[2023-03-15 08:11:05,970] [INFO] DFAST_QC pipeline started.
[2023-03-15 08:11:05,970] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 08:11:05,970] [INFO] DQC Reference Directory: /var/lib/cwl/stgd5c16ee1-c43f-40e8-ba09-97e345443c3f/dqc_reference
[2023-03-15 08:11:07,057] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 08:11:07,058] [INFO] Task started: Prodigal
[2023-03-15 08:11:07,058] [INFO] Running command: cat /var/lib/cwl/stg6f0f10e3-e2df-4109-af6a-aa483b1d7573/OceanDNA-a3224.fa | prodigal -d OceanDNA-a3224/cds.fna -a OceanDNA-a3224/protein.faa -g 11 -q > /dev/null
[2023-03-15 08:11:15,363] [INFO] Task succeeded: Prodigal
[2023-03-15 08:11:15,363] [INFO] Task started: HMMsearch
[2023-03-15 08:11:15,363] [INFO] Running command: hmmsearch --tblout OceanDNA-a3224/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd5c16ee1-c43f-40e8-ba09-97e345443c3f/dqc_reference/reference_markers.hmm OceanDNA-a3224/protein.faa > /dev/null
[2023-03-15 08:11:15,531] [INFO] Task succeeded: HMMsearch
[2023-03-15 08:11:15,531] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg6f0f10e3-e2df-4109-af6a-aa483b1d7573/OceanDNA-a3224.fa]
[2023-03-15 08:11:15,598] [INFO] Query marker FASTA was written to OceanDNA-a3224/markers.fasta
[2023-03-15 08:11:15,598] [INFO] Task started: Blastn
[2023-03-15 08:11:15,598] [INFO] Running command: blastn -query OceanDNA-a3224/markers.fasta -db /var/lib/cwl/stgd5c16ee1-c43f-40e8-ba09-97e345443c3f/dqc_reference/reference_markers.fasta -out OceanDNA-a3224/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:11:16,045] [INFO] Task succeeded: Blastn
[2023-03-15 08:11:16,068] [INFO] Selected 5 target genomes.
[2023-03-15 08:11:16,068] [INFO] Target genome list was writen to OceanDNA-a3224/target_genomes.txt
[2023-03-15 08:11:16,071] [INFO] Task started: fastANI
[2023-03-15 08:11:16,071] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f0f10e3-e2df-4109-af6a-aa483b1d7573/OceanDNA-a3224.fa --refList OceanDNA-a3224/target_genomes.txt --output OceanDNA-a3224/fastani_result.tsv --threads 1
[2023-03-15 08:11:17,725] [INFO] Task succeeded: fastANI
[2023-03-15 08:11:17,726] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd5c16ee1-c43f-40e8-ba09-97e345443c3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 08:11:17,726] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd5c16ee1-c43f-40e8-ba09-97e345443c3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 08:11:17,726] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 08:11:17,726] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 08:11:17,726] [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
--------------------------------------------------------------------------------
[2023-03-15 08:11:17,737] [INFO] DFAST Taxonomy check result was written to OceanDNA-a3224/tc_result.tsv
[2023-03-15 08:11:17,749] [INFO] ===== Taxonomy check completed =====
[2023-03-15 08:11:17,750] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 08:11:17,750] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd5c16ee1-c43f-40e8-ba09-97e345443c3f/dqc_reference/checkm_data
[2023-03-15 08:11:17,753] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 08:11:17,759] [INFO] Task started: CheckM
[2023-03-15 08:11:17,760] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a3224/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a3224/checkm_input OceanDNA-a3224/checkm_result
[2023-03-15 08:11:43,909] [INFO] Task succeeded: CheckM
[2023-03-15 08:11:43,910] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.90%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 08:11:43,953] [INFO] ===== Completeness check finished =====
[2023-03-15 08:11:43,953] [INFO] ===== Start GTDB Search =====
[2023-03-15 08:11:43,954] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a3224/markers.fasta)
[2023-03-15 08:11:43,955] [INFO] Task started: Blastn
[2023-03-15 08:11:43,955] [INFO] Running command: blastn -query OceanDNA-a3224/markers.fasta -db /var/lib/cwl/stgd5c16ee1-c43f-40e8-ba09-97e345443c3f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a3224/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:11:44,414] [INFO] Task succeeded: Blastn
[2023-03-15 08:11:44,415] [INFO] Selected 7 target genomes.
[2023-03-15 08:11:44,415] [INFO] Target genome list was writen to OceanDNA-a3224/target_genomes_gtdb.txt
[2023-03-15 08:11:44,421] [INFO] Task started: fastANI
[2023-03-15 08:11:44,421] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f0f10e3-e2df-4109-af6a-aa483b1d7573/OceanDNA-a3224.fa --refList OceanDNA-a3224/target_genomes_gtdb.txt --output OceanDNA-a3224/fastani_result_gtdb.tsv --threads 1
[2023-03-15 08:11:46,723] [INFO] Task succeeded: fastANI
[2023-03-15 08:11:46,728] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 08:11:46,728] [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_002170775.2	s__MGIIb-N1 sp002170775	99.6559	421	462	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-N1	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002712645.1	s__MGIIb-N1 sp002712645	90.9217	403	462	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-N1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002497295.1	s__MGIIb-N1 sp002497295	89.1245	384	462	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-N1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002504845.1	s__MGIIb-N1 sp002504845	88.5011	346	462	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-N1	95.0	98.34	97.20	0.81	0.69	5	-
GCA_002505455.1	s__MGIIb-N1 sp002505455	84.3124	374	462	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-N1	95.0	98.69	95.53	0.89	0.80	5	-
GCA_002717835.1	s__MGIIb-N1 sp002717835	82.667	308	462	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-N1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 08:11:46,728] [INFO] GTDB search result was written to OceanDNA-a3224/result_gtdb.tsv
[2023-03-15 08:11:46,728] [INFO] ===== GTDB Search completed =====
[2023-03-15 08:11:46,729] [INFO] DFAST_QC result json was written to OceanDNA-a3224/dqc_result.json
[2023-03-15 08:11:46,729] [INFO] DFAST_QC completed!
[2023-03-15 08:11:46,729] [INFO] Total running time: 0h0m41s