[2023-03-18 08:42:34,397] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:42:34,397] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:42:34,397] [INFO] DQC Reference Directory: /var/lib/cwl/stga6d26951-0066-496b-a541-df1bfc48b887/dqc_reference
[2023-03-18 08:42:35,510] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:42:35,510] [INFO] Task started: Prodigal
[2023-03-18 08:42:35,510] [INFO] Running command: cat /var/lib/cwl/stg7113f930-925b-4d00-b6c1-7b93949b2c59/OceanDNA-b46224.fa | prodigal -d OceanDNA-b46224/cds.fna -a OceanDNA-b46224/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:42:54,588] [INFO] Task succeeded: Prodigal
[2023-03-18 08:42:54,589] [INFO] Task started: HMMsearch
[2023-03-18 08:42:54,589] [INFO] Running command: hmmsearch --tblout OceanDNA-b46224/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga6d26951-0066-496b-a541-df1bfc48b887/dqc_reference/reference_markers.hmm OceanDNA-b46224/protein.faa > /dev/null
[2023-03-18 08:42:54,756] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:42:54,757] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg7113f930-925b-4d00-b6c1-7b93949b2c59/OceanDNA-b46224.fa]
[2023-03-18 08:42:54,779] [INFO] Query marker FASTA was written to OceanDNA-b46224/markers.fasta
[2023-03-18 08:42:54,780] [INFO] Task started: Blastn
[2023-03-18 08:42:54,781] [INFO] Running command: blastn -query OceanDNA-b46224/markers.fasta -db /var/lib/cwl/stga6d26951-0066-496b-a541-df1bfc48b887/dqc_reference/reference_markers.fasta -out OceanDNA-b46224/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:42:55,263] [INFO] Task succeeded: Blastn
[2023-03-18 08:42:55,275] [INFO] Selected 6 target genomes.
[2023-03-18 08:42:55,275] [INFO] Target genome list was writen to OceanDNA-b46224/target_genomes.txt
[2023-03-18 08:42:55,279] [INFO] Task started: fastANI
[2023-03-18 08:42:55,279] [INFO] Running command: fastANI --query /var/lib/cwl/stg7113f930-925b-4d00-b6c1-7b93949b2c59/OceanDNA-b46224.fa --refList OceanDNA-b46224/target_genomes.txt --output OceanDNA-b46224/fastani_result.tsv --threads 1
[2023-03-18 08:42:57,346] [INFO] Task succeeded: fastANI
[2023-03-18 08:42:57,346] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga6d26951-0066-496b-a541-df1bfc48b887/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:42:57,346] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga6d26951-0066-496b-a541-df1bfc48b887/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:42:57,346] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:42:57,347] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 08:42:57,347] [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
--------------------------------------------------------------------------------
[2023-03-18 08:42:57,349] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46224/tc_result.tsv
[2023-03-18 08:42:57,351] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:42:57,351] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:42:57,351] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga6d26951-0066-496b-a541-df1bfc48b887/dqc_reference/checkm_data
[2023-03-18 08:42:57,354] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:42:57,362] [INFO] Task started: CheckM
[2023-03-18 08:42:57,363] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46224/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46224/checkm_input OceanDNA-b46224/checkm_result
[2023-03-18 08:43:51,420] [INFO] Task succeeded: CheckM
[2023-03-18 08:43:51,421] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.94%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 08:43:51,487] [INFO] ===== Completeness check finished =====
[2023-03-18 08:43:51,487] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:43:51,487] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46224/markers.fasta)
[2023-03-18 08:43:51,488] [INFO] Task started: Blastn
[2023-03-18 08:43:51,488] [INFO] Running command: blastn -query OceanDNA-b46224/markers.fasta -db /var/lib/cwl/stga6d26951-0066-496b-a541-df1bfc48b887/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46224/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:43:52,109] [INFO] Task succeeded: Blastn
[2023-03-18 08:43:52,119] [INFO] Selected 16 target genomes.
[2023-03-18 08:43:52,120] [INFO] Target genome list was writen to OceanDNA-b46224/target_genomes_gtdb.txt
[2023-03-18 08:43:52,133] [INFO] Task started: fastANI
[2023-03-18 08:43:52,133] [INFO] Running command: fastANI --query /var/lib/cwl/stg7113f930-925b-4d00-b6c1-7b93949b2c59/OceanDNA-b46224.fa --refList OceanDNA-b46224/target_genomes_gtdb.txt --output OceanDNA-b46224/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:43:58,920] [INFO] Task succeeded: fastANI
[2023-03-18 08:43:58,922] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 08:43:58,923] [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_002690655.1	s__AAA164-E04 sp002690655	92.1624	466	567	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__AAA164-E04;g__AAA164-E04	95.0	99.74	99.61	0.83	0.80	9	-
GCA_000383715.1	s__AAA164-E04 sp000383715	91.9346	361	567	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__AAA164-E04;g__AAA164-E04	95.0	99.36	99.32	0.79	0.69	9	-
--------------------------------------------------------------------------------
[2023-03-18 08:43:58,925] [INFO] GTDB search result was written to OceanDNA-b46224/result_gtdb.tsv
[2023-03-18 08:43:58,929] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:43:58,931] [INFO] DFAST_QC result json was written to OceanDNA-b46224/dqc_result.json
[2023-03-18 08:43:58,931] [INFO] DFAST_QC completed!
[2023-03-18 08:43:58,931] [INFO] Total running time: 0h1m25s