[2023-03-17 05:26:45,798] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:26:45,800] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:26:45,801] [INFO] DQC Reference Directory: /var/lib/cwl/stg4f207250-34df-4423-8e83-a46a866dacf7/dqc_reference
[2023-03-17 05:26:46,920] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:26:46,921] [INFO] Task started: Prodigal
[2023-03-17 05:26:46,921] [INFO] Running command: cat /var/lib/cwl/stg3c3889b5-b3a6-490c-9107-f933b9131009/OceanDNA-b7503.fa | prodigal -d OceanDNA-b7503/cds.fna -a OceanDNA-b7503/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:27:12,984] [INFO] Task succeeded: Prodigal
[2023-03-17 05:27:12,984] [INFO] Task started: HMMsearch
[2023-03-17 05:27:12,984] [INFO] Running command: hmmsearch --tblout OceanDNA-b7503/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4f207250-34df-4423-8e83-a46a866dacf7/dqc_reference/reference_markers.hmm OceanDNA-b7503/protein.faa > /dev/null
[2023-03-17 05:27:13,209] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:27:13,209] [INFO] Found 6/6 markers.
[2023-03-17 05:27:13,233] [INFO] Query marker FASTA was written to OceanDNA-b7503/markers.fasta
[2023-03-17 05:27:13,234] [INFO] Task started: Blastn
[2023-03-17 05:27:13,235] [INFO] Running command: blastn -query OceanDNA-b7503/markers.fasta -db /var/lib/cwl/stg4f207250-34df-4423-8e83-a46a866dacf7/dqc_reference/reference_markers.fasta -out OceanDNA-b7503/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:27:13,830] [INFO] Task succeeded: Blastn
[2023-03-17 05:27:13,831] [INFO] Selected 9 target genomes.
[2023-03-17 05:27:13,831] [INFO] Target genome list was writen to OceanDNA-b7503/target_genomes.txt
[2023-03-17 05:27:13,836] [INFO] Task started: fastANI
[2023-03-17 05:27:13,836] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c3889b5-b3a6-490c-9107-f933b9131009/OceanDNA-b7503.fa --refList OceanDNA-b7503/target_genomes.txt --output OceanDNA-b7503/fastani_result.tsv --threads 1
[2023-03-17 05:27:22,137] [INFO] Task succeeded: fastANI
[2023-03-17 05:27:22,138] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4f207250-34df-4423-8e83-a46a866dacf7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:27:22,138] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4f207250-34df-4423-8e83-a46a866dacf7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:27:22,144] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2023-03-17 05:27:22,144] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-17 05:27:22,144] [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
Leeuwenhoekiella blandensis	strain=MED217	GCA_000152985.1	360293	360293	type	True	97.835	1162	1264	95	conclusive
Leeuwenhoekiella palythoae	strain=LMG 24856	GCA_004104045.1	573501	573501	type	True	85.2249	891	1264	95	below_threshold
Leeuwenhoekiella palythoae	strain=DSM 19859	GCA_900130045.1	573501	573501	type	True	85.1945	889	1264	95	below_threshold
Leeuwenhoekiella marinoflava	strain=DSM 3653	GCA_900129005.1	988	988	type	True	79.9465	687	1264	95	below_threshold
Leeuwenhoekiella marinoflava	strain=LMG 1345	GCA_004104035.1	988	988	type	True	79.946	688	1264	95	below_threshold
Leeuwenhoekiella aestuarii	strain=R-48165	GCA_004104055.1	2249426	2249426	type	True	79.9317	664	1264	95	below_threshold
Zobellia barbeyronii	strain=KMM 6746	GCA_018603515.1	2748009	2748009	type	True	75.9677	74	1264	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 05:27:22,145] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7503/tc_result.tsv
[2023-03-17 05:27:22,145] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:27:22,145] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:27:22,145] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4f207250-34df-4423-8e83-a46a866dacf7/dqc_reference/checkm_data
[2023-03-17 05:27:22,146] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:27:22,158] [INFO] Task started: CheckM
[2023-03-17 05:27:22,158] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7503/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7503/checkm_input OceanDNA-b7503/checkm_result
[2023-03-17 05:28:27,200] [INFO] Task succeeded: CheckM
[2023-03-17 05:28:27,200] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 05:28:27,236] [INFO] ===== Completeness check finished =====
[2023-03-17 05:28:27,236] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:28:27,236] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7503/markers.fasta)
[2023-03-17 05:28:27,237] [INFO] Task started: Blastn
[2023-03-17 05:28:27,237] [INFO] Running command: blastn -query OceanDNA-b7503/markers.fasta -db /var/lib/cwl/stg4f207250-34df-4423-8e83-a46a866dacf7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7503/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:28:28,107] [INFO] Task succeeded: Blastn
[2023-03-17 05:28:28,108] [INFO] Selected 9 target genomes.
[2023-03-17 05:28:28,108] [INFO] Target genome list was writen to OceanDNA-b7503/target_genomes_gtdb.txt
[2023-03-17 05:28:28,263] [INFO] Task started: fastANI
[2023-03-17 05:28:28,263] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c3889b5-b3a6-490c-9107-f933b9131009/OceanDNA-b7503.fa --refList OceanDNA-b7503/target_genomes_gtdb.txt --output OceanDNA-b7503/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:28:35,954] [INFO] Task succeeded: fastANI
[2023-03-17 05:28:35,960] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 05:28:35,960] [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_000152985.1	s__Leeuwenhoekiella blandensis	97.8551	1161	1264	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	97.86	97.58	0.89	0.73	11	conclusive
GCF_900130045.1	s__Leeuwenhoekiella palythoae	85.1874	890	1264	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	96.69	96.09	0.92	0.86	9	-
GCF_004104075.1	s__Leeuwenhoekiella polynyae	79.9913	685	1264	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129005.1	s__Leeuwenhoekiella marinoflava	79.9454	688	1264	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	99.99	99.99	0.99	0.99	2	-
GCF_004104055.1	s__Leeuwenhoekiella aestuarii	79.9354	664	1264	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	99.75	99.75	0.97	0.97	2	-
GCF_002744755.1	s__Leeuwenhoekiella nanhaiensis	79.229	465	1264	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	96.22	96.22	0.78	0.78	2	-
GCF_000687915.1	s__Leeuwenhoekiella sp000687915	78.5023	470	1264	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002708845.1	s__Leeuwenhoekiella sp002708845	78.4302	449	1264	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	99.96	99.95	0.93	0.90	5	-
GCF_003337215.1	s__Oceanihabitans sediminis	76.0319	75	1264	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-17 05:28:35,960] [INFO] GTDB search result was written to OceanDNA-b7503/result_gtdb.tsv
[2023-03-17 05:28:35,961] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:28:35,962] [INFO] DFAST_QC result json was written to OceanDNA-b7503/dqc_result.json
[2023-03-17 05:28:35,962] [INFO] DFAST_QC completed!
[2023-03-17 05:28:35,962] [INFO] Total running time: 0h1m50s