[2024-01-24 14:12:47,658] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:12:47,661] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:12:47,662] [INFO] DQC Reference Directory: /var/lib/cwl/stgcf242bca-3757-48e7-aa35-9dd89d91f86b/dqc_reference
[2024-01-24 14:12:48,894] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:12:48,895] [INFO] Task started: Prodigal
[2024-01-24 14:12:48,895] [INFO] Running command: gunzip -c /var/lib/cwl/stg2fa17e19-c02b-4cc2-9a9e-d346cd270c96/GCF_018736045.1_ASM1873604v1_genomic.fna.gz | prodigal -d GCF_018736045.1_ASM1873604v1_genomic.fna/cds.fna -a GCF_018736045.1_ASM1873604v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:13:14,936] [INFO] Task succeeded: Prodigal
[2024-01-24 14:13:14,936] [INFO] Task started: HMMsearch
[2024-01-24 14:13:14,937] [INFO] Running command: hmmsearch --tblout GCF_018736045.1_ASM1873604v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcf242bca-3757-48e7-aa35-9dd89d91f86b/dqc_reference/reference_markers.hmm GCF_018736045.1_ASM1873604v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:13:15,272] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:13:15,273] [INFO] Found 6/6 markers.
[2024-01-24 14:13:15,327] [INFO] Query marker FASTA was written to GCF_018736045.1_ASM1873604v1_genomic.fna/markers.fasta
[2024-01-24 14:13:15,328] [INFO] Task started: Blastn
[2024-01-24 14:13:15,328] [INFO] Running command: blastn -query GCF_018736045.1_ASM1873604v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcf242bca-3757-48e7-aa35-9dd89d91f86b/dqc_reference/reference_markers.fasta -out GCF_018736045.1_ASM1873604v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:15,914] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:15,919] [INFO] Selected 8 target genomes.
[2024-01-24 14:13:15,920] [INFO] Target genome list was writen to GCF_018736045.1_ASM1873604v1_genomic.fna/target_genomes.txt
[2024-01-24 14:13:15,924] [INFO] Task started: fastANI
[2024-01-24 14:13:15,925] [INFO] Running command: fastANI --query /var/lib/cwl/stg2fa17e19-c02b-4cc2-9a9e-d346cd270c96/GCF_018736045.1_ASM1873604v1_genomic.fna.gz --refList GCF_018736045.1_ASM1873604v1_genomic.fna/target_genomes.txt --output GCF_018736045.1_ASM1873604v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:13:26,817] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:26,818] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcf242bca-3757-48e7-aa35-9dd89d91f86b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:13:26,819] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcf242bca-3757-48e7-aa35-9dd89d91f86b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:13:26,831] [INFO] Found 7 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:13:26,831] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:13:26,831] [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 yaeyamensis	strain=NBRC:100898	GCA_018736045.1	367791	367791	type	True	100.0	2475	2477	95	conclusive
Flammeovirga yaeyamensis	strain=DSM 25626	GCA_014195575.1	367791	367791	type	True	99.9866	2446	2477	95	conclusive
Flammeovirga yaeyamensis	strain=NBRC 100898	GCA_012844325.1	367791	367791	type	True	99.982	2436	2477	95	conclusive
Flammeovirga pacifica	strain=WPAGA1	GCA_000807855.2	915059	915059	type	True	81.4774	1289	2477	95	below_threshold
Flammeovirga agarivorans	strain=SR4	GCA_012641475.1	2726742	2726742	type	True	79.2929	718	2477	95	below_threshold
Flammeovirga pectinis	strain=L12M1	GCA_003970675.1	2494373	2494373	type	True	78.2348	561	2477	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	75.3828	50	2477	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:13:26,832] [INFO] DFAST Taxonomy check result was written to GCF_018736045.1_ASM1873604v1_genomic.fna/tc_result.tsv
[2024-01-24 14:13:26,833] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:13:26,833] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:13:26,833] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcf242bca-3757-48e7-aa35-9dd89d91f86b/dqc_reference/checkm_data
[2024-01-24 14:13:26,834] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:13:26,902] [INFO] Task started: CheckM
[2024-01-24 14:13:26,902] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018736045.1_ASM1873604v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018736045.1_ASM1873604v1_genomic.fna/checkm_input GCF_018736045.1_ASM1873604v1_genomic.fna/checkm_result
[2024-01-24 14:14:42,862] [INFO] Task succeeded: CheckM
[2024-01-24 14:14:42,863] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:14:42,884] [INFO] ===== Completeness check finished =====
[2024-01-24 14:14:42,885] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:14:42,885] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018736045.1_ASM1873604v1_genomic.fna/markers.fasta)
[2024-01-24 14:14:42,885] [INFO] Task started: Blastn
[2024-01-24 14:14:42,886] [INFO] Running command: blastn -query GCF_018736045.1_ASM1873604v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcf242bca-3757-48e7-aa35-9dd89d91f86b/dqc_reference/reference_markers_gtdb.fasta -out GCF_018736045.1_ASM1873604v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:43,672] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:43,676] [INFO] Selected 11 target genomes.
[2024-01-24 14:14:43,677] [INFO] Target genome list was writen to GCF_018736045.1_ASM1873604v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:14:43,694] [INFO] Task started: fastANI
[2024-01-24 14:14:43,694] [INFO] Running command: fastANI --query /var/lib/cwl/stg2fa17e19-c02b-4cc2-9a9e-d346cd270c96/GCF_018736045.1_ASM1873604v1_genomic.fna.gz --refList GCF_018736045.1_ASM1873604v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018736045.1_ASM1873604v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:14:58,270] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:58,283] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:14:58,284] [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_018736045.1	s__Flammeovirga yaeyamensis	100.0	2474	2477	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Flammeovirgaceae;g__Flammeovirga	95.0	98.83	96.49	0.96	0.89	4	conclusive
GCF_000807855.2	s__Flammeovirga pacifica	81.4771	1289	2477	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Flammeovirgaceae;g__Flammeovirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012641475.1	s__Flammeovirga sp012641475	79.2864	719	2477	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	78.8541	651	2477	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	78.8296	603	2477	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Flammeovirgaceae;g__Flammeovirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000812565.1	s__Flammeovirga sp000812565	78.7949	628	2477	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	78.3451	567	2477	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	78.2341	560	2477	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Flammeovirgaceae;g__Flammeovirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003149185.1	s__Sediminitomix flava	76.4372	128	2477	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Flammeovirgaceae;g__Sediminitomix	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:14:58,286] [INFO] GTDB search result was written to GCF_018736045.1_ASM1873604v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:14:58,286] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:14:58,289] [INFO] DFAST_QC result json was written to GCF_018736045.1_ASM1873604v1_genomic.fna/dqc_result.json
[2024-01-24 14:14:58,289] [INFO] DFAST_QC completed!
[2024-01-24 14:14:58,289] [INFO] Total running time: 0h2m11s