA_014195575.1	367791	367791	type	True	79.2739	721	2413	95	below_threshold
Flammeovirga yaeyamensis	strain=NBRC 100898	GCA_012844325.1	367791	367791	type	True	79.2495	719	2413	95	below_threshold
Flammeovirga pacifica	strain=WPAGA1	GCA_000807855.2	915059	915059	type	True	79.0179	715	2413	95	below_threshold
Lutibacter citreus	strain=1KV19	GCA_003260195.1	2138210	2138210	type	True	75.0813	66	2413	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:51:41,462] [INFO] DFAST Taxonomy check result was written to GCF_012641475.1_ASM1264147v1_genomic.fna/tc_result.tsv
[2024-01-24 12:51:41,462] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:51:41,462] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:51:41,463] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg70cab832-ab7d-4e4a-ab92-677396e2f911/dqc_reference/checkm_data
[2024-01-24 12:51:41,464] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:51:41,539] [INFO] Task started: CheckM
[2024-01-24 12:51:41,539] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012641475.1_ASM1264147v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012641475.1_ASM1264147v1_genomic.fna/checkm_input GCF_012641475.1_ASM1264147v1_genomic.fna/checkm_result
[2024-01-24 12:52:51,017] [INFO] Task succeeded: CheckM
[2024-01-24 12:52:51,018] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:52:51,048] [INFO] ===== Completeness check finished =====
[2024-01-24 12:52:51,048] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:52:51,048] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012641475.1_ASM1264147v1_genomic.fna/markers.fasta)
[2024-01-24 12:52:51,049] [INFO] Task started: Blastn
[2024-01-24 12:52:51,049] [INFO] Running command: blastn -query GCF_012641475.1_ASM1264147v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg70cab832-ab7d-4e4a-ab92-677396e2f911/dqc_reference/reference_markers_gtdb.fasta -out GCF_012641475.1_ASM1264147v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:52:51,836] [INFO] Task succeeded: Blastn
[2024-01-24 12:52:51,840] [INFO] Selected 12 target genomes.
[2024-01-24 12:52:51,840] [INFO] Target genome list was writen to GCF_012641475.1_ASM1264147v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:52:51,875] [INFO] Task started: fastANI
[2024-01-24 12:52:51,875] [INFO] Running command: fastANI --query /var/lib/cwl/stgfaddc5d1-a40d-4444-9560-259417ab0d75/GCF_012641475.1_ASM1264147v1_genomic.fna.gz --refList GCF_012641475.1_ASM1264147v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012641475.1_ASM1264147v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:53:06,337] [INFO] Task succeeded: fastANI
[2024-01-24 12:53:06,349] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:53:06,349] [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_012641475.1	s__Flammeovirga sp012641475	100.0	2410	2413	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Flammeovirgaceae;g__Flammeovirga	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018736045.1	s__Flammeovirga yaeyamensis	79.3026	724	2413	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Flammeovirgaceae;g__Flammeovirga	95.0	98.83	96.49	0.96	0.89	4	-
GCF_000812565.1	s__Flammeovirga sp000812565	79.124	667	2413	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Flammeovirgaceae;g__Flammeovirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001583495.1	s__Flammeovirga sp001583495	79.1213	657	2413	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Flammeovirgaceae;g__Flammeovirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000807855.2	s__Flammeovirga pacifica	78.9992	718	2413	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Flammeovirgaceae;g__Flammeovirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012844305.1	s__Flammeovirga aprica	78.8915	638	2413	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Flammeovirgaceae;g__Flammeovirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014534745.1	s__Flammeovirga sp014534745	78.8828	667	2413	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Flammeovirgaceae;g__Flammeovirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018736065.1	s__Flammeovirga kamogawensis	78.3238	687	2413	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Flammeovirgaceae;g__Flammeovirga	95.0	100.00	100.00	1.00	1.00	3	-
GCF_003970675.1	s__Flammeovirga pectinis	78.3075	658	2413	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Flammeovirgaceae;g__Flammeovirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003260195.1	s__Lutibacter citreus	75.0813	66	2413	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:53:06,351] [INFO] GTDB search result was written to GCF_012641475.1_ASM1264147v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:53:06,352] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:53:06,354] [INFO] DFAST_QC result json was written to GCF_012641475.1_ASM1264147v1_genomic.fna/dqc_result.json
[2024-01-24 12:53:06,355] [INFO] DFAST_QC completed!
[2024-01-24 12:53:06,355] [INFO] Total running time: 0h2m1s