[2023-03-18 08:42:34,402] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:42:34,402] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:42:34,402] [INFO] DQC Reference Directory: /var/lib/cwl/stg20f5ff6f-1010-40ec-b2d1-9f8d96bbabe7/dqc_reference
[2023-03-18 08:42:35,540] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:42:35,540] [INFO] Task started: Prodigal
[2023-03-18 08:42:35,541] [INFO] Running command: cat /var/lib/cwl/stg2130ea86-d4a3-48f7-b5f2-0e8a433fcc0f/OceanDNA-a4114.fa | prodigal -d OceanDNA-a4114/cds.fna -a OceanDNA-a4114/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:42:41,763] [INFO] Task succeeded: Prodigal
[2023-03-18 08:42:41,764] [INFO] Task started: HMMsearch
[2023-03-18 08:42:41,764] [INFO] Running command: hmmsearch --tblout OceanDNA-a4114/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg20f5ff6f-1010-40ec-b2d1-9f8d96bbabe7/dqc_reference/reference_markers.hmm OceanDNA-a4114/protein.faa > /dev/null
[2023-03-18 08:42:41,923] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:42:41,923] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg2130ea86-d4a3-48f7-b5f2-0e8a433fcc0f/OceanDNA-a4114.fa]
[2023-03-18 08:42:41,951] [INFO] Query marker FASTA was written to OceanDNA-a4114/markers.fasta
[2023-03-18 08:42:41,952] [INFO] Task started: Blastn
[2023-03-18 08:42:41,952] [INFO] Running command: blastn -query OceanDNA-a4114/markers.fasta -db /var/lib/cwl/stg20f5ff6f-1010-40ec-b2d1-9f8d96bbabe7/dqc_reference/reference_markers.fasta -out OceanDNA-a4114/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:42:42,430] [INFO] Task succeeded: Blastn
[2023-03-18 08:42:42,437] [INFO] Selected 5 target genomes.
[2023-03-18 08:42:42,437] [INFO] Target genome list was writen to OceanDNA-a4114/target_genomes.txt
[2023-03-18 08:42:42,440] [INFO] Task started: fastANI
[2023-03-18 08:42:42,440] [INFO] Running command: fastANI --query /var/lib/cwl/stg2130ea86-d4a3-48f7-b5f2-0e8a433fcc0f/OceanDNA-a4114.fa --refList OceanDNA-a4114/target_genomes.txt --output OceanDNA-a4114/fastani_result.tsv --threads 1
[2023-03-18 08:42:47,098] [INFO] Task succeeded: fastANI
[2023-03-18 08:42:47,098] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg20f5ff6f-1010-40ec-b2d1-9f8d96bbabe7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:42:47,099] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg20f5ff6f-1010-40ec-b2d1-9f8d96bbabe7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:42:47,099] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:42:47,099] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 08:42:47,099] [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 08:42:47,101] [INFO] DFAST Taxonomy check result was written to OceanDNA-a4114/tc_result.tsv
[2023-03-18 08:42:47,106] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:42:47,106] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:42:47,106] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg20f5ff6f-1010-40ec-b2d1-9f8d96bbabe7/dqc_reference/checkm_data
[2023-03-18 08:42:47,109] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:42:47,113] [INFO] Task started: CheckM
[2023-03-18 08:42:47,113] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4114/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4114/checkm_input OceanDNA-a4114/checkm_result
[2023-03-18 08:43:12,131] [INFO] Task succeeded: CheckM
[2023-03-18 08:43:12,131] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.11%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 08:43:12,156] [INFO] ===== Completeness check finished =====
[2023-03-18 08:43:12,156] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:43:12,156] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4114/markers.fasta)
[2023-03-18 08:43:12,157] [INFO] Task started: Blastn
[2023-03-18 08:43:12,157] [INFO] Running command: blastn -query OceanDNA-a4114/markers.fasta -db /var/lib/cwl/stg20f5ff6f-1010-40ec-b2d1-9f8d96bbabe7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4114/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:43:12,755] [INFO] Task succeeded: Blastn
[2023-03-18 08:43:12,760] [INFO] Selected 7 target genomes.
[2023-03-18 08:43:12,760] [INFO] Target genome list was writen to OceanDNA-a4114/target_genomes_gtdb.txt
[2023-03-18 08:43:12,767] [INFO] Task started: fastANI
[2023-03-18 08:43:12,767] [INFO] Running command: fastANI --query /var/lib/cwl/stg2130ea86-d4a3-48f7-b5f2-0e8a433fcc0f/OceanDNA-a4114.fa --refList OceanDNA-a4114/target_genomes_gtdb.txt --output OceanDNA-a4114/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:43:14,381] [INFO] Task succeeded: fastANI
[2023-03-18 08:43:14,384] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 08:43:14,384] [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_002722735.1	s__MGIIb-O3 sp002722735	82.4035	248	333	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	99.60	99.54	0.93	0.90	4	-
GCA_003193925.1	s__Thalassarchaeum betae	78.8805	118	333	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	99.52	98.11	0.96	0.90	6	-
GCA_002507125.1	s__Thalassarchaeum sp002507125	78.0401	74	333	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	98.54	98.42	0.77	0.74	3	-
GCA_002725315.1	s__MGIIb-O3 sp002725315	76.8022	62	333	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	99.12	98.81	0.90	0.86	5	-
--------------------------------------------------------------------------------
[2023-03-18 08:43:14,386] [INFO] GTDB search result was written to OceanDNA-a4114/result_gtdb.tsv
[2023-03-18 08:43:14,386] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:43:14,388] [INFO] DFAST_QC result json was written to OceanDNA-a4114/dqc_result.json
[2023-03-18 08:43:14,388] [INFO] DFAST_QC completed!
[2023-03-18 08:43:14,388] [INFO] Total running time: 0h0m40s