[2023-03-15 14:29:06,012] [INFO] DFAST_QC pipeline started.
[2023-03-15 14:29:06,012] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 14:29:06,012] [INFO] DQC Reference Directory: /var/lib/cwl/stg4e5da098-8684-42e5-831a-85b3b03f53c3/dqc_reference
[2023-03-15 14:29:07,112] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 14:29:07,112] [INFO] Task started: Prodigal
[2023-03-15 14:29:07,113] [INFO] Running command: cat /var/lib/cwl/stg4c045065-22cc-4138-bc70-bd3f3b37bd25/OceanDNA-b9726.fa | prodigal -d OceanDNA-b9726/cds.fna -a OceanDNA-b9726/protein.faa -g 11 -q > /dev/null
[2023-03-15 14:29:18,335] [INFO] Task succeeded: Prodigal
[2023-03-15 14:29:18,336] [INFO] Task started: HMMsearch
[2023-03-15 14:29:18,336] [INFO] Running command: hmmsearch --tblout OceanDNA-b9726/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4e5da098-8684-42e5-831a-85b3b03f53c3/dqc_reference/reference_markers.hmm OceanDNA-b9726/protein.faa > /dev/null
[2023-03-15 14:29:18,506] [INFO] Task succeeded: HMMsearch
[2023-03-15 14:29:18,506] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4c045065-22cc-4138-bc70-bd3f3b37bd25/OceanDNA-b9726.fa]
[2023-03-15 14:29:18,523] [INFO] Query marker FASTA was written to OceanDNA-b9726/markers.fasta
[2023-03-15 14:29:18,525] [INFO] Task started: Blastn
[2023-03-15 14:29:18,525] [INFO] Running command: blastn -query OceanDNA-b9726/markers.fasta -db /var/lib/cwl/stg4e5da098-8684-42e5-831a-85b3b03f53c3/dqc_reference/reference_markers.fasta -out OceanDNA-b9726/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:29:19,066] [INFO] Task succeeded: Blastn
[2023-03-15 14:29:19,067] [INFO] Selected 16 target genomes.
[2023-03-15 14:29:19,067] [INFO] Target genome list was writen to OceanDNA-b9726/target_genomes.txt
[2023-03-15 14:29:19,075] [INFO] Task started: fastANI
[2023-03-15 14:29:19,075] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c045065-22cc-4138-bc70-bd3f3b37bd25/OceanDNA-b9726.fa --refList OceanDNA-b9726/target_genomes.txt --output OceanDNA-b9726/fastani_result.tsv --threads 1
[2023-03-15 14:29:28,417] [INFO] Task succeeded: fastANI
[2023-03-15 14:29:28,418] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4e5da098-8684-42e5-831a-85b3b03f53c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 14:29:28,418] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4e5da098-8684-42e5-831a-85b3b03f53c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 14:29:28,426] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2023-03-15 14:29:28,426] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-15 14:29:28,426] [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
Mesonia algae	strain=DSM 15361	GCA_003253545.1	213248	213248	type	True	95.0406	489	553	95	conclusive
Mesonia oceanica	strain=ISS653	GCA_902499555.1	2687242	2687242	type	True	77.9185	169	553	95	below_threshold
Mesonia phycicola	strain=DSM 21425	GCA_900141885.1	579105	579105	type	True	77.6428	203	553	95	below_threshold
Mesonia mobilis	strain=KCTC 12708	GCA_014651475.1	369791	369791	type	True	77.385	180	553	95	below_threshold
Mesonia mobilis	strain=DSM 19841	GCA_000423405.1	369791	369791	type	True	77.3665	182	553	95	below_threshold
Zunongwangia atlantica	strain=22II14-10F7	GCA_002094855.1	1502297	1502297	type	True	76.6585	77	553	95	below_threshold
Zunongwangia mangrovi	strain=DSM 24499	GCA_900112105.1	1334022	1334022	type	True	76.4773	75	553	95	below_threshold
Joostella marina	strain=DSM 19592	GCA_000260115.1	453852	453852	type	True	76.3898	55	553	95	below_threshold
Bizionia algoritergicola	strain=APA-1	GCA_008086165.1	291187	291187	type	True	76.2626	52	553	95	below_threshold
Aurantibacter aestuarii	strain=KCTC 32269	GCA_003008425.1	1266046	1266046	type	True	76.1504	54	553	95	below_threshold
