[2023-03-15 13:55:04,050] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:55:04,052] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:55:04,052] [INFO] DQC Reference Directory: /var/lib/cwl/stgf6ad6074-93d9-4ab5-a8ae-263846d6f33b/dqc_reference
[2023-03-15 13:55:05,147] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:55:05,148] [INFO] Task started: Prodigal
[2023-03-15 13:55:05,148] [INFO] Running command: cat /var/lib/cwl/stgd05787e9-783f-483e-8cc2-785e175d3326/OceanDNA-b6745.fa | prodigal -d OceanDNA-b6745/cds.fna -a OceanDNA-b6745/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:55:23,454] [INFO] Task succeeded: Prodigal
[2023-03-15 13:55:23,455] [INFO] Task started: HMMsearch
[2023-03-15 13:55:23,455] [INFO] Running command: hmmsearch --tblout OceanDNA-b6745/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf6ad6074-93d9-4ab5-a8ae-263846d6f33b/dqc_reference/reference_markers.hmm OceanDNA-b6745/protein.faa > /dev/null
[2023-03-15 13:55:23,619] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:55:23,619] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgd05787e9-783f-483e-8cc2-785e175d3326/OceanDNA-b6745.fa]
[2023-03-15 13:55:23,643] [INFO] Query marker FASTA was written to OceanDNA-b6745/markers.fasta
[2023-03-15 13:55:23,644] [INFO] Task started: Blastn
[2023-03-15 13:55:23,644] [INFO] Running command: blastn -query OceanDNA-b6745/markers.fasta -db /var/lib/cwl/stgf6ad6074-93d9-4ab5-a8ae-263846d6f33b/dqc_reference/reference_markers.fasta -out OceanDNA-b6745/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:55:24,281] [INFO] Task succeeded: Blastn
[2023-03-15 13:55:24,283] [INFO] Selected 10 target genomes.
[2023-03-15 13:55:24,283] [INFO] Target genome list was writen to OceanDNA-b6745/target_genomes.txt
[2023-03-15 13:55:24,287] [INFO] Task started: fastANI
[2023-03-15 13:55:24,288] [INFO] Running command: fastANI --query /var/lib/cwl/stgd05787e9-783f-483e-8cc2-785e175d3326/OceanDNA-b6745.fa --refList OceanDNA-b6745/target_genomes.txt --output OceanDNA-b6745/fastani_result.tsv --threads 1
[2023-03-15 13:55:30,198] [INFO] Task succeeded: fastANI
[2023-03-15 13:55:30,199] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf6ad6074-93d9-4ab5-a8ae-263846d6f33b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:55:30,199] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf6ad6074-93d9-4ab5-a8ae-263846d6f33b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:55:30,205] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 13:55:30,205] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 13:55:30,205] [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
Dokdonia donghaensis	strain=DSW-1	GCA_000769435.1	326320	326320	type	True	81.5836	516	956	95	below_threshold
Dokdonia donghaensis	strain=DSW-1	GCA_001653755.1	326320	326320	type	True	81.5247	509	956	95	below_threshold
Dokdonia sinensis	strain=SH27	GCA_003688895.1	2479847	2479847	type	True	77.4492	215	956	95	below_threshold
Dokdonia pacifica	strain=DSM 25597	GCA_900188275.1	1627892	1627892	type	True	77.2103	213	956	95	below_threshold
Dokdonia pacifica	strain=CGMCC 1.12184	GCA_014636685.1	1627892	1627892	type	True	77.1777	214	956	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	76.2661	62	956	95	below_threshold
Halomarinibacterium sedimenti	strain=CAU 1614	GCA_019312585.1	2857106	2857106	type	True	76.1828	51	956	95	below_threshold
Maribacter stanieri	strain=DSM 19891	GCA_900112245.1	440514	440514	type	True	76.0704	60	956	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 13:55:30,207] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6745/tc_result.tsv
[2023-03-15 13:55:30,207] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:55:30,207] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:55:30,207] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf6ad6074-93d9-4ab5-a8ae-263846d6f33b/dqc_reference/checkm_data
[2023-03-15 13:55:30,208] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:55:30,385] [INFO] Task started: CheckM
[2023-03-15 13:55:30,385] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6745/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6745/checkm_input OceanDNA-b6745/checkm_result
[2023-03-15 13:56:17,357] [INFO] Task succeeded: CheckM
[2023-03-15 13:56:17,358] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 8.33%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-15 13:56:17,360] [INFO] ===== Completeness check finished =====
[2023-03-15 13:56:17,360] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:56:17,360] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6745/markers.fasta)
[2023-03-15 13:56:17,361] [INFO] Task started: Blastn
[2023-03-15 13:56:17,361] [INFO] Running command: blastn -query OceanDNA-b6745/markers.fasta -db /var/lib/cwl/stgf6ad6074-93d9-4ab5-a8ae-263846d6f33b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6745/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:56:18,193] [INFO] Task succeeded: Blastn
[2023-03-15 13:56:18,194] [INFO] Selected 7 target genomes.
[2023-03-15 13:56:18,194] [INFO] Target genome list was writen to OceanDNA-b6745/target_genomes_gtdb.txt
[2023-03-15 13:56:18,202] [INFO] Task started: fastANI
[2023-03-15 13:56:18,202] [INFO] Running command: fastANI --query /var/lib/cwl/stgd05787e9-783f-483e-8cc2-785e175d3326/OceanDNA-b6745.fa --refList OceanDNA-b6745/target_genomes_gtdb.txt --output OceanDNA-b6745/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:56:22,940] [INFO] Task succeeded: fastANI
[2023-03-15 13:56:22,945] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 13:56:22,945] [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_000212355.1	s__Dokdonia sp000212355	93.5168	808	956	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	98.49	98.49	0.97	0.97	2	-
GCF_003095655.1	s__Dokdonia sp003095655	92.8384	825	956	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000355805.1	s__Dokdonia sp000355805	91.1154	806	956	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001653755.1	s__Dokdonia donghaensis	81.511	510	956	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	97.85	95.71	0.96	0.91	3	-
GCF_007827465.1	s__Dokdonia sp007827465	78.7913	274	956	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003688895.1	s__Dokdonia sinensis	77.4593	214	956	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143755.1	s__Algibacter_B sp003143755	76.2689	55	956	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 13:56:22,945] [INFO] GTDB search result was written to OceanDNA-b6745/result_gtdb.tsv
[2023-03-15 13:56:22,946] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:56:22,947] [INFO] DFAST_QC result json was written to OceanDNA-b6745/dqc_result.json
[2023-03-15 13:56:22,947] [INFO] DFAST_QC completed!
[2023-03-15 13:56:22,947] [INFO] Total running time: 0h1m19s