[2023-03-18 20:59:43,927] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:59:43,927] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:59:43,927] [INFO] DQC Reference Directory: /var/lib/cwl/stg58ab04ad-c9cf-40fc-bda0-ae65295aa2b9/dqc_reference
[2023-03-18 20:59:45,682] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:59:45,683] [INFO] Task started: Prodigal
[2023-03-18 20:59:45,683] [INFO] Running command: cat /var/lib/cwl/stg7e7a7d37-d6af-42f4-bbb5-fd41b7c1add3/OceanDNA-b269.fa | prodigal -d OceanDNA-b269/cds.fna -a OceanDNA-b269/protein.faa -g 11 -q > /dev/null
[2023-03-18 21:00:00,309] [INFO] Task succeeded: Prodigal
[2023-03-18 21:00:00,309] [INFO] Task started: HMMsearch
[2023-03-18 21:00:00,309] [INFO] Running command: hmmsearch --tblout OceanDNA-b269/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg58ab04ad-c9cf-40fc-bda0-ae65295aa2b9/dqc_reference/reference_markers.hmm OceanDNA-b269/protein.faa > /dev/null
[2023-03-18 21:00:00,475] [INFO] Task succeeded: HMMsearch
[2023-03-18 21:00:00,476] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg7e7a7d37-d6af-42f4-bbb5-fd41b7c1add3/OceanDNA-b269.fa]
[2023-03-18 21:00:00,492] [INFO] Query marker FASTA was written to OceanDNA-b269/markers.fasta
[2023-03-18 21:00:00,493] [INFO] Task started: Blastn
[2023-03-18 21:00:00,493] [INFO] Running command: blastn -query OceanDNA-b269/markers.fasta -db /var/lib/cwl/stg58ab04ad-c9cf-40fc-bda0-ae65295aa2b9/dqc_reference/reference_markers.fasta -out OceanDNA-b269/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:00:00,969] [INFO] Task succeeded: Blastn
[2023-03-18 21:00:00,970] [INFO] Selected 10 target genomes.
[2023-03-18 21:00:00,970] [INFO] Target genome list was writen to OceanDNA-b269/target_genomes.txt
[2023-03-18 21:00:00,982] [INFO] Task started: fastANI
[2023-03-18 21:00:00,982] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e7a7d37-d6af-42f4-bbb5-fd41b7c1add3/OceanDNA-b269.fa --refList OceanDNA-b269/target_genomes.txt --output OceanDNA-b269/fastani_result.tsv --threads 1
[2023-03-18 21:00:09,505] [INFO] Task succeeded: fastANI
[2023-03-18 21:00:09,505] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg58ab04ad-c9cf-40fc-bda0-ae65295aa2b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:00:09,505] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg58ab04ad-c9cf-40fc-bda0-ae65295aa2b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:00:09,509] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:00:09,509] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 21:00:09,509] [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	75.8812	74	788	95	below_threshold
Nonomuraea typhae	strain=p1410	GCA_009760925.1	2603600	2603600	type	True	74.7026	62	788	95	below_threshold
Nonomuraea dietziae	strain=DSM 44320	GCA_014195505.1	65515	65515	type	True	74.5558	53	788	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 21:00:09,510] [INFO] DFAST Taxonomy check result was written to OceanDNA-b269/tc_result.tsv
[2023-03-18 21:00:09,510] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:00:09,510] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:00:09,510] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg58ab04ad-c9cf-40fc-bda0-ae65295aa2b9/dqc_reference/checkm_data
[2023-03-18 21:00:09,511] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:00:09,570] [INFO] Task started: CheckM
[2023-03-18 21:00:09,570] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b269/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b269/checkm_input OceanDNA-b269/checkm_result
[2023-03-18 21:00:47,971] [INFO] Task succeeded: CheckM
[2023-03-18 21:00:47,972] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 21:00:47,997] [INFO] ===== Completeness check finished =====
[2023-03-18 21:00:47,997] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:00:47,997] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b269/markers.fasta)
[2023-03-18 21:00:47,998] [INFO] Task started: Blastn
[2023-03-18 21:00:47,998] [INFO] Running command: blastn -query OceanDNA-b269/markers.fasta -db /var/lib/cwl/stg58ab04ad-c9cf-40fc-bda0-ae65295aa2b9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b269/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:00:48,522] [INFO] Task succeeded: Blastn
[2023-03-18 21:00:48,528] [INFO] Selected 8 target genomes.
[2023-03-18 21:00:48,528] [INFO] Target genome list was writen to OceanDNA-b269/target_genomes_gtdb.txt
[2023-03-18 21:00:48,537] [INFO] Task started: fastANI
[2023-03-18 21:00:48,537] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e7a7d37-d6af-42f4-bbb5-fd41b7c1add3/OceanDNA-b269.fa --refList OceanDNA-b269/target_genomes_gtdb.txt --output OceanDNA-b269/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:00:54,843] [INFO] Task succeeded: fastANI
[2023-03-18 21:00:54,848] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 21:00:54,848] [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_015659035.1	s__NP936 sp015659035	96.1693	527	788	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_002726085.1	s__NP936 sp002726085	80.6179	467	788	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	77.522	257	788	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__UBA8438	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011523845.1	s__WTFV01 sp011523845	77.0326	252	788	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__WTFV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002346545.1	s__UBA2994 sp002346545	77.0229	184	788	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__UBA2994	95.0	99.87	99.87	0.91	0.91	2	-
GCA_012271165.1	s__JAAXGX01 sp012271165	76.5853	166	788	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__JAAXGX01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 21:00:54,850] [INFO] GTDB search result was written to OceanDNA-b269/result_gtdb.tsv
[2023-03-18 21:00:54,856] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:00:54,860] [INFO] DFAST_QC result json was written to OceanDNA-b269/dqc_result.json
[2023-03-18 21:00:54,860] [INFO] DFAST_QC completed!
[2023-03-18 21:00:54,860] [INFO] Total running time: 0h1m11s