[2023-06-19 04:29:06,117] [INFO] DFAST_QC pipeline started.
[2023-06-19 04:29:06,119] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 04:29:06,119] [INFO] DQC Reference Directory: /var/lib/cwl/stga18afeab-be36-4473-bf02-fe38beb864b9/dqc_reference
[2023-06-19 04:29:07,400] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 04:29:07,402] [INFO] Task started: Prodigal
[2023-06-19 04:29:07,402] [INFO] Running command: gunzip -c /var/lib/cwl/stg7c84be1e-eae7-4668-bc06-57ffaf42beb2/GCA_018062905.1_ASM1806290v1_genomic.fna.gz | prodigal -d GCA_018062905.1_ASM1806290v1_genomic.fna/cds.fna -a GCA_018062905.1_ASM1806290v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 04:29:15,272] [INFO] Task succeeded: Prodigal
[2023-06-19 04:29:15,273] [INFO] Task started: HMMsearch
[2023-06-19 04:29:15,273] [INFO] Running command: hmmsearch --tblout GCA_018062905.1_ASM1806290v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga18afeab-be36-4473-bf02-fe38beb864b9/dqc_reference/reference_markers.hmm GCA_018062905.1_ASM1806290v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 04:29:15,522] [INFO] Task succeeded: HMMsearch
[2023-06-19 04:29:15,524] [INFO] Found 6/6 markers.
[2023-06-19 04:29:15,564] [INFO] Query marker FASTA was written to GCA_018062905.1_ASM1806290v1_genomic.fna/markers.fasta
[2023-06-19 04:29:15,564] [INFO] Task started: Blastn
[2023-06-19 04:29:15,564] [INFO] Running command: blastn -query GCA_018062905.1_ASM1806290v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga18afeab-be36-4473-bf02-fe38beb864b9/dqc_reference/reference_markers.fasta -out GCA_018062905.1_ASM1806290v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 04:29:16,201] [INFO] Task succeeded: Blastn
[2023-06-19 04:29:16,206] [INFO] Selected 10 target genomes.
[2023-06-19 04:29:16,207] [INFO] Target genome list was writen to GCA_018062905.1_ASM1806290v1_genomic.fna/target_genomes.txt
[2023-06-19 04:29:16,210] [INFO] Task started: fastANI
[2023-06-19 04:29:16,210] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c84be1e-eae7-4668-bc06-57ffaf42beb2/GCA_018062905.1_ASM1806290v1_genomic.fna.gz --refList GCA_018062905.1_ASM1806290v1_genomic.fna/target_genomes.txt --output GCA_018062905.1_ASM1806290v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 04:29:22,309] [INFO] Task succeeded: fastANI
[2023-06-19 04:29:22,309] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga18afeab-be36-4473-bf02-fe38beb864b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 04:29:22,310] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga18afeab-be36-4473-bf02-fe38beb864b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 04:29:22,322] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 04:29:22,322] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 04:29:22,323] [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
Flavobacterium cheniae	strain=DSM 22462	GCA_004363695.1	295428	295428	type	True	86.9605	542	763	95	below_threshold
Flavobacterium cheniae	strain=CGMCC 1.6844	GCA_007830415.1	295428	295428	type	True	86.8558	545	763	95	below_threshold
Flavobacterium aquaticum	strain=CGMCC 1.12398	GCA_003259835.1	1236486	1236486	type	True	85.5616	568	763	95	below_threshold
Flavobacterium sasangense	strain=DSM 21067	GCA_000686885.1	503361	503361	type	True	85.4708	525	763	95	below_threshold
Flavobacterium proteolyticum	strain=1Y8A	GCA_015223105.1	2911683	2911683	type	True	85.4306	526	763	95	below_threshold
Flavobacterium cyclinae	strain=KSM-R2A25	GCA_021172145.1	2895947	2895947	type	True	84.3797	539	763	95	below_threshold
Flavobacterium celericrescens	strain=TWA-26	GCA_011392075.1	2709780	2709780	type	True	83.7798	491	763	95	below_threshold
Flavobacterium channae	strain=KSM-R2A30	GCA_021172165.1	2897181	2897181	type	True	83.4228	513	763	95	below_threshold
Flavobacterium branchiophilum	strain=DSM 24789	GCA_006716585.1	55197	55197	type	True	76.7802	119	763	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 04:29:22,324] [INFO] DFAST Taxonomy check result was written to GCA_018062905.1_ASM1806290v1_genomic.fna/tc_result.tsv
