[2023-03-15 13:58:53,792] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:58:53,792] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:58:53,792] [INFO] DQC Reference Directory: /var/lib/cwl/stg7d1c0692-10ab-4c6f-ad60-9dec5be3f0aa/dqc_reference
[2023-03-15 13:58:56,127] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:58:56,129] [INFO] Task started: Prodigal
[2023-03-15 13:58:56,129] [INFO] Running command: cat /var/lib/cwl/stga207633a-19fc-4a5a-995c-d9deb100fdbd/OceanDNA-b3716.fa | prodigal -d OceanDNA-b3716/cds.fna -a OceanDNA-b3716/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:59:18,107] [INFO] Task succeeded: Prodigal
[2023-03-15 13:59:18,108] [INFO] Task started: HMMsearch
[2023-03-15 13:59:18,108] [INFO] Running command: hmmsearch --tblout OceanDNA-b3716/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7d1c0692-10ab-4c6f-ad60-9dec5be3f0aa/dqc_reference/reference_markers.hmm OceanDNA-b3716/protein.faa > /dev/null
[2023-03-15 13:59:18,286] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:59:18,287] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga207633a-19fc-4a5a-995c-d9deb100fdbd/OceanDNA-b3716.fa]
[2023-03-15 13:59:18,310] [INFO] Query marker FASTA was written to OceanDNA-b3716/markers.fasta
[2023-03-15 13:59:18,311] [INFO] Task started: Blastn
[2023-03-15 13:59:18,311] [INFO] Running command: blastn -query OceanDNA-b3716/markers.fasta -db /var/lib/cwl/stg7d1c0692-10ab-4c6f-ad60-9dec5be3f0aa/dqc_reference/reference_markers.fasta -out OceanDNA-b3716/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:59:18,926] [INFO] Task succeeded: Blastn
[2023-03-15 13:59:18,929] [INFO] Selected 15 target genomes.
[2023-03-15 13:59:18,929] [INFO] Target genome list was writen to OceanDNA-b3716/target_genomes.txt
[2023-03-15 13:59:18,940] [INFO] Task started: fastANI
[2023-03-15 13:59:18,940] [INFO] Running command: fastANI --query /var/lib/cwl/stga207633a-19fc-4a5a-995c-d9deb100fdbd/OceanDNA-b3716.fa --refList OceanDNA-b3716/target_genomes.txt --output OceanDNA-b3716/fastani_result.tsv --threads 1
[2023-03-15 13:59:31,471] [INFO] Task succeeded: fastANI
[2023-03-15 13:59:31,471] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7d1c0692-10ab-4c6f-ad60-9dec5be3f0aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:59:31,471] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7d1c0692-10ab-4c6f-ad60-9dec5be3f0aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:59:31,479] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 13:59:31,479] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 13:59:31,479] [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 marina	strain=DSM 104084	GCA_011927705.1	438751	438751	type	True	78.3041	388	893	95	below_threshold
Neolewinella marina	strain=MKG-38	GCA_002631205.1	438751	438751	type	True	78.2942	384	893	95	below_threshold
Neolewinella maritima	strain=CECT 8419, type strain	GCA_923081025.1	1383882	1383882	type	True	77.4448	259	893	95	below_threshold
Neolewinella litorea	strain=HSMS-39	GCA_004803465.1	2562452	2562452	type	True	77.3871	253	893	95	below_threshold
Neolewinella lacunae	strain=KCTC 42187	GCA_014349155.1	1517758	1517758	type	True	77.1687	247	893	95	below_threshold
Neolewinella aquimaris	strain=DSM 105137	GCA_014197245.1	1835722	1835722	type	True	77.1424	235	893	95	below_threshold
Neolewinella xylanilytica	strain=DSM 29526	GCA_002934605.1	1514080	1514080	type	True	76.9944	209	893	95	below_threshold
Neolewinella aurantiaca	strain=SSH13	GCA_008014675.1	2602767	2602767	type	True	76.2274	96	893	95	below_threshold
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	75.4476	61	893	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	74.6963	62	893	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 13:59:31,482] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3716/tc_result.tsv
[2023-03-15 13:59:31,483] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:59:31,483] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:59:31,483] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7d1c0692-10ab-4c6f-ad60-9dec5be3f0aa/dqc_reference/checkm_data
[2023-03-15 13:59:31,484] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:59:31,556] [INFO] Task started: CheckM
[2023-03-15 13:59:31,556] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3716/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3716/checkm_input OceanDNA-b3716/checkm_result
[2023-03-15 14:00:25,325] [INFO] Task succeeded: CheckM
[2023-03-15 14:00:25,326] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 53.03%
Contamintation: 4.69%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 14:00:25,352] [INFO] ===== Completeness check finished =====
[2023-03-15 14:00:25,352] [INFO] ===== Start GTDB Search =====
[2023-03-15 14:00:25,352] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3716/markers.fasta)
[2023-03-15 14:00:25,353] [INFO] Task started: Blastn
[2023-03-15 14:00:25,353] [INFO] Running command: blastn -query OceanDNA-b3716/markers.fasta -db /var/lib/cwl/stg7d1c0692-10ab-4c6f-ad60-9dec5be3f0aa/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3716/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:00:26,410] [INFO] Task succeeded: Blastn
[2023-03-15 14:00:26,413] [INFO] Selected 10 target genomes.
[2023-03-15 14:00:26,413] [INFO] Target genome list was writen to OceanDNA-b3716/target_genomes_gtdb.txt
[2023-03-15 14:00:26,445] [INFO] Task started: fastANI
[2023-03-15 14:00:26,445] [INFO] Running command: fastANI --query /var/lib/cwl/stga207633a-19fc-4a5a-995c-d9deb100fdbd/OceanDNA-b3716.fa --refList OceanDNA-b3716/target_genomes_gtdb.txt --output OceanDNA-b3716/fastani_result_gtdb.tsv --threads 1
[2023-03-15 14:00:34,685] [INFO] Task succeeded: fastANI
[2023-03-15 14:00:34,690] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 14:00:34,690] [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_002631205.1	s__Lewinella_A marina	78.2902	384	893	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_003390915.1	s__Lewinella_A sp003390915	77.8397	327	893	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	77.3871	253	893	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	77.1687	247	893	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	77.1424	235	893	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	77.0981	196	893	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_002934605.1	s__Lewinella_A xylanilytica	77.0047	209	893	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	76.2274	96	893	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 14:00:34,690] [INFO] GTDB search result was written to OceanDNA-b3716/result_gtdb.tsv
[2023-03-15 14:00:34,690] [INFO] ===== GTDB Search completed =====
[2023-03-15 14:00:34,692] [INFO] DFAST_QC result json was written to OceanDNA-b3716/dqc_result.json
[2023-03-15 14:00:34,692] [INFO] DFAST_QC completed!
[2023-03-15 14:00:34,692] [INFO] Total running time: 0h1m41s