[2023-03-18 07:47:43,037] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:47:43,038] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:47:43,038] [INFO] DQC Reference Directory: /var/lib/cwl/stg350a4386-894e-4a05-b343-f21782c92aab/dqc_reference
[2023-03-18 07:47:44,202] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:47:44,202] [INFO] Task started: Prodigal
[2023-03-18 07:47:44,202] [INFO] Running command: cat /var/lib/cwl/stg961efcf7-3c61-4c52-bf20-4a007f6e5750/OceanDNA-a4490.fa | prodigal -d OceanDNA-a4490/cds.fna -a OceanDNA-a4490/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:47:51,767] [INFO] Task succeeded: Prodigal
[2023-03-18 07:47:51,768] [INFO] Task started: HMMsearch
[2023-03-18 07:47:51,768] [INFO] Running command: hmmsearch --tblout OceanDNA-a4490/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg350a4386-894e-4a05-b343-f21782c92aab/dqc_reference/reference_markers.hmm OceanDNA-a4490/protein.faa > /dev/null
[2023-03-18 07:47:51,924] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:47:51,924] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg961efcf7-3c61-4c52-bf20-4a007f6e5750/OceanDNA-a4490.fa]
[2023-03-18 07:47:51,934] [INFO] Query marker FASTA was written to OceanDNA-a4490/markers.fasta
[2023-03-18 07:47:51,934] [INFO] Task started: Blastn
[2023-03-18 07:47:51,934] [INFO] Running command: blastn -query OceanDNA-a4490/markers.fasta -db /var/lib/cwl/stg350a4386-894e-4a05-b343-f21782c92aab/dqc_reference/reference_markers.fasta -out OceanDNA-a4490/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:47:52,363] [INFO] Task succeeded: Blastn
[2023-03-18 07:47:52,363] [INFO] Selected 2 target genomes.
[2023-03-18 07:47:52,364] [INFO] Target genome list was writen to OceanDNA-a4490/target_genomes.txt
[2023-03-18 07:47:52,365] [INFO] Task started: fastANI
[2023-03-18 07:47:52,365] [INFO] Running command: fastANI --query /var/lib/cwl/stg961efcf7-3c61-4c52-bf20-4a007f6e5750/OceanDNA-a4490.fa --refList OceanDNA-a4490/target_genomes.txt --output OceanDNA-a4490/fastani_result.tsv --threads 1
[2023-03-18 07:47:53,492] [INFO] Task succeeded: fastANI
[2023-03-18 07:47:53,492] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg350a4386-894e-4a05-b343-f21782c92aab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:47:53,493] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg350a4386-894e-4a05-b343-f21782c92aab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:47:53,493] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 07:47:53,493] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 07:47:53,493] [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 07:47:53,493] [INFO] DFAST Taxonomy check result was written to OceanDNA-a4490/tc_result.tsv
[2023-03-18 07:47:53,493] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:47:53,493] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:47:53,493] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg350a4386-894e-4a05-b343-f21782c92aab/dqc_reference/checkm_data
[2023-03-18 07:47:53,496] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:47:53,498] [INFO] Task started: CheckM
[2023-03-18 07:47:53,498] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4490/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4490/checkm_input OceanDNA-a4490/checkm_result
[2023-03-18 07:48:17,452] [INFO] Task succeeded: CheckM
[2023-03-18 07:48:17,453] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.90%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 07:48:17,454] [INFO] ===== Completeness check finished =====
[2023-03-18 07:48:17,455] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:48:17,455] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4490/markers.fasta)
[2023-03-18 07:48:17,455] [INFO] Task started: Blastn
[2023-03-18 07:48:17,455] [INFO] Running command: blastn -query OceanDNA-a4490/markers.fasta -db /var/lib/cwl/stg350a4386-894e-4a05-b343-f21782c92aab/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4490/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:48:17,853] [INFO] Task succeeded: Blastn
[2023-03-18 07:48:17,854] [INFO] Selected 5 target genomes.
[2023-03-18 07:48:17,854] [INFO] Target genome list was writen to OceanDNA-a4490/target_genomes_gtdb.txt
[2023-03-18 07:48:17,861] [INFO] Task started: fastANI
[2023-03-18 07:48:17,861] [INFO] Running command: fastANI --query /var/lib/cwl/stg961efcf7-3c61-4c52-bf20-4a007f6e5750/OceanDNA-a4490.fa --refList OceanDNA-a4490/target_genomes_gtdb.txt --output OceanDNA-a4490/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:48:19,221] [INFO] Task succeeded: fastANI
[2023-03-18 07:48:19,225] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 07:48:19,225] [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_002498925.1	s__MGIIb-O5 sp002498925	99.6139	351	424	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O5	95.0	99.31	97.86	0.85	0.82	9	conclusive
GCA_002718995.2	s__MGIIb-O5 sp002718995	88.7751	387	424	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O5	95.0	99.42	98.33	0.97	0.95	5	-
GCA_002504435.1	s__MGIIb-O5 sp002504435	81.1267	299	424	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O5	95.0	99.62	99.62	0.76	0.76	2	-
GCA_002497985.1	s__MGIIb-O5 sp002497985	79.4796	148	424	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O5	95.0	95.38	95.38	0.60	0.60	2	-
--------------------------------------------------------------------------------
[2023-03-18 07:48:19,225] [INFO] GTDB search result was written to OceanDNA-a4490/result_gtdb.tsv
[2023-03-18 07:48:19,225] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:48:19,226] [INFO] DFAST_QC result json was written to OceanDNA-a4490/dqc_result.json
[2023-03-18 07:48:19,226] [INFO] DFAST_QC completed!
[2023-03-18 07:48:19,226] [INFO] Total running time: 0h0m36s