[2023-03-17 23:14:48,715] [INFO] DFAST_QC pipeline started.
[2023-03-17 23:14:48,717] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 23:14:48,717] [INFO] DQC Reference Directory: /var/lib/cwl/stge29ba6df-8bc8-4c68-9542-8d223dd92381/dqc_reference
[2023-03-17 23:14:49,833] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 23:14:49,834] [INFO] Task started: Prodigal
[2023-03-17 23:14:49,834] [INFO] Running command: cat /var/lib/cwl/stg00c13966-311e-4245-b1e5-b3634a9451e4/OceanDNA-b294.fa | prodigal -d OceanDNA-b294/cds.fna -a OceanDNA-b294/protein.faa -g 11 -q > /dev/null
[2023-03-17 23:15:11,887] [INFO] Task succeeded: Prodigal
[2023-03-17 23:15:11,888] [INFO] Task started: HMMsearch
[2023-03-17 23:15:11,888] [INFO] Running command: hmmsearch --tblout OceanDNA-b294/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge29ba6df-8bc8-4c68-9542-8d223dd92381/dqc_reference/reference_markers.hmm OceanDNA-b294/protein.faa > /dev/null
[2023-03-17 23:15:12,108] [INFO] Task succeeded: HMMsearch
[2023-03-17 23:15:12,108] [INFO] Found 6/6 markers.
[2023-03-17 23:15:12,130] [INFO] Query marker FASTA was written to OceanDNA-b294/markers.fasta
[2023-03-17 23:15:12,132] [INFO] Task started: Blastn
[2023-03-17 23:15:12,132] [INFO] Running command: blastn -query OceanDNA-b294/markers.fasta -db /var/lib/cwl/stge29ba6df-8bc8-4c68-9542-8d223dd92381/dqc_reference/reference_markers.fasta -out OceanDNA-b294/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:15:12,895] [INFO] Task succeeded: Blastn
[2023-03-17 23:15:12,897] [INFO] Selected 26 target genomes.
[2023-03-17 23:15:12,897] [INFO] Target genome list was writen to OceanDNA-b294/target_genomes.txt
[2023-03-17 23:15:12,920] [INFO] Task started: fastANI
[2023-03-17 23:15:12,921] [INFO] Running command: fastANI --query /var/lib/cwl/stg00c13966-311e-4245-b1e5-b3634a9451e4/OceanDNA-b294.fa --refList OceanDNA-b294/target_genomes.txt --output OceanDNA-b294/fastani_result.tsv --threads 1
[2023-03-17 23:15:33,437] [INFO] Task succeeded: fastANI
[2023-03-17 23:15:33,437] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge29ba6df-8bc8-4c68-9542-8d223dd92381/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 23:15:33,438] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge29ba6df-8bc8-4c68-9542-8d223dd92381/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 23:15:33,442] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 23:15:33,442] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 23:15:33,442] [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
Luteitalea pratensis	strain=DSM 100886; HEG_-6_39	GCA_001618865.1	1855912	1855912	type	True	75.9892	67	1151	95	below_threshold
Anaeromyxobacter dehalogenans	strain=2CP-1	GCA_000022145.1	161493	161493	type	True	74.8392	56	1151	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	74.82	64	1151	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 23:15:33,442] [INFO] DFAST Taxonomy check result was written to OceanDNA-b294/tc_result.tsv
[2023-03-17 23:15:33,443] [INFO] ===== Taxonomy check completed =====
[2023-03-17 23:15:33,443] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 23:15:33,443] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge29ba6df-8bc8-4c68-9542-8d223dd92381/dqc_reference/checkm_data
[2023-03-17 23:15:33,444] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 23:15:33,449] [INFO] Task started: CheckM
[2023-03-17 23:15:33,449] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b294/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b294/checkm_input OceanDNA-b294/checkm_result
[2023-03-17 23:16:27,907] [INFO] Task succeeded: CheckM
[2023-03-17 23:16:27,907] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 23:16:27,909] [INFO] ===== Completeness check finished =====
[2023-03-17 23:16:27,909] [INFO] ===== Start GTDB Search =====
[2023-03-17 23:16:27,910] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b294/markers.fasta)
[2023-03-17 23:16:27,911] [INFO] Task started: Blastn
[2023-03-17 23:16:27,911] [INFO] Running command: blastn -query OceanDNA-b294/markers.fasta -db /var/lib/cwl/stge29ba6df-8bc8-4c68-9542-8d223dd92381/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b294/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:16:28,999] [INFO] Task succeeded: Blastn
[2023-03-17 23:16:29,000] [INFO] Selected 19 target genomes.
