[2023-03-15 13:00:04,933] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:00:04,933] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:00:04,933] [INFO] DQC Reference Directory: /var/lib/cwl/stg174246a9-4a18-4235-a887-e4970bd4a116/dqc_reference
[2023-03-15 13:00:06,090] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:00:06,091] [INFO] Task started: Prodigal
[2023-03-15 13:00:06,091] [INFO] Running command: cat /var/lib/cwl/stgf848f528-c9fb-4629-88a5-5fbd2a23d792/OceanDNA-a4040.fa | prodigal -d OceanDNA-a4040/cds.fna -a OceanDNA-a4040/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:00:12,563] [INFO] Task succeeded: Prodigal
[2023-03-15 13:00:12,563] [INFO] Task started: HMMsearch
[2023-03-15 13:00:12,563] [INFO] Running command: hmmsearch --tblout OceanDNA-a4040/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg174246a9-4a18-4235-a887-e4970bd4a116/dqc_reference/reference_markers.hmm OceanDNA-a4040/protein.faa > /dev/null
[2023-03-15 13:00:12,729] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:00:12,730] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgf848f528-c9fb-4629-88a5-5fbd2a23d792/OceanDNA-a4040.fa]
[2023-03-15 13:00:12,740] [INFO] Query marker FASTA was written to OceanDNA-a4040/markers.fasta
[2023-03-15 13:00:12,740] [INFO] Task started: Blastn
[2023-03-15 13:00:12,740] [INFO] Running command: blastn -query OceanDNA-a4040/markers.fasta -db /var/lib/cwl/stg174246a9-4a18-4235-a887-e4970bd4a116/dqc_reference/reference_markers.fasta -out OceanDNA-a4040/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:00:13,164] [INFO] Task succeeded: Blastn
[2023-03-15 13:00:13,165] [INFO] Selected 5 target genomes.
[2023-03-15 13:00:13,165] [INFO] Target genome list was writen to OceanDNA-a4040/target_genomes.txt
[2023-03-15 13:00:13,170] [INFO] Task started: fastANI
[2023-03-15 13:00:13,170] [INFO] Running command: fastANI --query /var/lib/cwl/stgf848f528-c9fb-4629-88a5-5fbd2a23d792/OceanDNA-a4040.fa --refList OceanDNA-a4040/target_genomes.txt --output OceanDNA-a4040/fastani_result.tsv --threads 1
[2023-03-15 13:00:14,436] [INFO] Task succeeded: fastANI
[2023-03-15 13:00:14,437] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg174246a9-4a18-4235-a887-e4970bd4a116/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:00:14,437] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg174246a9-4a18-4235-a887-e4970bd4a116/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:00:14,437] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 13:00:14,437] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 13:00:14,437] [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 13:00:14,437] [INFO] DFAST Taxonomy check result was written to OceanDNA-a4040/tc_result.tsv
[2023-03-15 13:00:14,438] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:00:14,438] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:00:14,438] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg174246a9-4a18-4235-a887-e4970bd4a116/dqc_reference/checkm_data
[2023-03-15 13:00:14,491] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:00:14,494] [INFO] Task started: CheckM
[2023-03-15 13:00:14,494] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4040/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4040/checkm_input OceanDNA-a4040/checkm_result
[2023-03-15 13:00:38,643] [INFO] Task succeeded: CheckM
[2023-03-15 13:00:38,643] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.82%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 13:00:38,645] [INFO] ===== Completeness check finished =====
[2023-03-15 13:00:38,645] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:00:38,645] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4040/markers.fasta)
[2023-03-15 13:00:38,645] [INFO] Task started: Blastn
[2023-03-15 13:00:38,645] [INFO] Running command: blastn -query OceanDNA-a4040/markers.fasta -db /var/lib/cwl/stg174246a9-4a18-4235-a887-e4970bd4a116/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4040/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:00:39,081] [INFO] Task succeeded: Blastn
[2023-03-15 13:00:39,081] [INFO] Selected 8 target genomes.
[2023-03-15 13:00:39,082] [INFO] Target genome list was writen to OceanDNA-a4040/target_genomes_gtdb.txt
[2023-03-15 13:00:39,170] [INFO] Task started: fastANI
[2023-03-15 13:00:39,170] [INFO] Running command: fastANI --query /var/lib/cwl/stgf848f528-c9fb-4629-88a5-5fbd2a23d792/OceanDNA-a4040.fa --refList OceanDNA-a4040/target_genomes_gtdb.txt --output OceanDNA-a4040/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:00:41,206] [INFO] Task succeeded: fastANI
[2023-03-15 13:00:41,211] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 13:00:41,211] [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_002686525.1	s__MGIIb-O2 sp002686525	96.9403	333	395	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O2	95.0	97.02	96.68	0.82	0.74	10	conclusive
GCA_902593945.1	s__MGIIb-O2 sp902593945	80.1545	227	395	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002497245.1	s__MGIIb-O2 sp002497245	80.0099	281	395	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O2	95.0	97.50	97.50	0.90	0.90	2	-
GCA_002498985.1	s__MGIIb-O2 sp002498985	79.8104	228	395	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O2	95.0	97.30	95.20	0.78	0.62	4	-
GCA_002504905.1	s__MGIIb-O2 sp002504905	79.6582	281	395	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O2	95.0	99.85	99.68	0.95	0.91	6	-
GCA_002685315.1	s__MGIIb-O2 sp002685315	79.2608	166	395	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016777225.1	s__MGIIb-O2 sp016777225	78.703	176	395	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902514485.1	s__MGIIb-O2 sp902514485	78.1269	95	395	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O2	95.0	98.21	98.21	0.74	0.74	2	-
--------------------------------------------------------------------------------
[2023-03-15 13:00:41,212] [INFO] GTDB search result was written to OceanDNA-a4040/result_gtdb.tsv
[2023-03-15 13:00:41,212] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:00:41,212] [INFO] DFAST_QC result json was written to OceanDNA-a4040/dqc_result.json
[2023-03-15 13:00:41,213] [INFO] DFAST_QC completed!
[2023-03-15 13:00:41,213] [INFO] Total running time: 0h0m36s