[2023-03-17 11:00:13,049] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:00:13,050] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:00:13,050] [INFO] DQC Reference Directory: /var/lib/cwl/stga0d09ee4-a116-4ef5-94c7-356d75a99a3c/dqc_reference
[2023-03-17 11:00:14,151] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:00:14,151] [INFO] Task started: Prodigal
[2023-03-17 11:00:14,152] [INFO] Running command: cat /var/lib/cwl/stg33671e4d-2e40-4d3e-9a33-06858228576d/OceanDNA-b25918.fa | prodigal -d OceanDNA-b25918/cds.fna -a OceanDNA-b25918/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:00:19,094] [INFO] Task succeeded: Prodigal
[2023-03-17 11:00:19,094] [INFO] Task started: HMMsearch
[2023-03-17 11:00:19,094] [INFO] Running command: hmmsearch --tblout OceanDNA-b25918/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga0d09ee4-a116-4ef5-94c7-356d75a99a3c/dqc_reference/reference_markers.hmm OceanDNA-b25918/protein.faa > /dev/null
[2023-03-17 11:00:19,245] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:00:19,245] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg33671e4d-2e40-4d3e-9a33-06858228576d/OceanDNA-b25918.fa]
[2023-03-17 11:00:19,254] [INFO] Query marker FASTA was written to OceanDNA-b25918/markers.fasta
[2023-03-17 11:00:19,255] [INFO] Task started: Blastn
[2023-03-17 11:00:19,255] [INFO] Running command: blastn -query OceanDNA-b25918/markers.fasta -db /var/lib/cwl/stga0d09ee4-a116-4ef5-94c7-356d75a99a3c/dqc_reference/reference_markers.fasta -out OceanDNA-b25918/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:00:19,778] [INFO] Task succeeded: Blastn
[2023-03-17 11:00:19,780] [INFO] Selected 22 target genomes.
[2023-03-17 11:00:19,781] [INFO] Target genome list was writen to OceanDNA-b25918/target_genomes.txt
[2023-03-17 11:00:19,888] [INFO] Task started: fastANI
[2023-03-17 11:00:19,888] [INFO] Running command: fastANI --query /var/lib/cwl/stg33671e4d-2e40-4d3e-9a33-06858228576d/OceanDNA-b25918.fa --refList OceanDNA-b25918/target_genomes.txt --output OceanDNA-b25918/fastani_result.tsv --threads 1
[2023-03-17 11:00:28,668] [INFO] Task succeeded: fastANI
[2023-03-17 11:00:28,668] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga0d09ee4-a116-4ef5-94c7-356d75a99a3c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:00:28,668] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga0d09ee4-a116-4ef5-94c7-356d75a99a3c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:00:28,668] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:00:28,668] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 11:00:28,668] [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
--------------------------------------------------------------------------------
[2023-03-17 11:00:28,669] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25918/tc_result.tsv
[2023-03-17 11:00:28,669] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:00:28,669] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:00:28,669] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga0d09ee4-a116-4ef5-94c7-356d75a99a3c/dqc_reference/checkm_data
[2023-03-17 11:00:28,934] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:00:28,967] [INFO] Task started: CheckM
[2023-03-17 11:00:28,967] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25918/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25918/checkm_input OceanDNA-b25918/checkm_result
[2023-03-17 11:00:49,715] [INFO] Task succeeded: CheckM
[2023-03-17 11:00:49,715] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 11:00:49,719] [INFO] ===== Completeness check finished =====
[2023-03-17 11:00:49,720] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:00:49,720] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25918/markers.fasta)
[2023-03-17 11:00:49,720] [INFO] Task started: Blastn
[2023-03-17 11:00:49,720] [INFO] Running command: blastn -query OceanDNA-b25918/markers.fasta -db /var/lib/cwl/stga0d09ee4-a116-4ef5-94c7-356d75a99a3c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25918/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:00:50,946] [INFO] Task succeeded: Blastn
[2023-03-17 11:00:50,955] [INFO] Selected 19 target genomes.
[2023-03-17 11:00:50,956] [INFO] Target genome list was writen to OceanDNA-b25918/target_genomes_gtdb.txt
[2023-03-17 11:00:51,062] [INFO] Task started: fastANI
[2023-03-17 11:00:51,062] [INFO] Running command: fastANI --query /var/lib/cwl/stg33671e4d-2e40-4d3e-9a33-06858228576d/OceanDNA-b25918.fa --refList OceanDNA-b25918/target_genomes_gtdb.txt --output OceanDNA-b25918/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:00:55,980] [INFO] Task succeeded: fastANI
[2023-03-17 11:00:55,990] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 11:00:55,990] [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_905182395.1	s__CAJJBL01 sp905182395	78.5852	129	316	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__CAJJBL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902558885.1	s__AAA536-G10 sp902558885	77.0539	64	316	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902623995.1	s__AAA536-G10 sp902623995	77.0028	85	316	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	98.83	98.83	0.84	0.84	2	-
GCA_902622875.1	s__AAA536-G10 sp902622875	76.9853	71	316	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902619805.1	s__AAA536-G10 sp902619805	76.8729	86	316	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902529515.1	s__AAA536-G10 sp902529515	76.8354	54	316	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	97.18	97.18	0.52	0.52	2	-
GCA_003283875.1	s__AAA536-G10 sp003283875	76.8091	59	316	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	95.33	95.28	0.67	0.61	3	-
GCA_000421325.1	s__AAA536-G10 sp000421325	76.7968	100	316	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902595145.1	s__AAA536-G10 sp902595145	76.7943	65	316	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902537945.1	s__AAA536-G10 sp902537945	76.7032	76	316	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003278095.1	s__AAA536-G10 sp003278095	76.7018	102	316	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	97.84	95.67	0.90	0.81	3	-
GCA_902583415.1	s__AAA536-G10 sp902583415	76.644	68	316	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902619615.1	s__AAA536-G10 sp902619615	76.5815	92	316	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902592615.1	s__AAA536-G10 sp902592615	76.5145	66	316	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902589185.1	s__AAA536-G10 sp902589185	76.4872	70	316	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000384615.1	s__AAA536-G10 sp000384615	76.4237	102	316	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902530325.1	s__AAA536-G10 sp902530325	76.3812	64	316	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902578805.1	s__AAA536-G10 sp902578805	76.2932	51	316	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 11:00:55,990] [INFO] GTDB search result was written to OceanDNA-b25918/result_gtdb.tsv
[2023-03-17 11:00:55,990] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:00:55,992] [INFO] DFAST_QC result json was written to OceanDNA-b25918/dqc_result.json
[2023-03-17 11:00:55,992] [INFO] DFAST_QC completed!
[2023-03-17 11:00:55,992] [INFO] Total running time: 0h0m43s