[2023-03-19 00:15:41,730] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:15:41,730] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:15:41,730] [INFO] DQC Reference Directory: /var/lib/cwl/stga186d896-71fa-4233-b1e0-8224a98ef855/dqc_reference
[2023-03-19 00:15:43,444] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:15:43,444] [INFO] Task started: Prodigal
[2023-03-19 00:15:43,444] [INFO] Running command: cat /var/lib/cwl/stg8f40af05-15aa-426b-b258-9bbbf9a37ee8/OceanDNA-b305.fa | prodigal -d OceanDNA-b305/cds.fna -a OceanDNA-b305/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:16:07,366] [INFO] Task succeeded: Prodigal
[2023-03-19 00:16:07,366] [INFO] Task started: HMMsearch
[2023-03-19 00:16:07,366] [INFO] Running command: hmmsearch --tblout OceanDNA-b305/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga186d896-71fa-4233-b1e0-8224a98ef855/dqc_reference/reference_markers.hmm OceanDNA-b305/protein.faa > /dev/null
[2023-03-19 00:16:07,579] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:16:07,580] [INFO] Found 6/6 markers.
[2023-03-19 00:16:07,604] [INFO] Query marker FASTA was written to OceanDNA-b305/markers.fasta
[2023-03-19 00:16:07,606] [INFO] Task started: Blastn
[2023-03-19 00:16:07,606] [INFO] Running command: blastn -query OceanDNA-b305/markers.fasta -db /var/lib/cwl/stga186d896-71fa-4233-b1e0-8224a98ef855/dqc_reference/reference_markers.fasta -out OceanDNA-b305/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:16:08,192] [INFO] Task succeeded: Blastn
[2023-03-19 00:16:08,193] [INFO] Selected 30 target genomes.
[2023-03-19 00:16:08,193] [INFO] Target genome list was writen to OceanDNA-b305/target_genomes.txt
[2023-03-19 00:16:08,215] [INFO] Task started: fastANI
[2023-03-19 00:16:08,215] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f40af05-15aa-426b-b258-9bbbf9a37ee8/OceanDNA-b305.fa --refList OceanDNA-b305/target_genomes.txt --output OceanDNA-b305/fastani_result.tsv --threads 1
[2023-03-19 00:16:35,927] [INFO] Task succeeded: fastANI
[2023-03-19 00:16:35,927] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga186d896-71fa-4233-b1e0-8224a98ef855/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:16:35,927] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga186d896-71fa-4233-b1e0-8224a98ef855/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:16:35,937] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:16:35,937] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 00:16:35,937] [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	75.6016	94	1292	95	below_threshold
Methylobacterium aquaticum	strain=DSM 16371	GCA_001043915.1	270351	270351	type	True	74.7867	63	1292	95	below_threshold
Amycolatopsis acididurans	strain=K13G38	GCA_012328925.1	2724524	2724524	type	True	74.7794	69	1292	95	below_threshold
Nocardioides litoris	strain=DSM 103718	GCA_006346315.1	1926648	1926648	type	True	74.7723	59	1292	95	below_threshold
Corallococcus coralloides	strain=DSM 2259	GCA_000255295.1	184914	184914	type	True	74.7599	56	1292	95	below_threshold
Corallococcus sicarius	strain=CA040B	GCA_003611735.1	2316726	2316726	type	True	74.7463	55	1292	95	below_threshold
Methylobacterium tarhaniae	strain=DSM 25844	GCA_001043955.1	1187852	1187852	type	True	74.7435	54	1292	95	below_threshold
Methylobacterium frigidaeris	strain=JCM 32048	GCA_022179185.1	2038277	2038277	type	True	74.74	63	1292	95	below_threshold
Pyxidicoccus trucidator	strain=CA060A	GCA_010894435.1	2709662	2709662	type	True	74.6876	65	1292	95	below_threshold
Amycolatopsis acidiphila	strain=KCTC 39523	GCA_021391495.1	715473	715473	type	True	74.6539	77	1292	95	below_threshold
Haliangium ochraceum	strain=DSM 14365	GCA_000024805.1	80816	80816	type	True	74.6252	90	1292	95	below_threshold
Pyxidicoccus caerfyrddinensis	strain=CA032A	GCA_010894405.1	2709663	2709663	type	True	74.5917	73	1292	95	below_threshold
Amycolatopsis acidiphila	strain=JCM 30562	GCA_007713745.1	715473	715473	type	True	74.5911	77	1292	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 00:16:35,937] [INFO] DFAST Taxonomy check result was written to OceanDNA-b305/tc_result.tsv
[2023-03-19 00:16:35,937] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:16:35,937] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:16:35,938] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga186d896-71fa-4233-b1e0-8224a98ef855/dqc_reference/checkm_data
