[2023-03-16 02:38:04,897] [INFO] DFAST_QC pipeline started.
[2023-03-16 02:38:04,897] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 02:38:04,897] [INFO] DQC Reference Directory: /var/lib/cwl/stg25fd9580-2a16-4a8c-aec1-60161d8cc538/dqc_reference
[2023-03-16 02:38:06,138] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 02:38:06,139] [INFO] Task started: Prodigal
[2023-03-16 02:38:06,139] [INFO] Running command: cat /var/lib/cwl/stgc700fa2e-e960-48a7-acf9-1cb7da69d2f1/OceanDNA-a4212.fa | prodigal -d OceanDNA-a4212/cds.fna -a OceanDNA-a4212/protein.faa -g 11 -q > /dev/null
[2023-03-16 02:38:14,341] [INFO] Task succeeded: Prodigal
[2023-03-16 02:38:14,341] [INFO] Task started: HMMsearch
[2023-03-16 02:38:14,341] [INFO] Running command: hmmsearch --tblout OceanDNA-a4212/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg25fd9580-2a16-4a8c-aec1-60161d8cc538/dqc_reference/reference_markers.hmm OceanDNA-a4212/protein.faa > /dev/null
[2023-03-16 02:38:14,495] [INFO] Task succeeded: HMMsearch
[2023-03-16 02:38:14,495] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgc700fa2e-e960-48a7-acf9-1cb7da69d2f1/OceanDNA-a4212.fa]
[2023-03-16 02:38:14,505] [INFO] Query marker FASTA was written to OceanDNA-a4212/markers.fasta
[2023-03-16 02:38:14,505] [INFO] Task started: Blastn
[2023-03-16 02:38:14,505] [INFO] Running command: blastn -query OceanDNA-a4212/markers.fasta -db /var/lib/cwl/stg25fd9580-2a16-4a8c-aec1-60161d8cc538/dqc_reference/reference_markers.fasta -out OceanDNA-a4212/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 02:38:14,942] [INFO] Task succeeded: Blastn
[2023-03-16 02:38:14,943] [INFO] Selected 0 target genomes.
[2023-03-16 02:38:14,943] [INFO] Target genome list was writen to OceanDNA-a4212/target_genomes.txt
[2023-03-16 02:38:14,943] [ERROR] File is empty. [OceanDNA-a4212/target_genomes.txt]
[2023-03-16 02:38:14,943] [ERROR] Task failed. No target genome found.
[2023-03-16 02:38:14,943] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 02:38:14,944] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg25fd9580-2a16-4a8c-aec1-60161d8cc538/dqc_reference/checkm_data
[2023-03-16 02:38:14,946] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 02:38:14,949] [INFO] Task started: CheckM
[2023-03-16 02:38:14,949] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4212/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4212/checkm_input OceanDNA-a4212/checkm_result
[2023-03-16 02:38:40,609] [INFO] Task succeeded: CheckM
[2023-03-16 02:38:40,609] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.73%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 02:38:40,611] [INFO] ===== Completeness check finished =====
[2023-03-16 02:38:40,611] [INFO] ===== Start GTDB Search =====
[2023-03-16 02:38:40,611] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4212/markers.fasta)
[2023-03-16 02:38:40,611] [INFO] Task started: Blastn
[2023-03-16 02:38:40,611] [INFO] Running command: blastn -query OceanDNA-a4212/markers.fasta -db /var/lib/cwl/stg25fd9580-2a16-4a8c-aec1-60161d8cc538/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4212/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 02:38:41,082] [INFO] Task succeeded: Blastn
[2023-03-16 02:38:41,083] [INFO] Selected 2 target genomes.
[2023-03-16 02:38:41,083] [INFO] Target genome list was writen to OceanDNA-a4212/target_genomes_gtdb.txt
[2023-03-16 02:38:41,144] [INFO] Task started: fastANI
[2023-03-16 02:38:41,145] [INFO] Running command: fastANI --query /var/lib/cwl/stgc700fa2e-e960-48a7-acf9-1cb7da69d2f1/OceanDNA-a4212.fa --refList OceanDNA-a4212/target_genomes_gtdb.txt --output OceanDNA-a4212/fastani_result_gtdb.tsv --threads 1
[2023-03-16 02:38:42,011] [INFO] Task succeeded: fastANI
[2023-03-16 02:38:42,013] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 02:38:42,014] [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_004195615.1	s__MGIIb-O3 sp004195615	95.7912	431	457	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	99.94	99.91	0.95	0.93	3	conclusive
GCA_014239955.1	s__MGIIb-O3 sp014239955	91.1795	387	457	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 02:38:42,014] [INFO] GTDB search result was written to OceanDNA-a4212/result_gtdb.tsv
[2023-03-16 02:38:42,014] [INFO] ===== GTDB Search completed =====
[2023-03-16 02:38:42,014] [INFO] DFAST_QC result json was written to OceanDNA-a4212/dqc_result.json
[2023-03-16 02:38:42,014] [INFO] DFAST_QC completed!
[2023-03-16 02:38:42,015] [INFO] Total running time: 0h0m37s