[2023-03-18 20:40:39,433] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:40:39,433] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:40:39,433] [INFO] DQC Reference Directory: /var/lib/cwl/stgabd5a418-75e0-4ed2-bbde-4c8d8f465094/dqc_reference
[2023-03-18 20:40:41,207] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:40:41,207] [INFO] Task started: Prodigal
[2023-03-18 20:40:41,207] [INFO] Running command: cat /var/lib/cwl/stg410ecd78-6b85-491b-855c-9c9d3f0f4e8b/OceanDNA-b3706.fa | prodigal -d OceanDNA-b3706/cds.fna -a OceanDNA-b3706/protein.faa -g 11 -q > /dev/null
[2023-03-18 20:41:08,886] [INFO] Task succeeded: Prodigal
[2023-03-18 20:41:08,886] [INFO] Task started: HMMsearch
[2023-03-18 20:41:08,886] [INFO] Running command: hmmsearch --tblout OceanDNA-b3706/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgabd5a418-75e0-4ed2-bbde-4c8d8f465094/dqc_reference/reference_markers.hmm OceanDNA-b3706/protein.faa > /dev/null
[2023-03-18 20:41:09,084] [INFO] Task succeeded: HMMsearch
[2023-03-18 20:41:09,085] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg410ecd78-6b85-491b-855c-9c9d3f0f4e8b/OceanDNA-b3706.fa]
[2023-03-18 20:41:09,108] [INFO] Query marker FASTA was written to OceanDNA-b3706/markers.fasta
[2023-03-18 20:41:09,108] [INFO] Task started: Blastn
[2023-03-18 20:41:09,108] [INFO] Running command: blastn -query OceanDNA-b3706/markers.fasta -db /var/lib/cwl/stgabd5a418-75e0-4ed2-bbde-4c8d8f465094/dqc_reference/reference_markers.fasta -out OceanDNA-b3706/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:41:09,685] [INFO] Task succeeded: Blastn
[2023-03-18 20:41:09,686] [INFO] Selected 12 target genomes.
[2023-03-18 20:41:09,686] [INFO] Target genome list was writen to OceanDNA-b3706/target_genomes.txt
[2023-03-18 20:41:09,693] [INFO] Task started: fastANI
[2023-03-18 20:41:09,693] [INFO] Running command: fastANI --query /var/lib/cwl/stg410ecd78-6b85-491b-855c-9c9d3f0f4e8b/OceanDNA-b3706.fa --refList OceanDNA-b3706/target_genomes.txt --output OceanDNA-b3706/fastani_result.tsv --threads 1
[2023-03-18 20:41:20,161] [INFO] Task succeeded: fastANI
[2023-03-18 20:41:20,162] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgabd5a418-75e0-4ed2-bbde-4c8d8f465094/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 20:41:20,162] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgabd5a418-75e0-4ed2-bbde-4c8d8f465094/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 20:41:20,169] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 20:41:20,169] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 20:41:20,169] [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
Neolewinella lacunae	strain=KCTC 42187	GCA_014349155.1	1517758	1517758	type	True	76.919	294	1171	95	below_threshold
Neolewinella aurantiaca	strain=SSH13	GCA_008014675.1	2602767	2602767	type	True	76.9028	224	1171	95	below_threshold
Neolewinella antarctica	strain=DSM 105096	GCA_011927835.1	442734	442734	type	True	76.818	231	1171	95	below_threshold
Neolewinella marina	strain=DSM 104084	GCA_011927705.1	438751	438751	type	True	76.7297	243	1171	95	below_threshold
Neolewinella marina	strain=MKG-38	GCA_002631205.1	438751	438751	type	True	76.7102	247	1171	95	below_threshold
Neolewinella persica	strain=DSM 23188	GCA_000373105.1	70998	70998	type	True	76.6548	214	1171	95	below_threshold
Neolewinella agarilytica	strain=DSM 24740	GCA_900110645.1	478744	478744	type	True	76.6108	221	1171	95	below_threshold
Neolewinella litorea	strain=HSMS-39	GCA_004803465.1	2562452	2562452	type	True	76.5289	185	1171	95	below_threshold
Neolewinella maritima	strain=CECT 8419, type strain	GCA_923081025.1	1383882	1383882	type	True	76.4199	170	1171	95	below_threshold
Neolewinella xylanilytica	strain=DSM 29526	GCA_002934605.1	1514080	1514080	type	True	76.3162	167	1171	95	below_threshold
