[2023-03-18 02:27:37,203] [INFO] DFAST_QC pipeline started.
[2023-03-18 02:27:37,203] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 02:27:37,203] [INFO] DQC Reference Directory: /var/lib/cwl/stg2b5bbe7e-668f-46d8-b411-8b93d41cce27/dqc_reference
[2023-03-18 02:27:38,463] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 02:27:38,463] [INFO] Task started: Prodigal
[2023-03-18 02:27:38,463] [INFO] Running command: cat /var/lib/cwl/stg3a3358af-528e-4e09-a959-d42d39edb969/OceanDNA-a2914.fa | prodigal -d OceanDNA-a2914/cds.fna -a OceanDNA-a2914/protein.faa -g 11 -q > /dev/null
[2023-03-18 02:27:45,300] [INFO] Task succeeded: Prodigal
[2023-03-18 02:27:45,300] [INFO] Task started: HMMsearch
[2023-03-18 02:27:45,300] [INFO] Running command: hmmsearch --tblout OceanDNA-a2914/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2b5bbe7e-668f-46d8-b411-8b93d41cce27/dqc_reference/reference_markers.hmm OceanDNA-a2914/protein.faa > /dev/null
[2023-03-18 02:27:45,438] [INFO] Task succeeded: HMMsearch
[2023-03-18 02:27:45,439] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg3a3358af-528e-4e09-a959-d42d39edb969/OceanDNA-a2914.fa]
[2023-03-18 02:27:45,451] [INFO] Query marker FASTA was written to OceanDNA-a2914/markers.fasta
[2023-03-18 02:27:45,452] [INFO] Task started: Blastn
[2023-03-18 02:27:45,452] [INFO] Running command: blastn -query OceanDNA-a2914/markers.fasta -db /var/lib/cwl/stg2b5bbe7e-668f-46d8-b411-8b93d41cce27/dqc_reference/reference_markers.fasta -out OceanDNA-a2914/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:27:45,897] [INFO] Task succeeded: Blastn
[2023-03-18 02:27:45,898] [INFO] Selected 9 target genomes.
[2023-03-18 02:27:45,898] [INFO] Target genome list was writen to OceanDNA-a2914/target_genomes.txt
[2023-03-18 02:27:45,903] [INFO] Task started: fastANI
[2023-03-18 02:27:45,903] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a3358af-528e-4e09-a959-d42d39edb969/OceanDNA-a2914.fa --refList OceanDNA-a2914/target_genomes.txt --output OceanDNA-a2914/fastani_result.tsv --threads 1
[2023-03-18 02:27:51,892] [INFO] Task succeeded: fastANI
[2023-03-18 02:27:51,893] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2b5bbe7e-668f-46d8-b411-8b93d41cce27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 02:27:51,893] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2b5bbe7e-668f-46d8-b411-8b93d41cce27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 02:27:51,893] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 02:27:51,893] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 02:27:51,893] [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 02:27:51,893] [INFO] DFAST Taxonomy check result was written to OceanDNA-a2914/tc_result.tsv
[2023-03-18 02:27:51,894] [INFO] ===== Taxonomy check completed =====
[2023-03-18 02:27:51,894] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 02:27:51,894] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2b5bbe7e-668f-46d8-b411-8b93d41cce27/dqc_reference/checkm_data
[2023-03-18 02:27:51,897] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 02:27:51,924] [INFO] Task started: CheckM
[2023-03-18 02:27:51,924] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2914/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2914/checkm_input OceanDNA-a2914/checkm_result
[2023-03-18 02:28:14,809] [INFO] Task succeeded: CheckM
[2023-03-18 02:28:14,809] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.16%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 02:28:14,811] [INFO] ===== Completeness check finished =====
[2023-03-18 02:28:14,811] [INFO] ===== Start GTDB Search =====
[2023-03-18 02:28:14,812] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2914/markers.fasta)
[2023-03-18 02:28:14,812] [INFO] Task started: Blastn
[2023-03-18 02:28:14,812] [INFO] Running command: blastn -query OceanDNA-a2914/markers.fasta -db /var/lib/cwl/stg2b5bbe7e-668f-46d8-b411-8b93d41cce27/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2914/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:28:15,263] [INFO] Task succeeded: Blastn
[2023-03-18 02:28:15,276] [INFO] Selected 9 target genomes.
[2023-03-18 02:28:15,276] [INFO] Target genome list was writen to OceanDNA-a2914/target_genomes_gtdb.txt
[2023-03-18 02:28:15,288] [INFO] Task started: fastANI
[2023-03-18 02:28:15,288] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a3358af-528e-4e09-a959-d42d39edb969/OceanDNA-a2914.fa --refList OceanDNA-a2914/target_genomes_gtdb.txt --output OceanDNA-a2914/fastani_result_gtdb.tsv --threads 1
[2023-03-18 02:28:17,963] [INFO] Task succeeded: fastANI
[2023-03-18 02:28:17,965] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 02:28:17,965] [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_002718195.1	s__MGIIa-L4 sp002718195	91.1573	303	359	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L4	95.0	99.84	99.84	0.65	0.65	2	-
--------------------------------------------------------------------------------
[2023-03-18 02:28:17,965] [INFO] GTDB search result was written to OceanDNA-a2914/result_gtdb.tsv
[2023-03-18 02:28:17,966] [INFO] ===== GTDB Search completed =====
[2023-03-18 02:28:17,966] [INFO] DFAST_QC result json was written to OceanDNA-a2914/dqc_result.json
[2023-03-18 02:28:17,966] [INFO] DFAST_QC completed!
[2023-03-18 02:28:17,966] [INFO] Total running time: 0h0m41s