[2023-03-18 23:32:58,551] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:32:58,552] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:32:58,552] [INFO] DQC Reference Directory: /var/lib/cwl/stg32222449-1d8c-4816-b5a6-d0eddea9f89c/dqc_reference
[2023-03-18 23:32:59,890] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:32:59,890] [INFO] Task started: Prodigal
[2023-03-18 23:32:59,890] [INFO] Running command: cat /var/lib/cwl/stgb0d5da34-db2a-4152-b625-8c532b172e82/OceanDNA-b27518.fa | prodigal -d OceanDNA-b27518/cds.fna -a OceanDNA-b27518/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:33:15,386] [INFO] Task succeeded: Prodigal
[2023-03-18 23:33:15,387] [INFO] Task started: HMMsearch
[2023-03-18 23:33:15,387] [INFO] Running command: hmmsearch --tblout OceanDNA-b27518/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg32222449-1d8c-4816-b5a6-d0eddea9f89c/dqc_reference/reference_markers.hmm OceanDNA-b27518/protein.faa > /dev/null
[2023-03-18 23:33:15,578] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:33:15,578] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgb0d5da34-db2a-4152-b625-8c532b172e82/OceanDNA-b27518.fa]
[2023-03-18 23:33:15,603] [INFO] Query marker FASTA was written to OceanDNA-b27518/markers.fasta
[2023-03-18 23:33:15,604] [INFO] Task started: Blastn
[2023-03-18 23:33:15,604] [INFO] Running command: blastn -query OceanDNA-b27518/markers.fasta -db /var/lib/cwl/stg32222449-1d8c-4816-b5a6-d0eddea9f89c/dqc_reference/reference_markers.fasta -out OceanDNA-b27518/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:33:16,214] [INFO] Task succeeded: Blastn
[2023-03-18 23:33:16,215] [INFO] Selected 16 target genomes.
[2023-03-18 23:33:16,215] [INFO] Target genome list was writen to OceanDNA-b27518/target_genomes.txt
[2023-03-18 23:33:16,224] [INFO] Task started: fastANI
[2023-03-18 23:33:16,225] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0d5da34-db2a-4152-b625-8c532b172e82/OceanDNA-b27518.fa --refList OceanDNA-b27518/target_genomes.txt --output OceanDNA-b27518/fastani_result.tsv --threads 1
[2023-03-18 23:33:28,122] [INFO] Task succeeded: fastANI
[2023-03-18 23:33:28,122] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg32222449-1d8c-4816-b5a6-d0eddea9f89c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:33:28,122] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg32222449-1d8c-4816-b5a6-d0eddea9f89c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:33:28,131] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:33:28,132] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 23:33:28,132] [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
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	80.9993	432	805	95	below_threshold
Zongyanglinia marina	strain=DSW4-44	GCA_005771405.1	2578117	2578117	type	True	80.9437	425	805	95	below_threshold
Pseudophaeobacter arcticus	strain=DSM 23566	GCA_000473205.1	385492	385492	type	True	77.7612	228	805	95	below_threshold
Phaeobacter gallaeciensis	strain=DSM 26640	GCA_000511385.1	60890	60890	type	True	77.5334	208	805	95	below_threshold
Phaeobacter gallaeciensis	strain=DSM 26640	GCA_000819625.1	60890	60890	type	True	77.5037	212	805	95	below_threshold
Leisingera aquaemixtae	strain=CECT 8399	GCA_001458395.1	1396826	1396826	type	True	77.4981	213	805	95	below_threshold
Pseudophaeobacter leonis	strain=306	GCA_002087335.1	1144477	1144477	type	True	77.4924	210	805	95	below_threshold
Phaeobacter inhibens	strain=DSM 16374	GCA_000473105.1	221822	221822	type	True	77.4664	210	805	95	below_threshold
Thalassobius autumnalis	strain=CECT 5118	GCA_001458255.1	2072972	2072972	type	True	77.2814	143	805	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	77.2748	223	805	95	below_threshold
Phaeobacter porticola	strain=P97	GCA_001888185.1	1844006	1844006	type	True	77.1943	200	805	95	below_threshold
Falsiruegeria mediterranea	strain=CECT 7615	GCA_900302455.1	1280832	1280832	type	True	77.1768	180	805	95	below_threshold
Falsiruegeria litorea	strain=CECT 7639	GCA_900172225.1	1280831	1280831	type	True	77.0636	190	805	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	76.3733	62	805	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	75.9536	64	805	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 23:33:28,132] [INFO] DFAST Taxonomy check result was written to OceanDNA-b27518/tc_result.tsv
