[2023-03-15 05:37:30,054] [INFO] DFAST_QC pipeline started.
[2023-03-15 05:37:30,054] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 05:37:30,054] [INFO] DQC Reference Directory: /var/lib/cwl/stg8bba79f3-e7dc-41f2-b6aa-92b205a90c1f/dqc_reference
[2023-03-15 05:37:31,173] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 05:37:31,174] [INFO] Task started: Prodigal
[2023-03-15 05:37:31,174] [INFO] Running command: cat /var/lib/cwl/stg585fbe74-e5c3-4518-896b-e91dc080c52b/OceanDNA-b6674.fa | prodigal -d OceanDNA-b6674/cds.fna -a OceanDNA-b6674/protein.faa -g 11 -q > /dev/null
[2023-03-15 05:37:52,306] [INFO] Task succeeded: Prodigal
[2023-03-15 05:37:52,307] [INFO] Task started: HMMsearch
[2023-03-15 05:37:52,307] [INFO] Running command: hmmsearch --tblout OceanDNA-b6674/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8bba79f3-e7dc-41f2-b6aa-92b205a90c1f/dqc_reference/reference_markers.hmm OceanDNA-b6674/protein.faa > /dev/null
[2023-03-15 05:37:52,502] [INFO] Task succeeded: HMMsearch
[2023-03-15 05:37:52,503] [INFO] Found 6/6 markers.
[2023-03-15 05:37:52,522] [INFO] Query marker FASTA was written to OceanDNA-b6674/markers.fasta
[2023-03-15 05:37:52,523] [INFO] Task started: Blastn
[2023-03-15 05:37:52,523] [INFO] Running command: blastn -query OceanDNA-b6674/markers.fasta -db /var/lib/cwl/stg8bba79f3-e7dc-41f2-b6aa-92b205a90c1f/dqc_reference/reference_markers.fasta -out OceanDNA-b6674/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:37:53,126] [INFO] Task succeeded: Blastn
[2023-03-15 05:37:53,127] [INFO] Selected 18 target genomes.
[2023-03-15 05:37:53,127] [INFO] Target genome list was writen to OceanDNA-b6674/target_genomes.txt
[2023-03-15 05:37:53,135] [INFO] Task started: fastANI
[2023-03-15 05:37:53,135] [INFO] Running command: fastANI --query /var/lib/cwl/stg585fbe74-e5c3-4518-896b-e91dc080c52b/OceanDNA-b6674.fa --refList OceanDNA-b6674/target_genomes.txt --output OceanDNA-b6674/fastani_result.tsv --threads 1
[2023-03-15 05:38:04,027] [INFO] Task succeeded: fastANI
[2023-03-15 05:38:04,028] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8bba79f3-e7dc-41f2-b6aa-92b205a90c1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 05:38:04,028] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8bba79f3-e7dc-41f2-b6aa-92b205a90c1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 05:38:04,039] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 05:38:04,039] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 05:38:04,039] [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
Cellulophaga fucicola	strain=DSM 24786	GCA_900119145.1	76595	76595	type	True	79.9492	513	1073	95	below_threshold
Cellulophaga omnivescoria	strain=W5C	GCA_001999725.1	1888890	1888890	type	True	79.6319	464	1073	95	below_threshold
Cellulophaga lytica	strain=DSM 7489	GCA_000190595.1	979	979	type	True	79.5105	491	1073	95	below_threshold
Maribacter vaceletii	strain=DSM 25230	GCA_003634105.1	1206816	1206816	type	True	77.1779	232	1073	95	below_threshold
Cellulophaga tyrosinoxydans	strain=DSM 21164	GCA_900176415.1	504486	504486	type	True	77.0447	204	1073	95	below_threshold
Cellulophaga baltica	strain=DSM 24729	GCA_900102165.1	76594	76594	type	True	77.0202	211	1073	95	below_threshold
Maribacter spongiicola	strain=DSM 25233	GCA_004364165.1	1206753	1206753	type	True	76.3648	152	1073	95	below_threshold
Maribacter arcticus	strain=DSM 23546	GCA_900167935.1	561365	561365	type	True	76.3492	142	1073	95	below_threshold
Algibacter pectinivorans	strain=DSM 25730	GCA_900112595.1	870482	870482	type	True	76.3248	107	1073	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	76.2482	95	1073	95	below_threshold
Croceivirga lutea	strain=CGMCC 1.15761	GCA_014643615.1	1775167	1775167	type	True	76.1097	131	1073	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	76.1029	93	1073	95	below_threshold
Winogradskyella endarachnes	strain=HL2-2	GCA_009741275.1	2681965	2681965	type	True	76.0357	112	1073	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	75.9616	70	1073	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	75.9431	102	1073	95	below_threshold
Aequorivita sinensis	strain=S1-10	GCA_006346335.1	1382458	1382458	type	True	75.8522	58	1073	95	below_threshold
