[2023-03-17 06:30:49,799] [INFO] DFAST_QC pipeline started.
[2023-03-17 06:30:49,799] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 06:30:49,800] [INFO] DQC Reference Directory: /var/lib/cwl/stgb96b6b25-4348-47f8-9e2f-140420c81b74/dqc_reference
[2023-03-17 06:30:51,354] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 06:30:51,354] [INFO] Task started: Prodigal
[2023-03-17 06:30:51,354] [INFO] Running command: cat /var/lib/cwl/stga7b70233-2034-4ac1-8779-c8d6d0433beb/OceanDNA-b280.fa | prodigal -d OceanDNA-b280/cds.fna -a OceanDNA-b280/protein.faa -g 11 -q > /dev/null
[2023-03-17 06:31:15,159] [INFO] Task succeeded: Prodigal
[2023-03-17 06:31:15,159] [INFO] Task started: HMMsearch
[2023-03-17 06:31:15,159] [INFO] Running command: hmmsearch --tblout OceanDNA-b280/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb96b6b25-4348-47f8-9e2f-140420c81b74/dqc_reference/reference_markers.hmm OceanDNA-b280/protein.faa > /dev/null
[2023-03-17 06:31:15,389] [INFO] Task succeeded: HMMsearch
[2023-03-17 06:31:15,389] [INFO] Found 6/6 markers.
[2023-03-17 06:31:15,413] [INFO] Query marker FASTA was written to OceanDNA-b280/markers.fasta
[2023-03-17 06:31:15,413] [INFO] Task started: Blastn
[2023-03-17 06:31:15,413] [INFO] Running command: blastn -query OceanDNA-b280/markers.fasta -db /var/lib/cwl/stgb96b6b25-4348-47f8-9e2f-140420c81b74/dqc_reference/reference_markers.fasta -out OceanDNA-b280/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 06:31:15,956] [INFO] Task succeeded: Blastn
[2023-03-17 06:31:15,957] [INFO] Selected 29 target genomes.
[2023-03-17 06:31:15,957] [INFO] Target genome list was writen to OceanDNA-b280/target_genomes.txt
[2023-03-17 06:31:15,972] [INFO] Task started: fastANI
[2023-03-17 06:31:15,972] [INFO] Running command: fastANI --query /var/lib/cwl/stga7b70233-2034-4ac1-8779-c8d6d0433beb/OceanDNA-b280.fa --refList OceanDNA-b280/target_genomes.txt --output OceanDNA-b280/fastani_result.tsv --threads 1
[2023-03-17 06:31:37,798] [INFO] Task succeeded: fastANI
[2023-03-17 06:31:37,798] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb96b6b25-4348-47f8-9e2f-140420c81b74/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 06:31:37,798] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb96b6b25-4348-47f8-9e2f-140420c81b74/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 06:31:37,803] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 06:31:37,803] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 06:31:37,803] [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	75.6113	76	1250	95	below_threshold
Plesiocystis pacifica	strain=SIR-1	GCA_000170895.1	191768	191768	type	True	74.6897	65	1250	95	below_threshold
Solirubrobacter pauli	strain=DSM 14954	GCA_003633755.1	166793	166793	type	True	74.5895	50	1250	95	below_threshold
Streptomyces antimycoticus	strain=NBRC 12839	GCA_005405925.1	68175	68175	type	True	74.5856	56	1250	95	below_threshold
Streptomyces genisteinicus	strain=CRPJ-33	GCA_014489615.1	2768068	2768068	type	True	74.5672	51	1250	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 06:31:37,803] [INFO] DFAST Taxonomy check result was written to OceanDNA-b280/tc_result.tsv
[2023-03-17 06:31:37,803] [INFO] ===== Taxonomy check completed =====
[2023-03-17 06:31:37,803] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 06:31:37,803] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb96b6b25-4348-47f8-9e2f-140420c81b74/dqc_reference/checkm_data
[2023-03-17 06:31:37,804] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 06:31:37,908] [INFO] Task started: CheckM
[2023-03-17 06:31:37,908] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b280/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b280/checkm_input OceanDNA-b280/checkm_result
[2023-03-17 06:32:35,756] [INFO] Task succeeded: CheckM
[2023-03-17 06:32:35,756] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 06:32:35,759] [INFO] ===== Completeness check finished =====
[2023-03-17 06:32:35,759] [INFO] ===== Start GTDB Search =====
[2023-03-17 06:32:35,760] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b280/markers.fasta)
[2023-03-17 06:32:35,760] [INFO] Task started: Blastn
[2023-03-17 06:32:35,760] [INFO] Running command: blastn -query OceanDNA-b280/markers.fasta -db /var/lib/cwl/stgb96b6b25-4348-47f8-9e2f-140420c81b74/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b280/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 06:32:36,556] [INFO] Task succeeded: Blastn
[2023-03-17 06:32:36,557] [INFO] Selected 24 target genomes.
