[2023-03-17 11:25:36,905] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:25:36,907] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:25:36,907] [INFO] DQC Reference Directory: /var/lib/cwl/stg4d9d0d91-0920-4c22-a9b1-f8ad84776ec5/dqc_reference
[2023-03-17 11:25:38,043] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:25:38,044] [INFO] Task started: Prodigal
[2023-03-17 11:25:38,044] [INFO] Running command: cat /var/lib/cwl/stg9cad50f1-9688-4480-abf2-1959910fb3db/OceanDNA-b5408.fa | prodigal -d OceanDNA-b5408/cds.fna -a OceanDNA-b5408/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:25:59,181] [INFO] Task succeeded: Prodigal
[2023-03-17 11:25:59,181] [INFO] Task started: HMMsearch
[2023-03-17 11:25:59,181] [INFO] Running command: hmmsearch --tblout OceanDNA-b5408/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4d9d0d91-0920-4c22-a9b1-f8ad84776ec5/dqc_reference/reference_markers.hmm OceanDNA-b5408/protein.faa > /dev/null
[2023-03-17 11:25:59,376] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:25:59,377] [INFO] Found 6/6 markers.
[2023-03-17 11:25:59,422] [INFO] Query marker FASTA was written to OceanDNA-b5408/markers.fasta
[2023-03-17 11:25:59,422] [INFO] Task started: Blastn
[2023-03-17 11:25:59,422] [INFO] Running command: blastn -query OceanDNA-b5408/markers.fasta -db /var/lib/cwl/stg4d9d0d91-0920-4c22-a9b1-f8ad84776ec5/dqc_reference/reference_markers.fasta -out OceanDNA-b5408/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:25:59,961] [INFO] Task succeeded: Blastn
[2023-03-17 11:25:59,971] [INFO] Selected 25 target genomes.
[2023-03-17 11:25:59,972] [INFO] Target genome list was writen to OceanDNA-b5408/target_genomes.txt
[2023-03-17 11:25:59,988] [INFO] Task started: fastANI
[2023-03-17 11:25:59,988] [INFO] Running command: fastANI --query /var/lib/cwl/stg9cad50f1-9688-4480-abf2-1959910fb3db/OceanDNA-b5408.fa --refList OceanDNA-b5408/target_genomes.txt --output OceanDNA-b5408/fastani_result.tsv --threads 1
[2023-03-17 11:26:14,423] [INFO] Task succeeded: fastANI
[2023-03-17 11:26:14,423] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4d9d0d91-0920-4c22-a9b1-f8ad84776ec5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:26:14,424] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4d9d0d91-0920-4c22-a9b1-f8ad84776ec5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:26:14,428] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:26:14,428] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 11:26:14,428] [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
Fluviicola taffensis	strain=DSM 16823	GCA_000194605.1	191579	191579	type	True	76.4778	85	861	95	below_threshold
Taishania pollutisoli	strain=CZZ-1	GCA_014518315.1	2766479	2766479	type	True	76.3026	57	861	95	below_threshold
Brumimicrobium glaciale	strain=IC156	GCA_004152935.1	200475	200475	type	True	75.6868	57	861	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 11:26:14,431] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5408/tc_result.tsv
[2023-03-17 11:26:14,434] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:26:14,434] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:26:14,434] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4d9d0d91-0920-4c22-a9b1-f8ad84776ec5/dqc_reference/checkm_data
[2023-03-17 11:26:14,435] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:26:14,445] [INFO] Task started: CheckM
[2023-03-17 11:26:14,445] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5408/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5408/checkm_input OceanDNA-b5408/checkm_result
[2023-03-17 11:27:11,311] [INFO] Task succeeded: CheckM
[2023-03-17 11:27:11,311] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 8.33%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-17 11:27:11,618] [INFO] ===== Completeness check finished =====
[2023-03-17 11:27:11,618] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:27:11,619] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5408/markers.fasta)
[2023-03-17 11:27:11,619] [INFO] Task started: Blastn
[2023-03-17 11:27:11,620] [INFO] Running command: blastn -query OceanDNA-b5408/markers.fasta -db /var/lib/cwl/stg4d9d0d91-0920-4c22-a9b1-f8ad84776ec5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5408/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:27:12,420] [INFO] Task succeeded: Blastn
[2023-03-17 11:27:12,429] [INFO] Selected 32 target genomes.
[2023-03-17 11:27:12,429] [INFO] Target genome list was writen to OceanDNA-b5408/target_genomes_gtdb.txt
[2023-03-17 11:27:12,481] [INFO] Task started: fastANI
[2023-03-17 11:27:12,481] [INFO] Running command: fastANI --query /var/lib/cwl/stg9cad50f1-9688-4480-abf2-1959910fb3db/OceanDNA-b5408.fa --refList OceanDNA-b5408/target_genomes_gtdb.txt --output OceanDNA-b5408/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:27:27,981] [INFO] Task succeeded: fastANI
[2023-03-17 11:27:27,989] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 11:27:27,990] [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_018402525.1	s__UBA4466 sp018402525	77.0382	75	861	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017984635.1	s__M0103 sp017984635	76.8852	95	861	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__M0103	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903945495.1	s__M0103 sp903945495	76.8529	139	861	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__M0103	95.0	99.87	99.80	0.95	0.92	6	-
GCA_002409405.1	s__Taishania sp002409405	76.7808	64	861	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Taishania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480145.1	s__UBA4466 sp905480145	76.6068	52	861	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000194605.1	s__Fluviicola taffensis	76.4956	84	861	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Fluviicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017983465.1	s__UBA952 sp017983465	76.362	52	861	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	99.99	99.99	0.99	0.99	2	-
GCA_002483265.1	s__Fluviicola sp002483265	76.3331	63	861	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Fluviicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002734065.2	s__UBA4466 sp002734065	76.3026	64	861	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009885545.1	s__M0103 sp009885545	76.2363	101	861	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__M0103	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009926905.1	s__UBA952 sp009926905	76.0822	56	861	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182335.1	s__UBA4466 sp905182335	75.9231	58	861	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	99.88	99.88	0.98	0.98	2	-
GCA_903930085.1	s__M0103 sp903930085	75.8501	69	861	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__M0103	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903873915.1	s__M0103 sp903873915	75.714	52	861	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__M0103	95.0	99.96	99.96	0.94	0.94	3	-
--------------------------------------------------------------------------------
[2023-03-17 11:27:27,995] [INFO] GTDB search result was written to OceanDNA-b5408/result_gtdb.tsv
[2023-03-17 11:27:28,000] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:27:28,006] [INFO] DFAST_QC result json was written to OceanDNA-b5408/dqc_result.json
[2023-03-17 11:27:28,006] [INFO] DFAST_QC completed!
[2023-03-17 11:27:28,006] [INFO] Total running time: 0h1m51s