Salegentibacter holothuriorum	strain=DSM 23405	GCA_900168045.1	241145	241145	type	True	76.1304	66	553	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	75.471	57	553	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 14:29:28,427] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9726/tc_result.tsv
[2023-03-15 14:29:28,427] [INFO] ===== Taxonomy check completed =====
[2023-03-15 14:29:28,427] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 14:29:28,427] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4e5da098-8684-42e5-831a-85b3b03f53c3/dqc_reference/checkm_data
[2023-03-15 14:29:28,428] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 14:29:28,431] [INFO] Task started: CheckM
[2023-03-15 14:29:28,431] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9726/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9726/checkm_input OceanDNA-b9726/checkm_result
[2023-03-15 14:30:00,226] [INFO] Task succeeded: CheckM
[2023-03-15 14:30:00,227] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.98%
Contamintation: 4.55%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 14:30:00,269] [INFO] ===== Completeness check finished =====
[2023-03-15 14:30:00,269] [INFO] ===== Start GTDB Search =====
[2023-03-15 14:30:00,269] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9726/markers.fasta)
[2023-03-15 14:30:00,269] [INFO] Task started: Blastn
[2023-03-15 14:30:00,269] [INFO] Running command: blastn -query OceanDNA-b9726/markers.fasta -db /var/lib/cwl/stg4e5da098-8684-42e5-831a-85b3b03f53c3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9726/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:30:00,947] [INFO] Task succeeded: Blastn
[2023-03-15 14:30:00,948] [INFO] Selected 15 target genomes.
[2023-03-15 14:30:00,948] [INFO] Target genome list was writen to OceanDNA-b9726/target_genomes_gtdb.txt
[2023-03-15 14:30:00,971] [INFO] Task started: fastANI
[2023-03-15 14:30:00,971] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c045065-22cc-4138-bc70-bd3f3b37bd25/OceanDNA-b9726.fa --refList OceanDNA-b9726/target_genomes_gtdb.txt --output OceanDNA-b9726/fastani_result_gtdb.tsv --threads 1
[2023-03-15 14:30:09,701] [INFO] Task succeeded: fastANI
[2023-03-15 14:30:09,707] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 14:30:09,707] [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_003253545.1	s__Mesonia algae	95.0406	489	553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	95.16	95.16	0.83	0.83	2	conclusive
GCF_902499555.1	s__Mesonia oceanica	77.9185	169	553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	99.91	99.87	0.96	0.92	8	-
GCF_900141885.1	s__Mesonia phycicola	77.6417	203	553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003667275.1	s__Mesonia aquimarina	77.5999	160	553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423405.1	s__Mesonia mobilis	77.3665	182	553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	99.98	99.98	0.99	0.99	2	-
GCA_012964435.1	s__Mesonia sp012964435	77.1904	152	553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	99.98	99.98	0.99	0.99	2	-
GCF_008692195.1	s__Mesonia sp008692195	76.8755	158	553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002094855.1	s__Zunongwangia atlantica	76.6585	77	553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zunongwangia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015319355.1	s__Psychroserpens luteus	75.8258	61	553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 14:30:09,707] [INFO] GTDB search result was written to OceanDNA-b9726/result_gtdb.tsv
[2023-03-15 14:30:09,707] [INFO] ===== GTDB Search completed =====
[2023-03-15 14:30:09,709] [INFO] DFAST_QC result json was written to OceanDNA-b9726/dqc_result.json
[2023-03-15 14:30:09,709] [INFO] DFAST_QC completed!
[2023-03-15 14:30:09,709] [INFO] Total running time: 0h1m4s