[2023-03-15 04:00:14,039] [INFO] DFAST_QC pipeline started.
[2023-03-15 04:00:14,039] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 04:00:14,039] [INFO] DQC Reference Directory: /var/lib/cwl/stg704d23ec-b593-4dad-8dd7-0eea98fcc5e8/dqc_reference
[2023-03-15 04:00:15,123] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 04:00:15,124] [INFO] Task started: Prodigal
[2023-03-15 04:00:15,124] [INFO] Running command: cat /var/lib/cwl/stgdfbecdc3-97ea-4f21-8a12-33104d700eb7/OceanDNA-a4836.fa | prodigal -d OceanDNA-a4836/cds.fna -a OceanDNA-a4836/protein.faa -g 11 -q > /dev/null
[2023-03-15 04:00:22,393] [INFO] Task succeeded: Prodigal
[2023-03-15 04:00:22,393] [INFO] Task started: HMMsearch
[2023-03-15 04:00:22,393] [INFO] Running command: hmmsearch --tblout OceanDNA-a4836/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg704d23ec-b593-4dad-8dd7-0eea98fcc5e8/dqc_reference/reference_markers.hmm OceanDNA-a4836/protein.faa > /dev/null
[2023-03-15 04:00:22,558] [INFO] Task succeeded: HMMsearch
[2023-03-15 04:00:22,559] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgdfbecdc3-97ea-4f21-8a12-33104d700eb7/OceanDNA-a4836.fa]
[2023-03-15 04:00:22,573] [INFO] Query marker FASTA was written to OceanDNA-a4836/markers.fasta
[2023-03-15 04:00:22,574] [INFO] Task started: Blastn
[2023-03-15 04:00:22,574] [INFO] Running command: blastn -query OceanDNA-a4836/markers.fasta -db /var/lib/cwl/stg704d23ec-b593-4dad-8dd7-0eea98fcc5e8/dqc_reference/reference_markers.fasta -out OceanDNA-a4836/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:00:23,074] [INFO] Task succeeded: Blastn
[2023-03-15 04:00:23,076] [INFO] Selected 0 target genomes.
[2023-03-15 04:00:23,077] [INFO] Target genome list was writen to OceanDNA-a4836/target_genomes.txt
[2023-03-15 04:00:23,077] [ERROR] File is empty. [OceanDNA-a4836/target_genomes.txt]
[2023-03-15 04:00:23,077] [ERROR] Task failed. No target genome found.
[2023-03-15 04:00:23,077] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 04:00:23,077] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg704d23ec-b593-4dad-8dd7-0eea98fcc5e8/dqc_reference/checkm_data
[2023-03-15 04:00:23,089] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 04:00:23,093] [INFO] Task started: CheckM
[2023-03-15 04:00:23,093] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4836/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4836/checkm_input OceanDNA-a4836/checkm_result
[2023-03-15 04:00:47,840] [INFO] Task succeeded: CheckM
[2023-03-15 04:00:47,841] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.03%
Contamintation: 2.23%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 04:00:47,846] [INFO] ===== Completeness check finished =====
[2023-03-15 04:00:47,846] [INFO] ===== Start GTDB Search =====
[2023-03-15 04:00:47,846] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4836/markers.fasta)
[2023-03-15 04:00:47,848] [INFO] Task started: Blastn
[2023-03-15 04:00:47,848] [INFO] Running command: blastn -query OceanDNA-a4836/markers.fasta -db /var/lib/cwl/stg704d23ec-b593-4dad-8dd7-0eea98fcc5e8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4836/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:00:48,733] [INFO] Task succeeded: Blastn
[2023-03-15 04:00:48,735] [INFO] Selected 5 target genomes.
[2023-03-15 04:00:48,735] [INFO] Target genome list was writen to OceanDNA-a4836/target_genomes_gtdb.txt
[2023-03-15 04:00:48,740] [INFO] Task started: fastANI
[2023-03-15 04:00:48,740] [INFO] Running command: fastANI --query /var/lib/cwl/stgdfbecdc3-97ea-4f21-8a12-33104d700eb7/OceanDNA-a4836.fa --refList OceanDNA-a4836/target_genomes_gtdb.txt --output OceanDNA-a4836/fastani_result_gtdb.tsv --threads 1
[2023-03-15 04:00:50,137] [INFO] Task succeeded: fastANI
[2023-03-15 04:00:50,139] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 04:00:50,139] [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_002685895.1	s__MGIIb-Q1 sp002685895	99.4126	302	390	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-Q1	95.0	99.01	99.01	0.75	0.75	3	conclusive
--------------------------------------------------------------------------------
[2023-03-15 04:00:50,142] [INFO] GTDB search result was written to OceanDNA-a4836/result_gtdb.tsv
[2023-03-15 04:00:50,143] [INFO] ===== GTDB Search completed =====
[2023-03-15 04:00:50,145] [INFO] DFAST_QC result json was written to OceanDNA-a4836/dqc_result.json
[2023-03-15 04:00:50,145] [INFO] DFAST_QC completed!
[2023-03-15 04:00:50,145] [INFO] Total running time: 0h0m36s