[2023-03-15 23:59:26,616] [INFO] DFAST_QC pipeline started.
[2023-03-15 23:59:26,616] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 23:59:26,616] [INFO] DQC Reference Directory: /var/lib/cwl/stgf4f20914-6c72-4b4f-8312-2ca536dd7580/dqc_reference
[2023-03-15 23:59:27,706] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 23:59:27,707] [INFO] Task started: Prodigal
[2023-03-15 23:59:27,707] [INFO] Running command: cat /var/lib/cwl/stg37622afa-6fab-4ab6-b48d-f5e3c5942888/OceanDNA-b6840.fa | prodigal -d OceanDNA-b6840/cds.fna -a OceanDNA-b6840/protein.faa -g 11 -q > /dev/null
[2023-03-15 23:59:37,057] [INFO] Task succeeded: Prodigal
[2023-03-15 23:59:37,057] [INFO] Task started: HMMsearch
[2023-03-15 23:59:37,057] [INFO] Running command: hmmsearch --tblout OceanDNA-b6840/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf4f20914-6c72-4b4f-8312-2ca536dd7580/dqc_reference/reference_markers.hmm OceanDNA-b6840/protein.faa > /dev/null
[2023-03-15 23:59:37,213] [INFO] Task succeeded: HMMsearch
[2023-03-15 23:59:37,213] [INFO] Found 6/6 markers.
[2023-03-15 23:59:37,226] [INFO] Query marker FASTA was written to OceanDNA-b6840/markers.fasta
[2023-03-15 23:59:37,227] [INFO] Task started: Blastn
[2023-03-15 23:59:37,227] [INFO] Running command: blastn -query OceanDNA-b6840/markers.fasta -db /var/lib/cwl/stgf4f20914-6c72-4b4f-8312-2ca536dd7580/dqc_reference/reference_markers.fasta -out OceanDNA-b6840/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:59:37,864] [INFO] Task succeeded: Blastn
[2023-03-15 23:59:37,865] [INFO] Selected 12 target genomes.
[2023-03-15 23:59:37,865] [INFO] Target genome list was writen to OceanDNA-b6840/target_genomes.txt
[2023-03-15 23:59:37,871] [INFO] Task started: fastANI
[2023-03-15 23:59:37,872] [INFO] Running command: fastANI --query /var/lib/cwl/stg37622afa-6fab-4ab6-b48d-f5e3c5942888/OceanDNA-b6840.fa --refList OceanDNA-b6840/target_genomes.txt --output OceanDNA-b6840/fastani_result.tsv --threads 1
[2023-03-15 23:59:44,347] [INFO] Task succeeded: fastANI
[2023-03-15 23:59:44,348] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf4f20914-6c72-4b4f-8312-2ca536dd7580/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 23:59:44,348] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf4f20914-6c72-4b4f-8312-2ca536dd7580/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 23:59:44,356] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 23:59:44,356] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 23:59:44,356] [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=CGMCC 1.6844	GCA_007830415.1	295428	295428	type	True	85.3802	342	427	95	below_threshold
Flavobacterium cheniae	strain=DSM 22462	GCA_004363695.1	295428	295428	type	True	85.3375	340	427	95	below_threshold
Flavobacterium aquaticum	strain=CGMCC 1.12398	GCA_003259835.1	1236486	1236486	type	True	84.5332	337	427	95	below_threshold
Flavobacterium sasangense	strain=DSM 21067	GCA_000686885.1	503361	503361	type	True	84.3218	332	427	95	below_threshold
Flavobacterium proteolyticum	strain=1Y8A	GCA_015223105.1	2911683	2911683	type	True	83.972	344	427	95	below_threshold
Flavobacterium cyclinae	strain=KSM-R2A25	GCA_021172145.1	2895947	2895947	type	True	83.3525	351	427	95	below_threshold
Flavobacterium channae	strain=KSM-R2A30	GCA_021172165.1	2897181	2897181	type	True	83.1274	333	427	95	below_threshold
Flavobacterium celericrescens	strain=TWA-26	GCA_011392075.1	2709780	2709780	type	True	82.8313	308	427	95	below_threshold
Flavobacterium cucumis	strain=DSM 18830	GCA_900148835.1	416016	416016	type	True	82.3816	305	427	95	below_threshold
Flavobacterium jumunjinense	strain=HME7102	GCA_021650975.2	998845	998845	type	True	78.2171	197	427	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	77.896	214	427	95	below_threshold