Neolewinella aquimaris	strain=DSM 105137	GCA_014197245.1	1835722	1835722	type	True	76.193	180	1171	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 20:41:20,169] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3706/tc_result.tsv
[2023-03-18 20:41:20,169] [INFO] ===== Taxonomy check completed =====
[2023-03-18 20:41:20,169] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 20:41:20,170] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgabd5a418-75e0-4ed2-bbde-4c8d8f465094/dqc_reference/checkm_data
[2023-03-18 20:41:20,170] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 20:41:20,175] [INFO] Task started: CheckM
[2023-03-18 20:41:20,175] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3706/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3706/checkm_input OceanDNA-b3706/checkm_result
[2023-03-18 20:42:27,131] [INFO] Task succeeded: CheckM
[2023-03-18 20:42:27,131] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 20:42:27,134] [INFO] ===== Completeness check finished =====
[2023-03-18 20:42:27,134] [INFO] ===== Start GTDB Search =====
[2023-03-18 20:42:27,134] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3706/markers.fasta)
[2023-03-18 20:42:27,134] [INFO] Task started: Blastn
[2023-03-18 20:42:27,134] [INFO] Running command: blastn -query OceanDNA-b3706/markers.fasta -db /var/lib/cwl/stgabd5a418-75e0-4ed2-bbde-4c8d8f465094/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3706/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:42:28,065] [INFO] Task succeeded: Blastn
[2023-03-18 20:42:28,065] [INFO] Selected 13 target genomes.
[2023-03-18 20:42:28,065] [INFO] Target genome list was writen to OceanDNA-b3706/target_genomes_gtdb.txt
[2023-03-18 20:42:28,102] [INFO] Task started: fastANI
[2023-03-18 20:42:28,102] [INFO] Running command: fastANI --query /var/lib/cwl/stg410ecd78-6b85-491b-855c-9c9d3f0f4e8b/OceanDNA-b3706.fa --refList OceanDNA-b3706/target_genomes_gtdb.txt --output OceanDNA-b3706/fastani_result_gtdb.tsv --threads 1
[2023-03-18 20:42:39,391] [INFO] Task succeeded: fastANI
[2023-03-18 20:42:39,399] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 20:42:39,399] [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_001625015.1	s__Lewinella_A sp001625015	76.9728	238	1171	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014349155.1	s__Lewinella_A lacunae	76.91	294	1171	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008014675.1	s__Lewinella_A aurantiaca	76.9043	225	1171	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011927835.1	s__Lewinella_A antarctica	76.818	231	1171	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004375085.3	s__Lewinella_A sp004375085	76.7216	205	1171	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002631205.1	s__Lewinella_A marina	76.7009	248	1171	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000373105.1	s__Lewinella_A persica	76.6549	214	1171	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110645.1	s__Lewinella_A agarilytica	76.6007	222	1171	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004803465.1	s__Lewinella_A litorea	76.5289	185	1171	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003390915.1	s__Lewinella_A sp003390915	76.4717	230	1171	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003390935.1	s__Lewinella_A sp003390935	76.3915	156	1171	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197245.1	s__Lewinella_A aquimaris	76.203	179	1171	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 20:42:39,399] [INFO] GTDB search result was written to OceanDNA-b3706/result_gtdb.tsv
[2023-03-18 20:42:39,399] [INFO] ===== GTDB Search completed =====
[2023-03-18 20:42:39,401] [INFO] DFAST_QC result json was written to OceanDNA-b3706/dqc_result.json
[2023-03-18 20:42:39,401] [INFO] DFAST_QC completed!
[2023-03-18 20:42:39,401] [INFO] Total running time: 0h1m60s