[2023-03-17 07:47:46,525] [INFO] DFAST_QC pipeline started.
[2023-03-17 07:47:46,525] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 07:47:46,525] [INFO] DQC Reference Directory: /var/lib/cwl/stgfe667c5d-a0f2-46ea-8370-068b729e9aff/dqc_reference
[2023-03-17 07:47:47,630] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 07:47:47,631] [INFO] Task started: Prodigal
[2023-03-17 07:47:47,631] [INFO] Running command: cat /var/lib/cwl/stg56bf8d2e-9018-4793-b97d-34df40c2f212/OceanDNA-a3466.fa | prodigal -d OceanDNA-a3466/cds.fna -a OceanDNA-a3466/protein.faa -g 11 -q > /dev/null
[2023-03-17 07:47:55,869] [INFO] Task succeeded: Prodigal
[2023-03-17 07:47:55,869] [INFO] Task started: HMMsearch
[2023-03-17 07:47:55,869] [INFO] Running command: hmmsearch --tblout OceanDNA-a3466/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfe667c5d-a0f2-46ea-8370-068b729e9aff/dqc_reference/reference_markers.hmm OceanDNA-a3466/protein.faa > /dev/null
[2023-03-17 07:47:56,025] [INFO] Task succeeded: HMMsearch
[2023-03-17 07:47:56,026] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg56bf8d2e-9018-4793-b97d-34df40c2f212/OceanDNA-a3466.fa]
[2023-03-17 07:47:56,035] [INFO] Query marker FASTA was written to OceanDNA-a3466/markers.fasta
[2023-03-17 07:47:56,035] [INFO] Task started: Blastn
[2023-03-17 07:47:56,035] [INFO] Running command: blastn -query OceanDNA-a3466/markers.fasta -db /var/lib/cwl/stgfe667c5d-a0f2-46ea-8370-068b729e9aff/dqc_reference/reference_markers.fasta -out OceanDNA-a3466/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:47:56,463] [INFO] Task succeeded: Blastn
[2023-03-17 07:47:56,464] [INFO] Selected 5 target genomes.
[2023-03-17 07:47:56,464] [INFO] Target genome list was writen to OceanDNA-a3466/target_genomes.txt
[2023-03-17 07:47:56,466] [INFO] Task started: fastANI
[2023-03-17 07:47:56,466] [INFO] Running command: fastANI --query /var/lib/cwl/stg56bf8d2e-9018-4793-b97d-34df40c2f212/OceanDNA-a3466.fa --refList OceanDNA-a3466/target_genomes.txt --output OceanDNA-a3466/fastani_result.tsv --threads 1
[2023-03-17 07:47:59,151] [INFO] Task succeeded: fastANI
[2023-03-17 07:47:59,151] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfe667c5d-a0f2-46ea-8370-068b729e9aff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 07:47:59,152] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfe667c5d-a0f2-46ea-8370-068b729e9aff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 07:47:59,152] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 07:47:59,152] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 07:47:59,152] [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 07:47:59,152] [INFO] DFAST Taxonomy check result was written to OceanDNA-a3466/tc_result.tsv
[2023-03-17 07:47:59,152] [INFO] ===== Taxonomy check completed =====
[2023-03-17 07:47:59,152] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 07:47:59,152] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfe667c5d-a0f2-46ea-8370-068b729e9aff/dqc_reference/checkm_data
[2023-03-17 07:47:59,155] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 07:47:59,158] [INFO] Task started: CheckM
[2023-03-17 07:47:59,158] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a3466/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a3466/checkm_input OceanDNA-a3466/checkm_result
[2023-03-17 07:48:24,608] [INFO] Task succeeded: CheckM
[2023-03-17 07:48:24,608] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.73%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 07:48:24,610] [INFO] ===== Completeness check finished =====
[2023-03-17 07:48:24,610] [INFO] ===== Start GTDB Search =====
[2023-03-17 07:48:24,610] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a3466/markers.fasta)
[2023-03-17 07:48:24,610] [INFO] Task started: Blastn
[2023-03-17 07:48:24,610] [INFO] Running command: blastn -query OceanDNA-a3466/markers.fasta -db /var/lib/cwl/stgfe667c5d-a0f2-46ea-8370-068b729e9aff/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a3466/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:48:25,043] [INFO] Task succeeded: Blastn
[2023-03-17 07:48:25,043] [INFO] Selected 9 target genomes.
[2023-03-17 07:48:25,043] [INFO] Target genome list was writen to OceanDNA-a3466/target_genomes_gtdb.txt
[2023-03-17 07:48:25,200] [INFO] Task started: fastANI
[2023-03-17 07:48:25,200] [INFO] Running command: fastANI --query /var/lib/cwl/stg56bf8d2e-9018-4793-b97d-34df40c2f212/OceanDNA-a3466.fa --refList OceanDNA-a3466/target_genomes_gtdb.txt --output OceanDNA-a3466/fastani_result_gtdb.tsv --threads 1
[2023-03-17 07:48:27,603] [INFO] Task succeeded: fastANI
[2023-03-17 07:48:27,607] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 07:48:27,607] [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_016845365.1	s__MGIIb-O1 sp016845365	83.5374	376	447	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013329905.1	s__MGIIb-O1 sp8684u	80.7833	281	447	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O1	95.0	99.67	99.41	0.91	0.86	4	-
GCA_002497895.1	s__MGIIb-O1 sp002497895	80.4535	216	447	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O1	95.0	99.30	99.27	0.83	0.71	4	-
GCA_902560445.1	s__MGIIb-O1 sp902560445	78.2139	62	447	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002498525.1	s__MGIIb-O1 sp002498525	77.7682	157	447	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O1	95.0	98.43	97.35	0.95	0.89	6	-
--------------------------------------------------------------------------------
[2023-03-17 07:48:27,608] [INFO] GTDB search result was written to OceanDNA-a3466/result_gtdb.tsv
[2023-03-17 07:48:27,608] [INFO] ===== GTDB Search completed =====
[2023-03-17 07:48:27,608] [INFO] DFAST_QC result json was written to OceanDNA-a3466/dqc_result.json
[2023-03-17 07:48:27,608] [INFO] DFAST_QC completed!
[2023-03-17 07:48:27,609] [INFO] Total running time: 0h0m41s