[2023-03-18 20:55:47,273] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:55:47,273] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:55:47,274] [INFO] DQC Reference Directory: /var/lib/cwl/stgefe47605-c64e-45cc-8b29-410520676993/dqc_reference
[2023-03-18 20:55:48,411] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:55:48,411] [INFO] Task started: Prodigal
[2023-03-18 20:55:48,412] [INFO] Running command: cat /var/lib/cwl/stg4545c0c7-d6cc-4d29-a59d-6208eb6581cb/OceanDNA-a5149.fa | prodigal -d OceanDNA-a5149/cds.fna -a OceanDNA-a5149/protein.faa -g 11 -q > /dev/null
[2023-03-18 20:55:55,411] [INFO] Task succeeded: Prodigal
[2023-03-18 20:55:55,411] [INFO] Task started: HMMsearch
[2023-03-18 20:55:55,411] [INFO] Running command: hmmsearch --tblout OceanDNA-a5149/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgefe47605-c64e-45cc-8b29-410520676993/dqc_reference/reference_markers.hmm OceanDNA-a5149/protein.faa > /dev/null
[2023-03-18 20:55:55,566] [INFO] Task succeeded: HMMsearch
[2023-03-18 20:55:55,567] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg4545c0c7-d6cc-4d29-a59d-6208eb6581cb/OceanDNA-a5149.fa]
[2023-03-18 20:55:55,577] [INFO] Query marker FASTA was written to OceanDNA-a5149/markers.fasta
[2023-03-18 20:55:55,577] [INFO] Task started: Blastn
[2023-03-18 20:55:55,577] [INFO] Running command: blastn -query OceanDNA-a5149/markers.fasta -db /var/lib/cwl/stgefe47605-c64e-45cc-8b29-410520676993/dqc_reference/reference_markers.fasta -out OceanDNA-a5149/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:55:55,997] [INFO] Task succeeded: Blastn
[2023-03-18 20:55:55,998] [INFO] Selected 2 target genomes.
[2023-03-18 20:55:55,998] [INFO] Target genome list was writen to OceanDNA-a5149/target_genomes.txt
[2023-03-18 20:55:56,000] [INFO] Task started: fastANI
[2023-03-18 20:55:56,000] [INFO] Running command: fastANI --query /var/lib/cwl/stg4545c0c7-d6cc-4d29-a59d-6208eb6581cb/OceanDNA-a5149.fa --refList OceanDNA-a5149/target_genomes.txt --output OceanDNA-a5149/fastani_result.tsv --threads 1
[2023-03-18 20:55:56,987] [INFO] Task succeeded: fastANI
[2023-03-18 20:55:56,987] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgefe47605-c64e-45cc-8b29-410520676993/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 20:55:56,987] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgefe47605-c64e-45cc-8b29-410520676993/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 20:55:56,988] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 20:55:56,988] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 20:55:56,988] [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 20:55:56,988] [INFO] DFAST Taxonomy check result was written to OceanDNA-a5149/tc_result.tsv
[2023-03-18 20:55:56,988] [INFO] ===== Taxonomy check completed =====
[2023-03-18 20:55:56,988] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 20:55:56,988] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgefe47605-c64e-45cc-8b29-410520676993/dqc_reference/checkm_data
[2023-03-18 20:55:57,041] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 20:55:57,043] [INFO] Task started: CheckM
[2023-03-18 20:55:57,044] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a5149/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a5149/checkm_input OceanDNA-a5149/checkm_result
[2023-03-18 20:56:19,945] [INFO] Task succeeded: CheckM
[2023-03-18 20:56:19,945] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.78%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 20:56:19,946] [INFO] ===== Completeness check finished =====
[2023-03-18 20:56:19,946] [INFO] ===== Start GTDB Search =====
[2023-03-18 20:56:19,947] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a5149/markers.fasta)
[2023-03-18 20:56:19,947] [INFO] Task started: Blastn
[2023-03-18 20:56:19,947] [INFO] Running command: blastn -query OceanDNA-a5149/markers.fasta -db /var/lib/cwl/stgefe47605-c64e-45cc-8b29-410520676993/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a5149/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:56:20,370] [INFO] Task succeeded: Blastn
[2023-03-18 20:56:20,371] [INFO] Selected 8 target genomes.
[2023-03-18 20:56:20,371] [INFO] Target genome list was writen to OceanDNA-a5149/target_genomes_gtdb.txt
[2023-03-18 20:56:20,445] [INFO] Task started: fastANI
[2023-03-18 20:56:20,446] [INFO] Running command: fastANI --query /var/lib/cwl/stg4545c0c7-d6cc-4d29-a59d-6208eb6581cb/OceanDNA-a5149.fa --refList OceanDNA-a5149/target_genomes_gtdb.txt --output OceanDNA-a5149/fastani_result_gtdb.tsv --threads 1
[2023-03-18 20:56:22,551] [INFO] Task succeeded: fastANI
[2023-03-18 20:56:22,555] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 20:56:22,555] [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_002714745.1	s__Thalassarchaeum sp002714745	98.7723	308	390	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	97.82	95.69	0.77	0.69	7	conclusive
GCA_002727275.1	s__Thalassarchaeum sp002727275	81.4331	259	390	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002698225.1	s__Thalassarchaeum sp002698225	80.5183	250	390	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	99.66	99.66	0.83	0.83	2	-
GCA_002501885.1	s__Thalassarchaeum sp002501885	79.0121	222	390	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	98.85	97.05	0.83	0.68	9	-
--------------------------------------------------------------------------------
[2023-03-18 20:56:22,555] [INFO] GTDB search result was written to OceanDNA-a5149/result_gtdb.tsv
[2023-03-18 20:56:22,555] [INFO] ===== GTDB Search completed =====
[2023-03-18 20:56:22,556] [INFO] DFAST_QC result json was written to OceanDNA-a5149/dqc_result.json
[2023-03-18 20:56:22,556] [INFO] DFAST_QC completed!
[2023-03-18 20:56:22,556] [INFO] Total running time: 0h0m35s