Olleya namhaensis	strain=DSM 28881	GCA_900114005.1	1144750	1144750	type	True	75.8302	102	1073	95	below_threshold
Flavobacterium channae	strain=KSM-R2A30	GCA_021172165.1	2897181	2897181	type	True	75.7685	67	1073	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 05:38:04,039] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6674/tc_result.tsv
[2023-03-15 05:38:04,039] [INFO] ===== Taxonomy check completed =====
[2023-03-15 05:38:04,039] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 05:38:04,040] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8bba79f3-e7dc-41f2-b6aa-92b205a90c1f/dqc_reference/checkm_data
[2023-03-15 05:38:04,040] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 05:38:04,060] [INFO] Task started: CheckM
[2023-03-15 05:38:04,060] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6674/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6674/checkm_input OceanDNA-b6674/checkm_result
[2023-03-15 05:38:55,990] [INFO] Task succeeded: CheckM
[2023-03-15 05:38:55,991] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 05:38:56,005] [INFO] ===== Completeness check finished =====
[2023-03-15 05:38:56,006] [INFO] ===== Start GTDB Search =====
[2023-03-15 05:38:56,006] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6674/markers.fasta)
[2023-03-15 05:38:56,007] [INFO] Task started: Blastn
[2023-03-15 05:38:56,007] [INFO] Running command: blastn -query OceanDNA-b6674/markers.fasta -db /var/lib/cwl/stg8bba79f3-e7dc-41f2-b6aa-92b205a90c1f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6674/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:38:56,844] [INFO] Task succeeded: Blastn
[2023-03-15 05:38:56,847] [INFO] Selected 12 target genomes.
[2023-03-15 05:38:56,847] [INFO] Target genome list was writen to OceanDNA-b6674/target_genomes_gtdb.txt
[2023-03-15 05:38:56,860] [INFO] Task started: fastANI
[2023-03-15 05:38:56,860] [INFO] Running command: fastANI --query /var/lib/cwl/stg585fbe74-e5c3-4518-896b-e91dc080c52b/OceanDNA-b6674.fa --refList OceanDNA-b6674/target_genomes_gtdb.txt --output OceanDNA-b6674/fastani_result_gtdb.tsv --threads 1
[2023-03-15 05:39:04,674] [INFO] Task succeeded: fastANI
[2023-03-15 05:39:04,682] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 05:39:04,682] [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_900119145.1	s__Cellulophaga fucicola	79.9554	512	1073	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002813425.1	s__Cellulophaga sp002813425	79.8051	477	1073	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001999725.1	s__Cellulophaga omnivescoria	79.6319	464	1073	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000190595.1	s__Cellulophaga lytica	79.5105	491	1073	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	99.01	98.71	0.94	0.93	6	-
GCF_003634105.1	s__Maribacter_B vaceletii	77.1866	232	1073	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019021925.1	s__Cellulophaga sp019021925	77.1153	230	1073	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176415.1	s__Cellulophaga tyrosinoxydans	77.0447	204	1073	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102165.1	s__Cellulophaga baltica	77.0078	212	1073	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	97.62	97.40	0.90	0.89	7	-
GCA_016744255.1	s__Maribacter_B sp016744255	76.8365	197	1073	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009649685.1	s__Aurantibacter_A sp009649685	76.5646	139	1073	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aurantibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167935.1	s__Maribacter arcticus	76.3492	142	1073	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114005.1	s__Olleya namhaensis	75.8302	102	1073	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	98.20	98.20	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2023-03-15 05:39:04,683] [INFO] GTDB search result was written to OceanDNA-b6674/result_gtdb.tsv
[2023-03-15 05:39:04,684] [INFO] ===== GTDB Search completed =====
[2023-03-15 05:39:04,686] [INFO] DFAST_QC result json was written to OceanDNA-b6674/dqc_result.json
[2023-03-15 05:39:04,686] [INFO] DFAST_QC completed!
[2023-03-15 05:39:04,686] [INFO] Total running time: 0h1m35s