[2023-03-17 06:32:36,557] [INFO] Target genome list was writen to OceanDNA-b280/target_genomes_gtdb.txt
[2023-03-17 06:32:37,438] [INFO] Task started: fastANI
[2023-03-17 06:32:37,438] [INFO] Running command: fastANI --query /var/lib/cwl/stga7b70233-2034-4ac1-8779-c8d6d0433beb/OceanDNA-b280.fa --refList OceanDNA-b280/target_genomes_gtdb.txt --output OceanDNA-b280/fastani_result_gtdb.tsv --threads 1
[2023-03-17 06:32:53,860] [INFO] Task succeeded: fastANI
[2023-03-17 06:32:53,871] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 06:32:53,871] [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_002712885.1	s__UBA8438 sp002712885	79.4342	666	1250	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__UBA8438	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005778315.1	s__UBA8438 sp005778315	78.4404	426	1250	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__UBA8438	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002726085.1	s__NP936 sp002726085	77.0372	306	1250	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__NP936	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015659035.1	s__NP936 sp015659035	76.8294	252	1250	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__NP936	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002346545.1	s__UBA2994 sp002346545	76.777	224	1250	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__UBA2994	95.0	99.87	99.87	0.91	0.91	2	-
GCA_003533545.1	s__UBA9620 sp003533545	76.3529	128	1250	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__UBA9620	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011523845.1	s__WTFV01 sp011523845	76.198	232	1250	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__WTFV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002730525.1	s__UBA2161 sp002730525	76.0928	86	1250	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA823;g__UBA2161	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009861545.1	s__WTFV01 sp009861545	76.017	208	1250	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__WTFV01	95.0	96.15	96.15	0.82	0.82	2	-
GCA_016871255.1	s__VFZH01 sp016871255	75.8025	79	1250	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__VFZH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001767195.1	s__Gp6-AA40 sp001767195	75.7611	66	1250	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA40	95.0	99.78	99.78	0.93	0.93	2	-
GCA_001724025.1	s__SCN-69-37 sp001724025	75.7034	63	1250	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_017883165.1	s__JADGOC01 sp017883165	75.6631	65	1250	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__JADGOC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003222395.1	s__Gp6-AA45 sp003222395	75.6575	83	1250	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_001768615.1	s__12-FULL-67-14b sp001768615	75.626	77	1250	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_016195265.1	s__Gp6-AA45 sp016195265	75.4843	72	1250	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_013362195.1	s__QHWT01 sp013362195	75.382	60	1250	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__2-12-FULL-66-21;g__QHWT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009380045.1	s__WHSN01 sp009380045	75.2983	67	1250	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__WHSN01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 06:32:53,871] [INFO] GTDB search result was written to OceanDNA-b280/result_gtdb.tsv
[2023-03-17 06:32:53,871] [INFO] ===== GTDB Search completed =====
[2023-03-17 06:32:53,873] [INFO] DFAST_QC result json was written to OceanDNA-b280/dqc_result.json
[2023-03-17 06:32:53,873] [INFO] DFAST_QC completed!
[2023-03-17 06:32:53,873] [INFO] Total running time: 0h2m4s