[2023-03-15 22:06:34,784] [INFO] DFAST_QC pipeline started.
[2023-03-15 22:06:34,784] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 22:06:34,784] [INFO] DQC Reference Directory: /var/lib/cwl/stg8ed4f308-0648-4a13-9b36-94c969bcb93a/dqc_reference
[2023-03-15 22:06:35,888] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 22:06:35,888] [INFO] Task started: Prodigal
[2023-03-15 22:06:35,889] [INFO] Running command: cat /var/lib/cwl/stg21cbfb0b-9d66-4535-8cb5-f0740b833d46/OceanDNA-b6847.fa | prodigal -d OceanDNA-b6847/cds.fna -a OceanDNA-b6847/protein.faa -g 11 -q > /dev/null
[2023-03-15 22:06:50,246] [INFO] Task succeeded: Prodigal
[2023-03-15 22:06:50,247] [INFO] Task started: HMMsearch
[2023-03-15 22:06:50,247] [INFO] Running command: hmmsearch --tblout OceanDNA-b6847/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8ed4f308-0648-4a13-9b36-94c969bcb93a/dqc_reference/reference_markers.hmm OceanDNA-b6847/protein.faa > /dev/null
[2023-03-15 22:06:50,425] [INFO] Task succeeded: HMMsearch
[2023-03-15 22:06:50,426] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg21cbfb0b-9d66-4535-8cb5-f0740b833d46/OceanDNA-b6847.fa]
[2023-03-15 22:06:50,442] [INFO] Query marker FASTA was written to OceanDNA-b6847/markers.fasta
[2023-03-15 22:06:50,444] [INFO] Task started: Blastn
[2023-03-15 22:06:50,444] [INFO] Running command: blastn -query OceanDNA-b6847/markers.fasta -db /var/lib/cwl/stg8ed4f308-0648-4a13-9b36-94c969bcb93a/dqc_reference/reference_markers.fasta -out OceanDNA-b6847/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:06:51,061] [INFO] Task succeeded: Blastn
[2023-03-15 22:06:51,062] [INFO] Selected 16 target genomes.
[2023-03-15 22:06:51,062] [INFO] Target genome list was writen to OceanDNA-b6847/target_genomes.txt
[2023-03-15 22:06:51,088] [INFO] Task started: fastANI
[2023-03-15 22:06:51,088] [INFO] Running command: fastANI --query /var/lib/cwl/stg21cbfb0b-9d66-4535-8cb5-f0740b833d46/OceanDNA-b6847.fa --refList OceanDNA-b6847/target_genomes.txt --output OceanDNA-b6847/fastani_result.tsv --threads 1
[2023-03-15 22:07:03,016] [INFO] Task succeeded: fastANI
[2023-03-15 22:07:03,017] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8ed4f308-0648-4a13-9b36-94c969bcb93a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 22:07:03,017] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8ed4f308-0648-4a13-9b36-94c969bcb93a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 22:07:03,028] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 22:07:03,028] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 22:07:03,028] [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 frigoris	strain=DSM 15719	GCA_900111075.1	229204	229204	type	True	86.0308	604	691	95	below_threshold
Flavobacterium gillisiae	strain=DSM 22376	GCA_900107635.1	150146	150146	type	True	85.7648	618	691	95	below_threshold
Flavobacterium hiemivividum	strain=TSA-D2	GCA_004349145.1	2541734	2541734	type	True	82.9954	537	691	95	below_threshold
Flavobacterium degerlachei	strain=DSM 15718	GCA_900106645.1	229203	229203	type	True	80.5347	457	691	95	below_threshold
Flavobacterium gawalongense	strain=GSP16	GCA_007097265.1	2594432	2594432	type	True	79.2396	368	691	95	below_threshold
Flavobacterium muglaense	strain=F-60	GCA_014305155.1	2764716	2764716	type	True	79.164	334	691	95	below_threshold
Flavobacterium psychrolimnae	strain=LMG 22018	GCA_003312425.1	249351	249351	type	True	79.1072	343	691	95	below_threshold
Flavobacterium xinjiangense	strain=CGMCC 1.2749	GCA_900142885.1	178356	178356	type	True	79.0677	356	691	95	below_threshold
Flavobacterium glaciei	strain=DSM 19728	GCA_003350545.1	386300	386300	type	True	79.0183	327	691	95	below_threshold
Flavobacterium frigidarium	strain=DSM 17623	GCA_000425505.1	99286	99286	type	True	78.8837	277	691	95	below_threshold
