[2023-03-18 00:53:42,860] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:53:42,860] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:53:42,860] [INFO] DQC Reference Directory: /var/lib/cwl/stg7c35d81c-ff5f-4053-8b00-b6c0c8542cd0/dqc_reference
[2023-03-18 00:53:44,411] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:53:44,412] [INFO] Task started: Prodigal
[2023-03-18 00:53:44,412] [INFO] Running command: cat /var/lib/cwl/stg1a9731f3-23d5-4af7-85c3-22d98ae849f7/OceanDNA-b4857.fa | prodigal -d OceanDNA-b4857/cds.fna -a OceanDNA-b4857/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:53:54,731] [INFO] Task succeeded: Prodigal
[2023-03-18 00:53:54,732] [INFO] Task started: HMMsearch
[2023-03-18 00:53:54,732] [INFO] Running command: hmmsearch --tblout OceanDNA-b4857/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7c35d81c-ff5f-4053-8b00-b6c0c8542cd0/dqc_reference/reference_markers.hmm OceanDNA-b4857/protein.faa > /dev/null
[2023-03-18 00:53:54,931] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:53:54,931] [INFO] Found 6/6 markers.
[2023-03-18 00:53:54,944] [INFO] Query marker FASTA was written to OceanDNA-b4857/markers.fasta
[2023-03-18 00:53:54,945] [INFO] Task started: Blastn
[2023-03-18 00:53:54,945] [INFO] Running command: blastn -query OceanDNA-b4857/markers.fasta -db /var/lib/cwl/stg7c35d81c-ff5f-4053-8b00-b6c0c8542cd0/dqc_reference/reference_markers.fasta -out OceanDNA-b4857/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:53:55,510] [INFO] Task succeeded: Blastn
[2023-03-18 00:53:55,511] [INFO] Selected 34 target genomes.
[2023-03-18 00:53:55,511] [INFO] Target genome list was writen to OceanDNA-b4857/target_genomes.txt
[2023-03-18 00:53:55,531] [INFO] Task started: fastANI
[2023-03-18 00:53:55,532] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a9731f3-23d5-4af7-85c3-22d98ae849f7/OceanDNA-b4857.fa --refList OceanDNA-b4857/target_genomes.txt --output OceanDNA-b4857/fastani_result.tsv --threads 1
[2023-03-18 00:54:12,158] [INFO] Task succeeded: fastANI
[2023-03-18 00:54:12,159] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7c35d81c-ff5f-4053-8b00-b6c0c8542cd0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:54:12,159] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7c35d81c-ff5f-4053-8b00-b6c0c8542cd0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:54:12,162] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:54:12,162] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 00:54:12,162] [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
Tenacibaculum ovolyticum	strain=DSM 18103	GCA_000430545.1	104270	104270	type	True	74.8499	50	572	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 00:54:12,163] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4857/tc_result.tsv
[2023-03-18 00:54:12,163] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:54:12,163] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:54:12,163] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7c35d81c-ff5f-4053-8b00-b6c0c8542cd0/dqc_reference/checkm_data
[2023-03-18 00:54:12,164] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:54:12,167] [INFO] Task started: CheckM
[2023-03-18 00:54:12,167] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4857/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4857/checkm_input OceanDNA-b4857/checkm_result
[2023-03-18 00:54:42,075] [INFO] Task succeeded: CheckM
[2023-03-18 00:54:42,075] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 00:54:42,077] [INFO] ===== Completeness check finished =====
[2023-03-18 00:54:42,077] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:54:42,077] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4857/markers.fasta)
[2023-03-18 00:54:42,078] [INFO] Task started: Blastn
[2023-03-18 00:54:42,079] [INFO] Running command: blastn -query OceanDNA-b4857/markers.fasta -db /var/lib/cwl/stg7c35d81c-ff5f-4053-8b00-b6c0c8542cd0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4857/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:54:43,013] [INFO] Task succeeded: Blastn
[2023-03-18 00:54:43,014] [INFO] Selected 22 target genomes.
[2023-03-18 00:54:43,014] [INFO] Target genome list was writen to OceanDNA-b4857/target_genomes_gtdb.txt
[2023-03-18 00:54:43,034] [INFO] Task started: fastANI
[2023-03-18 00:54:43,034] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a9731f3-23d5-4af7-85c3-22d98ae849f7/OceanDNA-b4857.fa --refList OceanDNA-b4857/target_genomes_gtdb.txt --output OceanDNA-b4857/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:54:49,894] [INFO] Task succeeded: fastANI
[2023-03-18 00:54:49,903] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 00:54:49,903] [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_002728175.1	s__GCA-2697505 sp002728175	87.2554	488	572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2697505	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002697505.1	s__GCA-2697505 sp002697505	86.7432	414	572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2697505	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002724895.1	s__GCA-2693335 sp002724895	77.1087	125	572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2693335	95.0	97.78	97.48	0.81	0.76	3	-
GCA_002715565.1	s__GCA-2715565 sp002715565	76.7915	121	572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2715565	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002689735.1	s__GCA-002715885 sp002689735	76.7564	53	572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002715885	95.0	96.30	96.30	0.76	0.76	2	-
GCA_018652335.1	s__GCA-2683775 sp018652335	76.6521	82	572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2683775	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478765.1	s__UWMA-0277 sp905478765	76.577	92	572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002711125.1	s__GCA-2711125 sp002711125	76.4166	122	572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2711125	95.0	97.93	96.61	0.96	0.94	3	-
GCA_002705205.1	s__GCA-2705205 sp002705205	76.3669	59	572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2705205	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478185.1	s__UWMA-0277 sp905478185	76.2879	97	572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	96.67	96.67	0.88	0.88	2	-
GCA_018675825.1	s__GCA-002715885 sp018675825	76.2602	67	572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002715885	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014239655.1	s__GCA-002715885 sp014239655	76.2488	65	572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002715885	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902579065.1	s__GCA-002715885 sp902579065	76.2004	77	572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002715885	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014384505.1	s__UWMA-0277 sp014384505	76.137	65	572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002693745.1	s__BACL11 sp002693745	76.0645	74	572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__BACL11	95.0	98.58	98.58	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2023-03-18 00:54:49,903] [INFO] GTDB search result was written to OceanDNA-b4857/result_gtdb.tsv
[2023-03-18 00:54:49,904] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:54:49,905] [INFO] DFAST_QC result json was written to OceanDNA-b4857/dqc_result.json
[2023-03-18 00:54:49,905] [INFO] DFAST_QC completed!
[2023-03-18 00:54:49,905] [INFO] Total running time: 0h1m7s