[2023-03-17 10:35:02,806] [INFO] DFAST_QC pipeline started.
[2023-03-17 10:35:02,806] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 10:35:02,806] [INFO] DQC Reference Directory: /var/lib/cwl/stgada6a9ac-b8f7-4379-a004-66f4a8dbcfa1/dqc_reference
[2023-03-17 10:35:04,553] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 10:35:04,554] [INFO] Task started: Prodigal
[2023-03-17 10:35:04,554] [INFO] Running command: cat /var/lib/cwl/stgbbcc0bb6-6136-4785-b366-0c93db5f601f/OceanDNA-b6665.fa | prodigal -d OceanDNA-b6665/cds.fna -a OceanDNA-b6665/protein.faa -g 11 -q > /dev/null
[2023-03-17 10:35:20,960] [INFO] Task succeeded: Prodigal
[2023-03-17 10:35:20,960] [INFO] Task started: HMMsearch
[2023-03-17 10:35:20,960] [INFO] Running command: hmmsearch --tblout OceanDNA-b6665/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgada6a9ac-b8f7-4379-a004-66f4a8dbcfa1/dqc_reference/reference_markers.hmm OceanDNA-b6665/protein.faa > /dev/null
[2023-03-17 10:35:21,156] [INFO] Task succeeded: HMMsearch
[2023-03-17 10:35:21,157] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgbbcc0bb6-6136-4785-b366-0c93db5f601f/OceanDNA-b6665.fa]
[2023-03-17 10:35:21,175] [INFO] Query marker FASTA was written to OceanDNA-b6665/markers.fasta
[2023-03-17 10:35:21,176] [INFO] Task started: Blastn
[2023-03-17 10:35:21,176] [INFO] Running command: blastn -query OceanDNA-b6665/markers.fasta -db /var/lib/cwl/stgada6a9ac-b8f7-4379-a004-66f4a8dbcfa1/dqc_reference/reference_markers.fasta -out OceanDNA-b6665/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:35:21,750] [INFO] Task succeeded: Blastn
[2023-03-17 10:35:21,751] [INFO] Selected 16 target genomes.
[2023-03-17 10:35:21,751] [INFO] Target genome list was writen to OceanDNA-b6665/target_genomes.txt
[2023-03-17 10:35:21,759] [INFO] Task started: fastANI
[2023-03-17 10:35:21,759] [INFO] Running command: fastANI --query /var/lib/cwl/stgbbcc0bb6-6136-4785-b366-0c93db5f601f/OceanDNA-b6665.fa --refList OceanDNA-b6665/target_genomes.txt --output OceanDNA-b6665/fastani_result.tsv --threads 1
[2023-03-17 10:35:32,901] [INFO] Task succeeded: fastANI
[2023-03-17 10:35:32,901] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgada6a9ac-b8f7-4379-a004-66f4a8dbcfa1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 10:35:32,901] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgada6a9ac-b8f7-4379-a004-66f4a8dbcfa1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 10:35:32,911] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 10:35:32,911] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 10:35:32,911] [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 tyrosinoxydans	strain=DSM 21164	GCA_900176415.1	504486	504486	type	True	78.8097	459	903	95	below_threshold
Cellulophaga algicola	strain=DSM 14237	GCA_000186265.1	59600	59600	type	True	78.6132	391	903	95	below_threshold
Cellulophaga baltica	strain=DSM 24729	GCA_900102165.1	76594	76594	type	True	78.3714	387	903	95	below_threshold
Maribacter vaceletii	strain=DSM 25230	GCA_003634105.1	1206816	1206816	type	True	77.1684	258	903	95	below_threshold
Cellulophaga omnivescoria	strain=W5C	GCA_001999725.1	1888890	1888890	type	True	76.9927	213	903	95	below_threshold
Cellulophaga fucicola	strain=DSM 24786	GCA_900119145.1	76595	76595	type	True	76.9924	211	903	95	below_threshold
Maribacter caenipelagi	strain=CECT 8455	GCA_004364175.1	1447781	1447781	type	True	76.5285	159	903	95	below_threshold
Maribacter hydrothermalis	strain=T28	GCA_001673755.1	1836467	1836467	type	True	76.5119	190	903	95	below_threshold
Maribacter hydrothermalis	strain=T28	GCA_001913155.1	1836467	1836467	type	True	76.4976	190	903	95	below_threshold
Maribacter algarum	strain=RZ26	GCA_005885635.1	2578118	2578118	type	True	76.2051	112	903	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	76.1824	76	903	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	75.857	123	903	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	75.7805	82	903	95	below_threshold
Aquimarina algicola	strain=M625	GCA_006443095.1	2589995	2589995	type	True	75.7219	89	903	95	below_threshold
Abyssalbus ytuae	strain=MT3330	GCA_022807975.1	2926907	2926907	type	True	75.7007	54	903	95	below_threshold