Flavobacterium urumqiense	strain=CGMCC 1.9230	GCA_900108015.1	935224	935224	type	True	78.8744	352	691	95	below_threshold
Flavobacterium taihuense	strain=NAS39	GCA_019351435.1	2857508	2857508	type	True	77.8789	252	691	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	77.7231	201	691	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	77.5662	216	691	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	76.4731	100	691	95	below_threshold
Flavobacterium amniphilum	strain=KYPY10	GCA_023634845.1	1834035	1834035	type	True	76.3943	75	691	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 22:07:03,028] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6847/tc_result.tsv
[2023-03-15 22:07:03,028] [INFO] ===== Taxonomy check completed =====
[2023-03-15 22:07:03,029] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 22:07:03,029] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8ed4f308-0648-4a13-9b36-94c969bcb93a/dqc_reference/checkm_data
[2023-03-15 22:07:03,029] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 22:07:03,034] [INFO] Task started: CheckM
[2023-03-15 22:07:03,034] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6847/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6847/checkm_input OceanDNA-b6847/checkm_result
[2023-03-15 22:07:42,304] [INFO] Task succeeded: CheckM
[2023-03-15 22:07:42,304] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 61.46%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 22:07:42,334] [INFO] ===== Completeness check finished =====
[2023-03-15 22:07:42,334] [INFO] ===== Start GTDB Search =====
[2023-03-15 22:07:42,334] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6847/markers.fasta)
[2023-03-15 22:07:42,335] [INFO] Task started: Blastn
[2023-03-15 22:07:42,335] [INFO] Running command: blastn -query OceanDNA-b6847/markers.fasta -db /var/lib/cwl/stg8ed4f308-0648-4a13-9b36-94c969bcb93a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6847/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:07:43,303] [INFO] Task succeeded: Blastn
[2023-03-15 22:07:43,322] [INFO] Selected 7 target genomes.
[2023-03-15 22:07:43,322] [INFO] Target genome list was writen to OceanDNA-b6847/target_genomes_gtdb.txt
[2023-03-15 22:07:43,366] [INFO] Task started: fastANI
[2023-03-15 22:07:43,366] [INFO] Running command: fastANI --query /var/lib/cwl/stg21cbfb0b-9d66-4535-8cb5-f0740b833d46/OceanDNA-b6847.fa --refList OceanDNA-b6847/target_genomes_gtdb.txt --output OceanDNA-b6847/fastani_result_gtdb.tsv --threads 1
[2023-03-15 22:07:48,447] [INFO] Task succeeded: fastANI
[2023-03-15 22:07:48,452] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 22:07:48,452] [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_002836475.1	s__Flavobacterium sp002836475	98.3848	686	691	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000264055.1	s__Flavobacterium sp000264055	87.7223	605	691	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111075.1	s__Flavobacterium frigoris	86.0308	604	691	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107635.1	s__Flavobacterium gillisiae	85.7648	618	691	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004349145.1	s__Flavobacterium hiemivividum	83.0115	536	691	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	95.37	95.37	0.86	0.86	2	-
GCF_014305155.1	s__Flavobacterium sp014305155	79.1505	335	691	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900108015.1	s__Flavobacterium urumqiense	78.8794	351	691	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 22:07:48,455] [INFO] GTDB search result was written to OceanDNA-b6847/result_gtdb.tsv
[2023-03-15 22:07:48,457] [INFO] ===== GTDB Search completed =====
[2023-03-15 22:07:48,461] [INFO] DFAST_QC result json was written to OceanDNA-b6847/dqc_result.json
[2023-03-15 22:07:48,461] [INFO] DFAST_QC completed!
[2023-03-15 22:07:48,461] [INFO] Total running time: 0h1m14s