[2023-03-17 23:16:29,000] [INFO] Target genome list was writen to OceanDNA-b294/target_genomes_gtdb.txt
[2023-03-17 23:16:29,011] [INFO] Task started: fastANI
[2023-03-17 23:16:29,011] [INFO] Running command: fastANI --query /var/lib/cwl/stg00c13966-311e-4245-b1e5-b3634a9451e4/OceanDNA-b294.fa --refList OceanDNA-b294/target_genomes_gtdb.txt --output OceanDNA-b294/fastani_result_gtdb.tsv --threads 1
[2023-03-17 23:16:44,213] [INFO] Task succeeded: fastANI
[2023-03-17 23:16:44,223] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 23:16:44,223] [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_002346545.1	s__UBA2994 sp002346545	96.4198	1085	1151	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__UBA2994	95.0	99.87	99.87	0.91	0.91	2	conclusive
GCA_015659035.1	s__NP936 sp015659035	76.9553	273	1151	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__NP936	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002726085.1	s__NP936 sp002726085	76.8982	310	1151	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__NP936	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002712885.1	s__UBA8438 sp002712885	76.4263	248	1151	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__UBA8438	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009861545.1	s__WTFV01 sp009861545	76.3981	239	1151	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__WTFV01	95.0	96.15	96.15	0.82	0.82	2	-
GCA_003242705.1	s__SCN-69-37 sp003242705	76.2933	72	1151	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__SCN-69-37;g__SCN-69-37	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011523845.1	s__WTFV01 sp011523845	76.2676	269	1151	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__WTFV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012271165.1	s__JAAXGX01 sp012271165	76.2263	157	1151	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__JAAXGX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003223775.1	s__Gp6-AA45 sp003223775	76.0822	66	1151	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA45	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003222395.1	s__Gp6-AA45 sp003222395	76.0728	85	1151	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA45	95.0	99.74	99.72	0.98	0.98	4	-
GCA_005778315.1	s__UBA8438 sp005778315	76.0342	158	1151	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__UBA8438	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001768615.1	s__12-FULL-67-14b sp001768615	75.9515	78	1151	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__12-FULL-67-14b	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003170135.1	s__Fen-181 sp003170135	75.9113	86	1151	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__Fen-181;g__Fen-181	95.0	99.94	99.94	0.97	0.97	2	-
GCA_013694845.1	s__JACDCA01 sp013694845	75.8347	54	1151	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__2-12-FULL-66-21;g__JACDCA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001767455.1	s__2-12-FULL-66-21 sp001767455	75.6872	90	1151	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__2-12-FULL-66-21;g__2-12-FULL-66-21	95.0	99.91	99.91	0.96	0.96	2	-
GCA_902825985.1	s__WHSN01 sp902825985	75.6175	118	1151	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__WHSN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016650245.1	s__JAENWD01 sp016650245	75.5899	61	1151	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__JAENWD01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 23:16:44,224] [INFO] GTDB search result was written to OceanDNA-b294/result_gtdb.tsv
[2023-03-17 23:16:44,224] [INFO] ===== GTDB Search completed =====
[2023-03-17 23:16:44,225] [INFO] DFAST_QC result json was written to OceanDNA-b294/dqc_result.json
[2023-03-17 23:16:44,225] [INFO] DFAST_QC completed!
[2023-03-17 23:16:44,225] [INFO] Total running time: 0h1m56s