[2023-03-19 00:16:35,938] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:16:35,968] [INFO] Task started: CheckM
[2023-03-19 00:16:35,968] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b305/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b305/checkm_input OceanDNA-b305/checkm_result
[2023-03-19 00:17:34,537] [INFO] Task succeeded: CheckM
[2023-03-19 00:17:34,537] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.77%
Contamintation: 4.63%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-19 00:17:34,540] [INFO] ===== Completeness check finished =====
[2023-03-19 00:17:34,540] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:17:34,540] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b305/markers.fasta)
[2023-03-19 00:17:34,541] [INFO] Task started: Blastn
[2023-03-19 00:17:34,541] [INFO] Running command: blastn -query OceanDNA-b305/markers.fasta -db /var/lib/cwl/stga186d896-71fa-4233-b1e0-8224a98ef855/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b305/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:17:35,406] [INFO] Task succeeded: Blastn
[2023-03-19 00:17:35,407] [INFO] Selected 21 target genomes.
[2023-03-19 00:17:35,407] [INFO] Target genome list was writen to OceanDNA-b305/target_genomes_gtdb.txt
[2023-03-19 00:17:35,420] [INFO] Task started: fastANI
[2023-03-19 00:17:35,420] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f40af05-15aa-426b-b258-9bbbf9a37ee8/OceanDNA-b305.fa --refList OceanDNA-b305/target_genomes_gtdb.txt --output OceanDNA-b305/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:17:49,754] [INFO] Task succeeded: fastANI
[2023-03-19 00:17:49,763] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 00:17:49,763] [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_002726085.1	s__NP936 sp002726085	99.1539	1126	1292	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__NP936	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_015659035.1	s__NP936 sp015659035	81.4099	582	1292	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	77.609	353	1292	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__UBA8438	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002346545.1	s__UBA2994 sp002346545	77.0749	295	1292	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__UBA2994	95.0	99.87	99.87	0.91	0.91	2	-
GCA_005778315.1	s__UBA8438 sp005778315	76.6311	196	1292	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__UBA8438	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002328835.1	s__UBA2161 sp002328835	76.4765	141	1292	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA823;g__UBA2161	95.0	99.85	99.81	0.96	0.95	4	-
GCA_012271165.1	s__JAAXGX01 sp012271165	76.4241	201	1292	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__JAAXGX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003533545.1	s__UBA9620 sp003533545	76.3895	141	1292	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__UBA9620	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002347025.1	s__UBA2990 sp002347025	76.037	54	1292	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__UBA2990	95.0	99.94	99.92	0.88	0.83	3	-
GCA_002730525.1	s__UBA2161 sp002730525	75.8767	123	1292	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA823;g__UBA2161	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464065.1	s__Luteitalea sp001464065	75.834	102	1292	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__Vicinamibacteraceae;g__Luteitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016865485.1	s__Luteitalea sp016865485	75.6579	108	1292	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__Vicinamibacteraceae;g__Luteitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016789705.1	s__CADEFD01 sp016789705	75.4696	102	1292	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__CADEFD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826515.1	s__CADEFD01 sp902826515	75.4361	110	1292	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__CADEFD01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 00:17:49,764] [INFO] GTDB search result was written to OceanDNA-b305/result_gtdb.tsv
[2023-03-19 00:17:49,764] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:17:49,765] [INFO] DFAST_QC result json was written to OceanDNA-b305/dqc_result.json
[2023-03-19 00:17:49,765] [INFO] DFAST_QC completed!
[2023-03-19 00:17:49,765] [INFO] Total running time: 0h2m8s