[2023-03-17 10:48:45,595] [INFO] DFAST_QC pipeline started.
[2023-03-17 10:48:45,595] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 10:48:45,595] [INFO] DQC Reference Directory: /var/lib/cwl/stgdc478d61-8e78-4394-9e98-76bb4310a408/dqc_reference
[2023-03-17 10:48:46,693] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 10:48:46,694] [INFO] Task started: Prodigal
[2023-03-17 10:48:46,694] [INFO] Running command: cat /var/lib/cwl/stg6d1fc075-bc7a-4ef6-a35d-479e4e64e453/OceanDNA-a4458.fa | prodigal -d OceanDNA-a4458/cds.fna -a OceanDNA-a4458/protein.faa -g 11 -q > /dev/null
[2023-03-17 10:48:55,032] [INFO] Task succeeded: Prodigal
[2023-03-17 10:48:55,032] [INFO] Task started: HMMsearch
[2023-03-17 10:48:55,032] [INFO] Running command: hmmsearch --tblout OceanDNA-a4458/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdc478d61-8e78-4394-9e98-76bb4310a408/dqc_reference/reference_markers.hmm OceanDNA-a4458/protein.faa > /dev/null
[2023-03-17 10:48:55,219] [INFO] Task succeeded: HMMsearch
[2023-03-17 10:48:55,220] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg6d1fc075-bc7a-4ef6-a35d-479e4e64e453/OceanDNA-a4458.fa]
[2023-03-17 10:48:55,234] [INFO] Query marker FASTA was written to OceanDNA-a4458/markers.fasta
[2023-03-17 10:48:55,235] [INFO] Task started: Blastn
[2023-03-17 10:48:55,235] [INFO] Running command: blastn -query OceanDNA-a4458/markers.fasta -db /var/lib/cwl/stgdc478d61-8e78-4394-9e98-76bb4310a408/dqc_reference/reference_markers.fasta -out OceanDNA-a4458/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:48:55,721] [INFO] Task succeeded: Blastn
[2023-03-17 10:48:55,722] [INFO] Selected 1 target genomes.
[2023-03-17 10:48:55,722] [INFO] Target genome list was writen to OceanDNA-a4458/target_genomes.txt
[2023-03-17 10:48:55,725] [INFO] Task started: fastANI
[2023-03-17 10:48:55,725] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d1fc075-bc7a-4ef6-a35d-479e4e64e453/OceanDNA-a4458.fa --refList OceanDNA-a4458/target_genomes.txt --output OceanDNA-a4458/fastani_result.tsv --threads 1
[2023-03-17 10:48:56,178] [INFO] Task succeeded: fastANI
[2023-03-17 10:48:56,178] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdc478d61-8e78-4394-9e98-76bb4310a408/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 10:48:56,178] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdc478d61-8e78-4394-9e98-76bb4310a408/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 10:48:56,178] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 10:48:56,179] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 10:48:56,179] [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
--------------------------------------------------------------------------------
[2023-03-17 10:48:56,179] [INFO] DFAST Taxonomy check result was written to OceanDNA-a4458/tc_result.tsv
[2023-03-17 10:48:56,179] [INFO] ===== Taxonomy check completed =====
[2023-03-17 10:48:56,179] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 10:48:56,179] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdc478d61-8e78-4394-9e98-76bb4310a408/dqc_reference/checkm_data
[2023-03-17 10:48:56,182] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 10:48:56,189] [INFO] Task started: CheckM
[2023-03-17 10:48:56,189] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4458/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4458/checkm_input OceanDNA-a4458/checkm_result
[2023-03-17 10:49:23,189] [INFO] Task succeeded: CheckM
[2023-03-17 10:49:23,189] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.90%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 10:49:23,191] [INFO] ===== Completeness check finished =====
[2023-03-17 10:49:23,191] [INFO] ===== Start GTDB Search =====
[2023-03-17 10:49:23,191] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4458/markers.fasta)
[2023-03-17 10:49:23,191] [INFO] Task started: Blastn
[2023-03-17 10:49:23,191] [INFO] Running command: blastn -query OceanDNA-a4458/markers.fasta -db /var/lib/cwl/stgdc478d61-8e78-4394-9e98-76bb4310a408/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4458/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:49:23,800] [INFO] Task succeeded: Blastn
[2023-03-17 10:49:23,800] [INFO] Selected 10 target genomes.
[2023-03-17 10:49:23,801] [INFO] Target genome list was writen to OceanDNA-a4458/target_genomes_gtdb.txt
[2023-03-17 10:49:23,945] [INFO] Task started: fastANI
[2023-03-17 10:49:23,945] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d1fc075-bc7a-4ef6-a35d-479e4e64e453/OceanDNA-a4458.fa --refList OceanDNA-a4458/target_genomes_gtdb.txt --output OceanDNA-a4458/fastani_result_gtdb.tsv --threads 1
[2023-03-17 10:49:26,605] [INFO] Task succeeded: fastANI
[2023-03-17 10:49:26,608] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 10:49:26,608] [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_002501605.1	s__MGIIb-O5 sp002501605	80.9233	276	463	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O5	95.0	99.05	98.72	0.89	0.86	6	-
GCA_002505775.1	s__MGIIb-O5 sp002505775	80.2601	303	463	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O5	95.0	99.25	97.62	0.92	0.83	5	-
GCA_002496725.1	s__MGIIb-O5 sp002496725	77.1483	100	463	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O5	95.0	99.85	99.85	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2023-03-17 10:49:26,609] [INFO] GTDB search result was written to OceanDNA-a4458/result_gtdb.tsv
[2023-03-17 10:49:26,609] [INFO] ===== GTDB Search completed =====
[2023-03-17 10:49:26,609] [INFO] DFAST_QC result json was written to OceanDNA-a4458/dqc_result.json
[2023-03-17 10:49:26,609] [INFO] DFAST_QC completed!
[2023-03-17 10:49:26,609] [INFO] Total running time: 0h0m41s