Flavobacterium branchiophilum	strain=DSM 24789	GCA_006716585.1	55197	55197	type	True	76.6505	60	427	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 23:59:44,356] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6840/tc_result.tsv
[2023-03-15 23:59:44,357] [INFO] ===== Taxonomy check completed =====
[2023-03-15 23:59:44,357] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 23:59:44,357] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf4f20914-6c72-4b4f-8312-2ca536dd7580/dqc_reference/checkm_data
[2023-03-15 23:59:44,357] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 23:59:44,416] [INFO] Task started: CheckM
[2023-03-15 23:59:44,416] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6840/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6840/checkm_input OceanDNA-b6840/checkm_result
[2023-03-16 00:00:12,282] [INFO] Task succeeded: CheckM
[2023-03-16 00:00:12,283] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.25%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 00:00:12,332] [INFO] ===== Completeness check finished =====
[2023-03-16 00:00:12,332] [INFO] ===== Start GTDB Search =====
[2023-03-16 00:00:12,333] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6840/markers.fasta)
[2023-03-16 00:00:12,334] [INFO] Task started: Blastn
[2023-03-16 00:00:12,334] [INFO] Running command: blastn -query OceanDNA-b6840/markers.fasta -db /var/lib/cwl/stgf4f20914-6c72-4b4f-8312-2ca536dd7580/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6840/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:00:13,376] [INFO] Task succeeded: Blastn
[2023-03-16 00:00:13,377] [INFO] Selected 9 target genomes.
[2023-03-16 00:00:13,377] [INFO] Target genome list was writen to OceanDNA-b6840/target_genomes_gtdb.txt
[2023-03-16 00:00:13,443] [INFO] Task started: fastANI
[2023-03-16 00:00:13,443] [INFO] Running command: fastANI --query /var/lib/cwl/stg37622afa-6fab-4ab6-b48d-f5e3c5942888/OceanDNA-b6840.fa --refList OceanDNA-b6840/target_genomes_gtdb.txt --output OceanDNA-b6840/fastani_result_gtdb.tsv --threads 1
[2023-03-16 00:00:17,762] [INFO] Task succeeded: fastANI
[2023-03-16 00:00:17,768] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 00:00:17,768] [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_000169355.1	s__Flavobacterium sp000169355	95.2947	389	427	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.75	96.74	0.84	0.84	3	conclusive
GCF_009495755.1	s__Flavobacterium sp009495755	85.7144	350	427	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004293165.1	s__Flavobacterium sp004293165	85.3928	350	427	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.30	97.30	0.81	0.81	2	-
GCF_004363695.1	s__Flavobacterium cheniae	85.3375	340	427	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003497625.1	s__Flavobacterium sp003497625	85.208	330	427	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.98	99.98	0.98	0.98	2	-
GCA_002483315.1	s__Flavobacterium sp002483315	85.0074	317	427	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259835.1	s__Flavobacterium aquaticum	84.5332	337	427	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	84.2928	333	427	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	83.5706	293	427	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 00:00:17,768] [INFO] GTDB search result was written to OceanDNA-b6840/result_gtdb.tsv
[2023-03-16 00:00:17,768] [INFO] ===== GTDB Search completed =====
[2023-03-16 00:00:17,770] [INFO] DFAST_QC result json was written to OceanDNA-b6840/dqc_result.json
[2023-03-16 00:00:17,771] [INFO] DFAST_QC completed!
[2023-03-16 00:00:17,771] [INFO] Total running time: 0h0m51s