[2023-03-19 00:15:41,732] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:15:41,732] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:15:41,732] [INFO] DQC Reference Directory: /var/lib/cwl/stg53d6de21-be4a-4052-bd0a-ccabdf587b36/dqc_reference
[2023-03-19 00:15:43,440] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:15:43,440] [INFO] Task started: Prodigal
[2023-03-19 00:15:43,440] [INFO] Running command: cat /var/lib/cwl/stgb41bce26-156b-44e4-9454-064ba61bc909/OceanDNA-b34123.fa | prodigal -d OceanDNA-b34123/cds.fna -a OceanDNA-b34123/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:15:56,636] [INFO] Task succeeded: Prodigal
[2023-03-19 00:15:56,637] [INFO] Task started: HMMsearch
[2023-03-19 00:15:56,637] [INFO] Running command: hmmsearch --tblout OceanDNA-b34123/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg53d6de21-be4a-4052-bd0a-ccabdf587b36/dqc_reference/reference_markers.hmm OceanDNA-b34123/protein.faa > /dev/null
[2023-03-19 00:15:56,883] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:15:56,884] [INFO] Found 6/6 markers.
[2023-03-19 00:15:56,907] [INFO] Query marker FASTA was written to OceanDNA-b34123/markers.fasta
[2023-03-19 00:15:56,907] [INFO] Task started: Blastn
[2023-03-19 00:15:56,907] [INFO] Running command: blastn -query OceanDNA-b34123/markers.fasta -db /var/lib/cwl/stg53d6de21-be4a-4052-bd0a-ccabdf587b36/dqc_reference/reference_markers.fasta -out OceanDNA-b34123/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:15:57,555] [INFO] Task succeeded: Blastn
[2023-03-19 00:15:57,556] [INFO] Selected 33 target genomes.
[2023-03-19 00:15:57,556] [INFO] Target genome list was writen to OceanDNA-b34123/target_genomes.txt
[2023-03-19 00:15:57,581] [INFO] Task started: fastANI
[2023-03-19 00:15:57,581] [INFO] Running command: fastANI --query /var/lib/cwl/stgb41bce26-156b-44e4-9454-064ba61bc909/OceanDNA-b34123.fa --refList OceanDNA-b34123/target_genomes.txt --output OceanDNA-b34123/fastani_result.tsv --threads 1
[2023-03-19 00:16:15,100] [INFO] Task succeeded: fastANI
[2023-03-19 00:16:15,101] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg53d6de21-be4a-4052-bd0a-ccabdf587b36/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:16:15,101] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg53d6de21-be4a-4052-bd0a-ccabdf587b36/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:16:15,107] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:16:15,107] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 00:16:15,107] [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
Rugosibacter aromaticivorans	strain=Ca6	GCA_000934545.1	1565605	1565605	type	True	79.527	319	683	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	76.5418	52	683	95	below_threshold
Denitratisoma oestradiolicum	strain=DSM 16959	GCA_902813185.1	311182	311182	type	True	76.3977	51	683	95	below_threshold
Denitratisoma oestradiolicum	strain=DSM 16959	GCA_007844305.1	311182	311182	type	True	76.3284	52	683	95	below_threshold
Georgfuchsia toluolica	strain=G5G6	GCA_907163265.1	424218	424218	type	True	76.2491	58	683	95	below_threshold
Azoarcus indigens	strain=VB32	GCA_012910835.1	29545	29545	type	True	75.9443	51	683	95	below_threshold
Zoogloea oleivorans	strain=Buc	GCA_008107625.1	1552750	1552750	type	True	75.8867	51	683	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 00:16:15,108] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34123/tc_result.tsv
[2023-03-19 00:16:15,108] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:16:15,108] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:16:15,108] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg53d6de21-be4a-4052-bd0a-ccabdf587b36/dqc_reference/checkm_data
[2023-03-19 00:16:15,109] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:16:15,172] [INFO] Task started: CheckM
[2023-03-19 00:16:15,172] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34123/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34123/checkm_input OceanDNA-b34123/checkm_result
[2023-03-19 00:16:51,535] [INFO] Task succeeded: CheckM
[2023-03-19 00:16:51,536] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:16:51,538] [INFO] ===== Completeness check finished =====
[2023-03-19 00:16:51,538] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:16:51,538] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34123/markers.fasta)
[2023-03-19 00:16:51,539] [INFO] Task started: Blastn
[2023-03-19 00:16:51,539] [INFO] Running command: blastn -query OceanDNA-b34123/markers.fasta -db /var/lib/cwl/stg53d6de21-be4a-4052-bd0a-ccabdf587b36/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34123/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:16:52,615] [INFO] Task succeeded: Blastn
[2023-03-19 00:16:52,616] [INFO] Selected 14 target genomes.
[2023-03-19 00:16:52,617] [INFO] Target genome list was writen to OceanDNA-b34123/target_genomes_gtdb.txt
[2023-03-19 00:16:52,626] [INFO] Task started: fastANI
[2023-03-19 00:16:52,626] [INFO] Running command: fastANI --query /var/lib/cwl/stgb41bce26-156b-44e4-9454-064ba61bc909/OceanDNA-b34123.fa --refList OceanDNA-b34123/target_genomes_gtdb.txt --output OceanDNA-b34123/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:16:59,857] [INFO] Task succeeded: fastANI
[2023-03-19 00:16:59,865] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 00:16:59,865] [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_002422995.1	s__Rugosibacter sp002422995	97.1623	373	683	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Rugosibacter	95.0	97.21	96.23	0.74	0.65	4	conclusive
GCA_002424865.1	s__Rugosibacter sp002424865	85.2601	393	683	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Rugosibacter	95.0	99.77	99.73	0.92	0.91	4	-
GCA_011620215.1	s__Rugosibacter sp011620215	80.0204	276	683	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Rugosibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004322535.1	s__Rugosibacter sp004322535	79.6506	310	683	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Rugosibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000934545.1	s__Rugosibacter aromaticivorans	79.5508	318	683	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Rugosibacter	95.0	99.39	99.39	0.96	0.96	2	-
GCA_016235025.1	s__Rugosibacter sp016235025	77.3712	152	683	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Rugosibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903959855.1	s__Sulfuritalea sp903959855	77.0476	78	683	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfuritalea	95.0	99.57	99.34	0.90	0.90	4	-
GCA_016192435.1	s__Sulfuritalea sp016192435	76.936	85	683	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfuritalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903946745.1	s__CAJAWW01 sp903946745	76.6385	95	683	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__CAJAWW01	95.0	99.25	99.21	0.88	0.87	4	-
GCA_016708585.1	s__Sulfuritalea sp016708585	76.6183	87	683	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfuritalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903848955.1	s__Sulfuritalea sp903848955	76.5519	84	683	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfuritalea	95.0	99.61	99.42	0.91	0.84	24	-
GCA_903933395.1	s__Sulfuritalea sp903933395	76.4684	74	683	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfuritalea	95.0	99.21	99.21	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2023-03-19 00:16:59,866] [INFO] GTDB search result was written to OceanDNA-b34123/result_gtdb.tsv
[2023-03-19 00:16:59,866] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:16:59,867] [INFO] DFAST_QC result json was written to OceanDNA-b34123/dqc_result.json
[2023-03-19 00:16:59,867] [INFO] DFAST_QC completed!
[2023-03-19 00:16:59,867] [INFO] Total running time: 0h1m18s