Maribacter luteus	strain=RZ05	GCA_009674825.1	2594478	2594478	type	True	75.5786	83	903	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 10:35:32,911] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6665/tc_result.tsv
[2023-03-17 10:35:32,911] [INFO] ===== Taxonomy check completed =====
[2023-03-17 10:35:32,911] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 10:35:32,912] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgada6a9ac-b8f7-4379-a004-66f4a8dbcfa1/dqc_reference/checkm_data
[2023-03-17 10:35:32,912] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 10:35:32,916] [INFO] Task started: CheckM
[2023-03-17 10:35:32,917] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6665/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6665/checkm_input OceanDNA-b6665/checkm_result
[2023-03-17 10:36:15,630] [INFO] Task succeeded: CheckM
[2023-03-17 10:36:15,631] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.31%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 10:36:15,633] [INFO] ===== Completeness check finished =====
[2023-03-17 10:36:15,633] [INFO] ===== Start GTDB Search =====
[2023-03-17 10:36:15,633] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6665/markers.fasta)
[2023-03-17 10:36:15,634] [INFO] Task started: Blastn
[2023-03-17 10:36:15,635] [INFO] Running command: blastn -query OceanDNA-b6665/markers.fasta -db /var/lib/cwl/stgada6a9ac-b8f7-4379-a004-66f4a8dbcfa1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6665/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:36:16,782] [INFO] Task succeeded: Blastn
[2023-03-17 10:36:16,783] [INFO] Selected 14 target genomes.
[2023-03-17 10:36:16,783] [INFO] Target genome list was writen to OceanDNA-b6665/target_genomes_gtdb.txt
[2023-03-17 10:36:16,981] [INFO] Task started: fastANI
[2023-03-17 10:36:16,982] [INFO] Running command: fastANI --query /var/lib/cwl/stgbbcc0bb6-6136-4785-b366-0c93db5f601f/OceanDNA-b6665.fa --refList OceanDNA-b6665/target_genomes_gtdb.txt --output OceanDNA-b6665/fastani_result_gtdb.tsv --threads 1
[2023-03-17 10:36:26,815] [INFO] Task succeeded: fastANI
[2023-03-17 10:36:26,823] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 10:36:26,823] [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_019021925.1	s__Cellulophaga sp019021925	79.0059	436	903	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	78.8181	458	903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000186265.1	s__Cellulophaga algicola	78.6071	392	903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	98.35	98.34	0.88	0.87	3	-
GCF_009797025.1	s__Cellulophaga sp009797025	78.4955	397	903	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	78.3714	387	903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	97.62	97.40	0.90	0.89	7	-
GCF_018861125.1	s__Cellulophaga baltica_A	78.3671	394	903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000799565.1	s__Cellulophaga sp000799565	77.5945	321	903	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	76.9927	213	903	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	76.7438	218	903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001913155.1	s__Maribacter hydrothermalis	76.4976	190	903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009649685.1	s__Aurantibacter_A sp009649685	76.4934	169	903	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_005047595.1	s__CAU-1491 sp005047595	76.1824	76	903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__CAU-1491	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006443095.1	s__Aquimarina sp006443095	75.7219	89	903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009674825.1	s__Maribacter_A luteus	75.5786	83	903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 10:36:26,824] [INFO] GTDB search result was written to OceanDNA-b6665/result_gtdb.tsv
[2023-03-17 10:36:26,824] [INFO] ===== GTDB Search completed =====
[2023-03-17 10:36:26,825] [INFO] DFAST_QC result json was written to OceanDNA-b6665/dqc_result.json
[2023-03-17 10:36:26,825] [INFO] DFAST_QC completed!
[2023-03-17 10:36:26,826] [INFO] Total running time: 0h1m24s