[2023-06-19 04:29:22,325] [INFO] ===== Taxonomy check completed =====
[2023-06-19 04:29:22,325] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 04:29:22,325] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga18afeab-be36-4473-bf02-fe38beb864b9/dqc_reference/checkm_data
[2023-06-19 04:29:22,327] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 04:29:22,356] [INFO] Task started: CheckM
[2023-06-19 04:29:22,356] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018062905.1_ASM1806290v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018062905.1_ASM1806290v1_genomic.fna/checkm_input GCA_018062905.1_ASM1806290v1_genomic.fna/checkm_result
[2023-06-19 04:29:51,873] [INFO] Task succeeded: CheckM
[2023-06-19 04:29:51,874] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 69.65%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 04:29:51,911] [INFO] ===== Completeness check finished =====
[2023-06-19 04:29:51,911] [INFO] ===== Start GTDB Search =====
[2023-06-19 04:29:51,912] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018062905.1_ASM1806290v1_genomic.fna/markers.fasta)
[2023-06-19 04:29:51,912] [INFO] Task started: Blastn
[2023-06-19 04:29:51,912] [INFO] Running command: blastn -query GCA_018062905.1_ASM1806290v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga18afeab-be36-4473-bf02-fe38beb864b9/dqc_reference/reference_markers_gtdb.fasta -out GCA_018062905.1_ASM1806290v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 04:29:52,798] [INFO] Task succeeded: Blastn
[2023-06-19 04:29:52,803] [INFO] Selected 11 target genomes.
[2023-06-19 04:29:52,804] [INFO] Target genome list was writen to GCA_018062905.1_ASM1806290v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 04:29:52,814] [INFO] Task started: fastANI
[2023-06-19 04:29:52,814] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c84be1e-eae7-4668-bc06-57ffaf42beb2/GCA_018062905.1_ASM1806290v1_genomic.fna.gz --refList GCA_018062905.1_ASM1806290v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018062905.1_ASM1806290v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 04:29:59,388] [INFO] Task succeeded: fastANI
[2023-06-19 04:29:59,399] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 04:29:59,399] [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
GCA_004293165.1	s__Flavobacterium sp004293165	97.2957	620	763	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.30	97.30	0.81	0.81	2	conclusive
GCF_004363695.1	s__Flavobacterium cheniae	86.9605	542	763	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002483315.1	s__Flavobacterium sp002483315	86.7786	516	763	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003497625.1	s__Flavobacterium sp003497625	86.6774	515	763	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.98	99.98	0.98	0.98	2	-
GCF_009495755.1	s__Flavobacterium sp009495755	85.9298	522	763	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000169355.1	s__Flavobacterium sp000169355	85.7541	536	763	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.75	96.74	0.84	0.84	3	-
GCF_003259835.1	s__Flavobacterium aquaticum	85.5813	567	763	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000686885.1	s__Flavobacterium sasangense	85.4898	524	763	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002422095.1	s__Flavobacterium sp002422095	84.9285	440	763	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011392075.1	s__Flavobacterium celericrescens	83.7585	493	763	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017984495.1	s__Flavobacterium sp017984495	80.7715	269	763	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 04:29:59,401] [INFO] GTDB search result was written to GCA_018062905.1_ASM1806290v1_genomic.fna/result_gtdb.tsv
[2023-06-19 04:29:59,402] [INFO] ===== GTDB Search completed =====
[2023-06-19 04:29:59,405] [INFO] DFAST_QC result json was written to GCA_018062905.1_ASM1806290v1_genomic.fna/dqc_result.json
[2023-06-19 04:29:59,405] [INFO] DFAST_QC completed!
[2023-06-19 04:29:59,405] [INFO] Total running time: 0h0m53s