[2024-01-24 13:57:56,309] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:56,311] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:56,311] [INFO] DQC Reference Directory: /var/lib/cwl/stgb53ac62e-fd7d-41db-a942-2c2fda3b6086/dqc_reference
[2024-01-24 13:57:57,644] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:57,645] [INFO] Task started: Prodigal
[2024-01-24 13:57:57,646] [INFO] Running command: gunzip -c /var/lib/cwl/stgfd015870-fcea-464e-88fd-1a77b09d43da/GCF_012844305.1_ASM1284430v1_genomic.fna.gz | prodigal -d GCF_012844305.1_ASM1284430v1_genomic.fna/cds.fna -a GCF_012844305.1_ASM1284430v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:33,255] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:33,255] [INFO] Task started: HMMsearch
[2024-01-24 13:58:33,255] [INFO] Running command: hmmsearch --tblout GCF_012844305.1_ASM1284430v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb53ac62e-fd7d-41db-a942-2c2fda3b6086/dqc_reference/reference_markers.hmm GCF_012844305.1_ASM1284430v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:33,651] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:33,652] [INFO] Found 6/6 markers.
[2024-01-24 13:58:33,722] [INFO] Query marker FASTA was written to GCF_012844305.1_ASM1284430v1_genomic.fna/markers.fasta
[2024-01-24 13:58:33,723] [INFO] Task started: Blastn
[2024-01-24 13:58:33,723] [INFO] Running command: blastn -query GCF_012844305.1_ASM1284430v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb53ac62e-fd7d-41db-a942-2c2fda3b6086/dqc_reference/reference_markers.fasta -out GCF_012844305.1_ASM1284430v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:34,332] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:34,336] [INFO] Selected 13 target genomes.
[2024-01-24 13:58:34,336] [INFO] Target genome list was writen to GCF_012844305.1_ASM1284430v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:34,343] [INFO] Task started: fastANI
[2024-01-24 13:58:34,343] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd015870-fcea-464e-88fd-1a77b09d43da/GCF_012844305.1_ASM1284430v1_genomic.fna.gz --refList GCF_012844305.1_ASM1284430v1_genomic.fna/target_genomes.txt --output GCF_012844305.1_ASM1284430v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:49,357] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:49,358] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb53ac62e-fd7d-41db-a942-2c2fda3b6086/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:49,358] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb53ac62e-fd7d-41db-a942-2c2fda3b6086/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:49,365] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:49,365] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:49,366] [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 aprica	strain=ATCC 23126	GCA_012844305.1	29528	29528	type	True	100.0	2905	2918	95	conclusive
Flammeovirga agarivorans	strain=SR4	GCA_012641475.1	2726742	2726742	type	True	78.7172	644	2918	95	below_threshold
Flammeovirga kamogawensis	strain=YS10	GCA_007097495.1	373891	373891	type	True	78.3455	598	2918	95	below_threshold
Flammeovirga kamogawensis	strain=DSM 26273	GCA_014207545.1	373891	373891	type	True	78.3181	597	2918	95	below_threshold
Flammeovirga pectinis	strain=L12M1	GCA_003970675.1	2494373	2494373	type	True	78.3059	576	2918	95	below_threshold
Flammeovirga kamogawensis	strain=YS10	GCA_018736065.1	373891	373891	type	True	78.3036	598	2918	95	below_threshold
Flammeovirga pacifica	strain=WPAGA1	GCA_000807855.2	915059	915059	type	True	78.2594	572	2918	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:49,367] [INFO] DFAST Taxonomy check result was written to GCF_012844305.1_ASM1284430v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:49,368] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:49,368] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:49,368] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb53ac62e-fd7d-41db-a942-2c2fda3b6086/dqc_reference/checkm_data
[2024-01-24 13:58:49,369] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:49,453] [INFO] Task started: CheckM
[2024-01-24 13:58:49,454] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012844305.1_ASM1284430v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012844305.1_ASM1284430v1_genomic.fna/checkm_input GCF_012844305.1_ASM1284430v1_genomic.fna/checkm_result
[2024-01-24 14:00:26,603] [INFO] Task succeeded: CheckM
[2024-01-24 14:00:26,605] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:00:26,643] [INFO] ===== Completeness check finished =====
[2024-01-24 14:00:26,644] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:00:26,644] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012844305.1_ASM1284430v1_genomic.fna/markers.fasta)
[2024-01-24 14:00:26,644] [INFO] Task started: Blastn
[2024-01-24 14:00:26,645] [INFO] Running command: blastn -query GCF_012844305.1_ASM1284430v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb53ac62e-fd7d-41db-a942-2c2fda3b6086/dqc_reference/reference_markers_gtdb.fasta -out GCF_012844305.1_ASM1284430v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:00:27,503] [INFO] Task succeeded: Blastn
[2024-01-24 14:00:27,506] [INFO] Selected 8 target genomes.
[2024-01-24 14:00:27,506] [INFO] Target genome list was writen to GCF_012844305.1_ASM1284430v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:00:27,525] [INFO] Task started: fastANI
[2024-01-24 14:00:27,525] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd015870-fcea-464e-88fd-1a77b09d43da/GCF_012844305.1_ASM1284430v1_genomic.fna.gz --refList GCF_012844305.1_ASM1284430v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012844305.1_ASM1284430v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:44,205] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:44,212] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:00:44,213] [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_012844305.1	s__Flammeovirga aprica	100.0	2905	2918	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_001583495.1	s__Flammeovirga sp001583495	87.7857	2036	2918	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	85.0856	1804	2918	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	84.7848	1791	2918	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	78.7397	640	2918	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	78.3121	598	2918	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	78.306	576	2918	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Flammeovirgaceae;g__Flammeovirga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:00:44,214] [INFO] GTDB search result was written to GCF_012844305.1_ASM1284430v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:44,215] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:44,218] [INFO] DFAST_QC result json was written to GCF_012844305.1_ASM1284430v1_genomic.fna/dqc_result.json
[2024-01-24 14:00:44,218] [INFO] DFAST_QC completed!
[2024-01-24 14:00:44,218] [INFO] Total running time: 0h2m48s