[2023-03-15 22:15:27,639] [INFO] DFAST_QC pipeline started.
[2023-03-15 22:15:27,639] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 22:15:27,640] [INFO] DQC Reference Directory: /var/lib/cwl/stgaa957ee5-0f57-4a8d-93da-aac38b4ebdd9/dqc_reference
[2023-03-15 22:15:29,360] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 22:15:29,361] [INFO] Task started: Prodigal
[2023-03-15 22:15:29,361] [INFO] Running command: cat /var/lib/cwl/stgbdef7088-665c-4cc0-8788-4308e87ff668/OceanDNA-b6427.fa | prodigal -d OceanDNA-b6427/cds.fna -a OceanDNA-b6427/protein.faa -g 11 -q > /dev/null
[2023-03-15 22:15:44,348] [INFO] Task succeeded: Prodigal
[2023-03-15 22:15:44,348] [INFO] Task started: HMMsearch
[2023-03-15 22:15:44,349] [INFO] Running command: hmmsearch --tblout OceanDNA-b6427/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaa957ee5-0f57-4a8d-93da-aac38b4ebdd9/dqc_reference/reference_markers.hmm OceanDNA-b6427/protein.faa > /dev/null
[2023-03-15 22:15:44,528] [INFO] Task succeeded: HMMsearch
[2023-03-15 22:15:44,529] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgbdef7088-665c-4cc0-8788-4308e87ff668/OceanDNA-b6427.fa]
[2023-03-15 22:15:44,566] [INFO] Query marker FASTA was written to OceanDNA-b6427/markers.fasta
[2023-03-15 22:15:44,567] [INFO] Task started: Blastn
[2023-03-15 22:15:44,567] [INFO] Running command: blastn -query OceanDNA-b6427/markers.fasta -db /var/lib/cwl/stgaa957ee5-0f57-4a8d-93da-aac38b4ebdd9/dqc_reference/reference_markers.fasta -out OceanDNA-b6427/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:15:45,144] [INFO] Task succeeded: Blastn
[2023-03-15 22:15:45,148] [INFO] Selected 11 target genomes.
[2023-03-15 22:15:45,148] [INFO] Target genome list was writen to OceanDNA-b6427/target_genomes.txt
[2023-03-15 22:15:45,154] [INFO] Task started: fastANI
[2023-03-15 22:15:45,154] [INFO] Running command: fastANI --query /var/lib/cwl/stgbdef7088-665c-4cc0-8788-4308e87ff668/OceanDNA-b6427.fa --refList OceanDNA-b6427/target_genomes.txt --output OceanDNA-b6427/fastani_result.tsv --threads 1
[2023-03-15 22:15:51,483] [INFO] Task succeeded: fastANI
[2023-03-15 22:15:51,483] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaa957ee5-0f57-4a8d-93da-aac38b4ebdd9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 22:15:51,483] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaa957ee5-0f57-4a8d-93da-aac38b4ebdd9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 22:15:51,489] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2023-03-15 22:15:51,489] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-15 22:15:51,489] [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
Aequorivita aquimaris	strain=D-24	GCA_001573155.1	1548749	1548749	type	True	96.9228	491	544	95	conclusive
Aequorivita vladivostokensis	strain=KMM 3516	GCA_000952855.1	171194	171194	type	True	90.7882	455	544	95	below_threshold
Aequorivita iocasae	strain=KX20305	GCA_016757735.1	2803865	2803865	type	True	85.1504	443	544	95	below_threshold
Aequorivita soesokkakensis	strain=RSSK-12	GCA_001641085.1	1385699	1385699	type	True	82.8396	378	544	95	below_threshold
Aequorivita antarctica	strain=SW49	GCA_007997155.1	153266	153266	type	True	80.3671	364	544	95	below_threshold
Aequorivita lipolytica	strain=Y10-2	GCA_007997135.1	153267	153267	type	True	80.2805	368	544	95	below_threshold
Aequorivita sublithincola	strain=DSM 14238	GCA_000265385.1	101385	101385	type	True	79.5596	316	544	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 22:15:51,491] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6427/tc_result.tsv
[2023-03-15 22:15:51,494] [INFO] ===== Taxonomy check completed =====
[2023-03-15 22:15:51,494] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 22:15:51,494] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaa957ee5-0f57-4a8d-93da-aac38b4ebdd9/dqc_reference/checkm_data
[2023-03-15 22:15:51,495] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 22:15:51,508] [INFO] Task started: CheckM
[2023-03-15 22:15:51,508] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6427/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6427/checkm_input OceanDNA-b6427/checkm_result
[2023-03-15 22:16:32,555] [INFO] Task succeeded: CheckM
[2023-03-15 22:16:32,555] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.15%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 22:16:32,655] [INFO] ===== Completeness check finished =====
[2023-03-15 22:16:32,656] [INFO] ===== Start GTDB Search =====
[2023-03-15 22:16:32,656] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6427/markers.fasta)
[2023-03-15 22:16:32,657] [INFO] Task started: Blastn
[2023-03-15 22:16:32,657] [INFO] Running command: blastn -query OceanDNA-b6427/markers.fasta -db /var/lib/cwl/stgaa957ee5-0f57-4a8d-93da-aac38b4ebdd9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6427/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:16:33,563] [INFO] Task succeeded: Blastn
[2023-03-15 22:16:33,569] [INFO] Selected 7 target genomes.
[2023-03-15 22:16:33,569] [INFO] Target genome list was writen to OceanDNA-b6427/target_genomes_gtdb.txt
[2023-03-15 22:16:33,612] [INFO] Task started: fastANI
[2023-03-15 22:16:33,612] [INFO] Running command: fastANI --query /var/lib/cwl/stgbdef7088-665c-4cc0-8788-4308e87ff668/OceanDNA-b6427.fa --refList OceanDNA-b6427/target_genomes_gtdb.txt --output OceanDNA-b6427/fastani_result_gtdb.tsv --threads 1
[2023-03-15 22:16:37,831] [INFO] Task succeeded: fastANI
[2023-03-15 22:16:37,836] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 22:16:37,836] [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_001573155.1	s__Aequorivita aquimaris	96.9228	491	544	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000952855.1	s__Aequorivita vladivostokensis	90.7882	455	544	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	98.24	98.00	0.93	0.90	7	-
GCA_002364215.1	s__Aequorivita sp002364215	90.0914	482	544	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.66	98.55	0.97	0.89	12	-
GCA_002715485.1	s__Aequorivita sp002715485	86.3951	430	544	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.49	99.49	0.87	0.87	2	-
GCF_016757735.1	s__Aequorivita sp016757735	85.1504	443	544	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733915.1	s__Aequorivita sp002733915	84.0039	429	544	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001641085.1	s__Aequorivita soesokkakensis	82.8396	378	544	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	97.26	97.26	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2023-03-15 22:16:37,837] [INFO] GTDB search result was written to OceanDNA-b6427/result_gtdb.tsv
[2023-03-15 22:16:37,840] [INFO] ===== GTDB Search completed =====
[2023-03-15 22:16:37,843] [INFO] DFAST_QC result json was written to OceanDNA-b6427/dqc_result.json
[2023-03-15 22:16:37,843] [INFO] DFAST_QC completed!
[2023-03-15 22:16:37,843] [INFO] Total running time: 0h1m10s