[2023-03-16 14:50:25,375] [INFO] DFAST_QC pipeline started.
[2023-03-16 14:50:25,376] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 14:50:25,376] [INFO] DQC Reference Directory: /var/lib/cwl/stg383eb99d-2f25-43a8-a722-78dba84b8083/dqc_reference
[2023-03-16 14:50:26,691] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 14:50:26,691] [INFO] Task started: Prodigal
[2023-03-16 14:50:26,691] [INFO] Running command: cat /var/lib/cwl/stgdb11c633-c8d7-4785-ba5c-1db74eceadbd/OceanDNA-b300.fa | prodigal -d OceanDNA-b300/cds.fna -a OceanDNA-b300/protein.faa -g 11 -q > /dev/null
[2023-03-16 14:50:48,752] [INFO] Task succeeded: Prodigal
[2023-03-16 14:50:48,752] [INFO] Task started: HMMsearch
[2023-03-16 14:50:48,753] [INFO] Running command: hmmsearch --tblout OceanDNA-b300/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg383eb99d-2f25-43a8-a722-78dba84b8083/dqc_reference/reference_markers.hmm OceanDNA-b300/protein.faa > /dev/null
[2023-03-16 14:50:48,980] [INFO] Task succeeded: HMMsearch
[2023-03-16 14:50:48,981] [INFO] Found 6/6 markers.
[2023-03-16 14:50:49,007] [INFO] Query marker FASTA was written to OceanDNA-b300/markers.fasta
[2023-03-16 14:50:49,008] [INFO] Task started: Blastn
[2023-03-16 14:50:49,008] [INFO] Running command: blastn -query OceanDNA-b300/markers.fasta -db /var/lib/cwl/stg383eb99d-2f25-43a8-a722-78dba84b8083/dqc_reference/reference_markers.fasta -out OceanDNA-b300/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 14:50:49,687] [INFO] Task succeeded: Blastn
[2023-03-16 14:50:49,688] [INFO] Selected 31 target genomes.
[2023-03-16 14:50:49,688] [INFO] Target genome list was writen to OceanDNA-b300/target_genomes.txt
[2023-03-16 14:50:49,711] [INFO] Task started: fastANI
[2023-03-16 14:50:49,711] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb11c633-c8d7-4785-ba5c-1db74eceadbd/OceanDNA-b300.fa --refList OceanDNA-b300/target_genomes.txt --output OceanDNA-b300/fastani_result.tsv --threads 1
[2023-03-16 14:51:24,379] [INFO] Task succeeded: fastANI
[2023-03-16 14:51:24,379] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg383eb99d-2f25-43a8-a722-78dba84b8083/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 14:51:24,379] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg383eb99d-2f25-43a8-a722-78dba84b8083/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 14:51:24,383] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 14:51:24,383] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 14:51:24,383] [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	75.4326	69	1145	95	below_threshold
Anaeromyxobacter dehalogenans	strain=2CP-1	GCA_000022145.1	161493	161493	type	True	74.8265	56	1145	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 14:51:24,384] [INFO] DFAST Taxonomy check result was written to OceanDNA-b300/tc_result.tsv
[2023-03-16 14:51:24,384] [INFO] ===== Taxonomy check completed =====
[2023-03-16 14:51:24,384] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 14:51:24,384] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg383eb99d-2f25-43a8-a722-78dba84b8083/dqc_reference/checkm_data
[2023-03-16 14:51:24,385] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 14:51:24,390] [INFO] Task started: CheckM
[2023-03-16 14:51:24,390] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b300/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b300/checkm_input OceanDNA-b300/checkm_result
[2023-03-16 14:52:24,245] [INFO] Task succeeded: CheckM
[2023-03-16 14:52:24,246] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 14:52:24,248] [INFO] ===== Completeness check finished =====
[2023-03-16 14:52:24,248] [INFO] ===== Start GTDB Search =====
[2023-03-16 14:52:24,249] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b300/markers.fasta)
[2023-03-16 14:52:24,250] [INFO] Task started: Blastn
[2023-03-16 14:52:24,250] [INFO] Running command: blastn -query OceanDNA-b300/markers.fasta -db /var/lib/cwl/stg383eb99d-2f25-43a8-a722-78dba84b8083/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b300/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 14:52:25,042] [INFO] Task succeeded: Blastn
[2023-03-16 14:52:25,043] [INFO] Selected 29 target genomes.