[2023-03-18 23:33:28,132] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:33:28,132] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:33:28,132] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg32222449-1d8c-4816-b5a6-d0eddea9f89c/dqc_reference/checkm_data
[2023-03-18 23:33:28,133] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:33:28,138] [INFO] Task started: CheckM
[2023-03-18 23:33:28,138] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b27518/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b27518/checkm_input OceanDNA-b27518/checkm_result
[2023-03-18 23:34:10,044] [INFO] Task succeeded: CheckM
[2023-03-18 23:34:10,044] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 47.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:34:10,073] [INFO] ===== Completeness check finished =====
[2023-03-18 23:34:10,073] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:34:10,073] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b27518/markers.fasta)
[2023-03-18 23:34:10,074] [INFO] Task started: Blastn
[2023-03-18 23:34:10,075] [INFO] Running command: blastn -query OceanDNA-b27518/markers.fasta -db /var/lib/cwl/stg32222449-1d8c-4816-b5a6-d0eddea9f89c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b27518/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:34:11,017] [INFO] Task succeeded: Blastn
[2023-03-18 23:34:11,019] [INFO] Selected 10 target genomes.
[2023-03-18 23:34:11,019] [INFO] Target genome list was writen to OceanDNA-b27518/target_genomes_gtdb.txt
[2023-03-18 23:34:11,028] [INFO] Task started: fastANI
[2023-03-18 23:34:11,028] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0d5da34-db2a-4152-b625-8c532b172e82/OceanDNA-b27518.fa --refList OceanDNA-b27518/target_genomes_gtdb.txt --output OceanDNA-b27518/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:34:18,994] [INFO] Task succeeded: fastANI
[2023-03-18 23:34:19,001] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 23:34:19,001] [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_011813015.1	s__Parasedimentitalea sp011813015	91.5296	724	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Parasedimentitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004006175.1	s__Parasedimentitalea marina	81.2027	548	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Parasedimentitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009753675.1	s__Parasedimentitalea huanghaiensis	80.9993	432	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Parasedimentitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013214575.1	s__Parasedimentitalea sp013214575	80.9588	568	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Parasedimentitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005771405.1	s__Parasedimentitalea marina_A	80.9289	426	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Parasedimentitalea	95.0	97.09	97.09	0.92	0.92	2	-
GCA_002162795.1	s__Parasedimentitalea sp002162795	79.9904	504	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Parasedimentitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002401945.1	s__Parasedimentitalea sp002401945	79.6694	415	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Parasedimentitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001457775.1	s__Pseudophaeobacter sp001457775	77.7936	210	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudophaeobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473205.1	s__Pseudophaeobacter arcticus	77.7612	228	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudophaeobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900313025.1	s__Pseudophaeobacter sp900313025	77.6018	237	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudophaeobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 23:34:19,001] [INFO] GTDB search result was written to OceanDNA-b27518/result_gtdb.tsv
[2023-03-18 23:34:19,001] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:34:19,003] [INFO] DFAST_QC result json was written to OceanDNA-b27518/dqc_result.json
[2023-03-18 23:34:19,003] [INFO] DFAST_QC completed!
[2023-03-18 23:34:19,003] [INFO] Total running time: 0h1m20s