[2023-03-16 23:42:36,132] [INFO] DFAST_QC pipeline started.
[2023-03-16 23:42:36,132] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 23:42:36,132] [INFO] DQC Reference Directory: /var/lib/cwl/stg4c03224a-2b5b-4eff-9de4-d2a2fd2d8e4f/dqc_reference
[2023-03-16 23:42:38,504] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 23:42:38,505] [INFO] Task started: Prodigal
[2023-03-16 23:42:38,506] [INFO] Running command: cat /var/lib/cwl/stgdee2a680-83a7-4ec9-8037-9a3c8ff7479a/OceanDNA-b6218.fa | prodigal -d OceanDNA-b6218/cds.fna -a OceanDNA-b6218/protein.faa -g 11 -q > /dev/null
[2023-03-16 23:42:55,090] [INFO] Task succeeded: Prodigal
[2023-03-16 23:42:55,090] [INFO] Task started: HMMsearch
[2023-03-16 23:42:55,090] [INFO] Running command: hmmsearch --tblout OceanDNA-b6218/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4c03224a-2b5b-4eff-9de4-d2a2fd2d8e4f/dqc_reference/reference_markers.hmm OceanDNA-b6218/protein.faa > /dev/null
[2023-03-16 23:42:55,286] [INFO] Task succeeded: HMMsearch
[2023-03-16 23:42:55,286] [INFO] Found 6/6 markers.
[2023-03-16 23:42:55,304] [INFO] Query marker FASTA was written to OceanDNA-b6218/markers.fasta
[2023-03-16 23:42:55,305] [INFO] Task started: Blastn
[2023-03-16 23:42:55,305] [INFO] Running command: blastn -query OceanDNA-b6218/markers.fasta -db /var/lib/cwl/stg4c03224a-2b5b-4eff-9de4-d2a2fd2d8e4f/dqc_reference/reference_markers.fasta -out OceanDNA-b6218/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:42:55,842] [INFO] Task succeeded: Blastn
[2023-03-16 23:42:55,847] [INFO] Selected 33 target genomes.
[2023-03-16 23:42:55,848] [INFO] Target genome list was writen to OceanDNA-b6218/target_genomes.txt
[2023-03-16 23:42:55,874] [INFO] Task started: fastANI
[2023-03-16 23:42:55,875] [INFO] Running command: fastANI --query /var/lib/cwl/stgdee2a680-83a7-4ec9-8037-9a3c8ff7479a/OceanDNA-b6218.fa --refList OceanDNA-b6218/target_genomes.txt --output OceanDNA-b6218/fastani_result.tsv --threads 1
[2023-03-16 23:43:14,514] [INFO] Task succeeded: fastANI
[2023-03-16 23:43:14,515] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4c03224a-2b5b-4eff-9de4-d2a2fd2d8e4f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 23:43:14,515] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4c03224a-2b5b-4eff-9de4-d2a2fd2d8e4f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 23:43:14,515] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 23:43:14,515] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 23:43:14,515] [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
--------------------------------------------------------------------------------
[2023-03-16 23:43:14,519] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6218/tc_result.tsv
[2023-03-16 23:43:14,524] [INFO] ===== Taxonomy check completed =====
[2023-03-16 23:43:14,524] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 23:43:14,525] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4c03224a-2b5b-4eff-9de4-d2a2fd2d8e4f/dqc_reference/checkm_data
[2023-03-16 23:43:14,528] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 23:43:14,535] [INFO] Task started: CheckM
[2023-03-16 23:43:14,535] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6218/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6218/checkm_input OceanDNA-b6218/checkm_result
[2023-03-16 23:43:58,822] [INFO] Task succeeded: CheckM
[2023-03-16 23:43:58,823] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.12%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 23:43:58,869] [INFO] ===== Completeness check finished =====
[2023-03-16 23:43:58,870] [INFO] ===== Start GTDB Search =====
[2023-03-16 23:43:58,870] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6218/markers.fasta)
[2023-03-16 23:43:58,871] [INFO] Task started: Blastn
[2023-03-16 23:43:58,871] [INFO] Running command: blastn -query OceanDNA-b6218/markers.fasta -db /var/lib/cwl/stg4c03224a-2b5b-4eff-9de4-d2a2fd2d8e4f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6218/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:43:59,620] [INFO] Task succeeded: Blastn
[2023-03-16 23:43:59,627] [INFO] Selected 24 target genomes.
[2023-03-16 23:43:59,627] [INFO] Target genome list was writen to OceanDNA-b6218/target_genomes_gtdb.txt
[2023-03-16 23:43:59,644] [INFO] Task started: fastANI
[2023-03-16 23:43:59,644] [INFO] Running command: fastANI --query /var/lib/cwl/stgdee2a680-83a7-4ec9-8037-9a3c8ff7479a/OceanDNA-b6218.fa --refList OceanDNA-b6218/target_genomes_gtdb.txt --output OceanDNA-b6218/fastani_result_gtdb.tsv --threads 1
[2023-03-16 23:44:09,728] [INFO] Task succeeded: fastANI
[2023-03-16 23:44:09,735] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 23:44:09,735] [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
GCA_018699935.1	s__MS024-2A sp018699935	99.8912	609	666	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.36	99.36	0.92	0.92	2	conclusive
GCA_017851655.1	s__MS024-2A sp017851655	76.8398	67	666	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.55	99.53	0.87	0.86	3	-
GCA_009886625.1	s__MS024-2A sp009886625	76.7248	85	666	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000173095.1	s__MS024-2A sp000173095	76.6706	82	666	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.61	99.48	0.88	0.84	16	-
GCA_002364535.1	s__UBA8316 sp002364535	76.5079	57	666	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	99.85	99.85	0.95	0.95	2	-
GCA_017858055.1	s__MS024-2A sp002384715	76.5012	78	666	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.54	99.54	0.94	0.94	2	-
GCA_002292265.1	s__MS024-2A sp002292265	76.4303	100	666	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.71	99.21	0.94	0.92	6	-
GCA_017852075.1	s__MS024-2A sp017852075	76.394	83	666	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.70	99.69	0.95	0.94	3	-
GCA_011525195.1	s__MS024-2A sp011525195	76.3589	56	666	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009936675.1	s__UBA8316 sp009936675	75.8255	53	666	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	99.40	99.39	0.87	0.79	3	-
GCA_905480425.1	s__MS024-2A sp905480425	75.6054	70	666	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	95.11	95.11	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2023-03-16 23:44:09,737] [INFO] GTDB search result was written to OceanDNA-b6218/result_gtdb.tsv
[2023-03-16 23:44:09,745] [INFO] ===== GTDB Search completed =====
[2023-03-16 23:44:09,750] [INFO] DFAST_QC result json was written to OceanDNA-b6218/dqc_result.json
[2023-03-16 23:44:09,750] [INFO] DFAST_QC completed!
[2023-03-16 23:44:09,750] [INFO] Total running time: 0h1m34s