[2023-03-16 14:52:25,043] [INFO] Target genome list was writen to OceanDNA-b300/target_genomes_gtdb.txt
[2023-03-16 14:52:26,264] [INFO] Task started: fastANI
[2023-03-16 14:52:26,264] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb11c633-c8d7-4785-ba5c-1db74eceadbd/OceanDNA-b300.fa --refList OceanDNA-b300/target_genomes_gtdb.txt --output OceanDNA-b300/fastani_result_gtdb.tsv --threads 1
[2023-03-16 14:52:46,857] [INFO] Task succeeded: fastANI
[2023-03-16 14:52:46,868] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 14:52:46,868] [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	99.4609	1007	1145	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__UBA8438	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_005778315.1	s__UBA8438 sp005778315	77.9239	390	1145	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	77.5738	366	1145	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	77.5572	324	1145	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__NP936	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011523845.1	s__WTFV01 sp011523845	76.6087	253	1145	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__WTFV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009861545.1	s__WTFV01 sp009861545	76.4531	244	1145	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__WTFV01	95.0	96.15	96.15	0.82	0.82	2	-
GCA_002346545.1	s__UBA2994 sp002346545	76.4258	245	1145	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__UBA2994	95.0	99.87	99.87	0.91	0.91	2	-
GCA_011523485.1	s__WTFV01 sp011523485	75.9435	145	1145	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__WTFV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002328835.1	s__UBA2161 sp002328835	75.9147	98	1145	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA823;g__UBA2161	95.0	99.85	99.81	0.96	0.95	4	-
GCA_016195265.1	s__Gp6-AA45 sp016195265	75.8027	80	1145	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_003222675.1	s__QHWT01 sp003222675	75.6499	59	1145	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_003170135.1	s__Fen-181 sp003170135	75.6495	61	1145	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_003222635.1	s__Gp6-AA40 sp003222635	75.6272	69	1145	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA40	95.0	98.94	98.94	0.87	0.87	2	-
GCA_002347025.1	s__UBA2990 sp002347025	75.6182	56	1145	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__UBA2990	95.0	99.94	99.92	0.88	0.83	3	-
GCA_001464065.1	s__Luteitalea sp001464065	75.5724	70	1145	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__Vicinamibacteraceae;g__Luteitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003222395.1	s__Gp6-AA45 sp003222395	75.5491	88	1145	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_016865485.1	s__Luteitalea sp016865485	75.4394	111	1145	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__Vicinamibacteraceae;g__Luteitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016871255.1	s__VFZH01 sp016871255	75.439	82	1145	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__VFZH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009380045.1	s__WHSN01 sp009380045	75.4278	70	1145	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__WHSN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001917905.1	s__Gp6-AA45 sp001917905	75.3214	75	1145	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA45	95.0	99.03	98.94	0.79	0.79	3	-
--------------------------------------------------------------------------------
[2023-03-16 14:52:46,868] [INFO] GTDB search result was written to OceanDNA-b300/result_gtdb.tsv
[2023-03-16 14:52:46,868] [INFO] ===== GTDB Search completed =====
[2023-03-16 14:52:46,870] [INFO] DFAST_QC result json was written to OceanDNA-b300/dqc_result.json
[2023-03-16 14:52:46,870] [INFO] DFAST_QC completed!
[2023-03-16 14:52:46,870] [INFO] Total running time: 0h2m21s