[2023-03-15 12:44:24,480] [INFO] DFAST_QC pipeline started.
[2023-03-15 12:44:24,480] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 12:44:24,480] [INFO] DQC Reference Directory: /var/lib/cwl/stg1d18b895-9239-471f-93f5-df5de94bfec1/dqc_reference
[2023-03-15 12:44:26,204] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 12:44:26,205] [INFO] Task started: Prodigal
[2023-03-15 12:44:26,205] [INFO] Running command: cat /var/lib/cwl/stg6d5813b6-a6bd-43d6-8d67-45811374cd85/OceanDNA-a5205.fa | prodigal -d OceanDNA-a5205/cds.fna -a OceanDNA-a5205/protein.faa -g 11 -q > /dev/null
[2023-03-15 12:44:28,658] [INFO] Task succeeded: Prodigal
[2023-03-15 12:44:28,659] [INFO] Task started: HMMsearch
[2023-03-15 12:44:28,659] [INFO] Running command: hmmsearch --tblout OceanDNA-a5205/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1d18b895-9239-471f-93f5-df5de94bfec1/dqc_reference/reference_markers.hmm OceanDNA-a5205/protein.faa > /dev/null
[2023-03-15 12:44:28,768] [INFO] Task succeeded: HMMsearch
[2023-03-15 12:44:28,769] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg6d5813b6-a6bd-43d6-8d67-45811374cd85/OceanDNA-a5205.fa]
[2023-03-15 12:44:28,773] [INFO] Query marker FASTA was written to OceanDNA-a5205/markers.fasta
[2023-03-15 12:44:28,774] [INFO] Task started: Blastn
[2023-03-15 12:44:28,774] [INFO] Running command: blastn -query OceanDNA-a5205/markers.fasta -db /var/lib/cwl/stg1d18b895-9239-471f-93f5-df5de94bfec1/dqc_reference/reference_markers.fasta -out OceanDNA-a5205/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:44:30,617] [INFO] Task succeeded: Blastn
[2023-03-15 12:44:30,617] [INFO] Selected 1 target genomes.
[2023-03-15 12:44:30,617] [INFO] Target genome list was writen to OceanDNA-a5205/target_genomes.txt
[2023-03-15 12:44:30,619] [INFO] Task started: fastANI
[2023-03-15 12:44:30,619] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d5813b6-a6bd-43d6-8d67-45811374cd85/OceanDNA-a5205.fa --refList OceanDNA-a5205/target_genomes.txt --output OceanDNA-a5205/fastani_result.tsv --threads 1
[2023-03-15 12:44:30,940] [INFO] Task succeeded: fastANI
[2023-03-15 12:44:30,941] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1d18b895-9239-471f-93f5-df5de94bfec1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 12:44:30,941] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1d18b895-9239-471f-93f5-df5de94bfec1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 12:44:30,941] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 12:44:30,941] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 12:44:30,941] [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
--------------------------------------------------------------------------------
[2023-03-15 12:44:30,941] [INFO] DFAST Taxonomy check result was written to OceanDNA-a5205/tc_result.tsv
[2023-03-15 12:44:30,942] [INFO] ===== Taxonomy check completed =====
[2023-03-15 12:44:30,942] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 12:44:30,942] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1d18b895-9239-471f-93f5-df5de94bfec1/dqc_reference/checkm_data
[2023-03-15 12:44:30,944] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 12:44:31,573] [INFO] Task started: CheckM
[2023-03-15 12:44:31,573] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a5205/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a5205/checkm_input OceanDNA-a5205/checkm_result
[2023-03-15 12:44:45,577] [INFO] Task succeeded: CheckM
[2023-03-15 12:44:45,578] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 12:44:45,579] [INFO] ===== Completeness check finished =====
[2023-03-15 12:44:45,579] [INFO] ===== Start GTDB Search =====
[2023-03-15 12:44:45,579] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a5205/markers.fasta)
[2023-03-15 12:44:45,580] [INFO] Task started: Blastn
[2023-03-15 12:44:45,580] [INFO] Running command: blastn -query OceanDNA-a5205/markers.fasta -db /var/lib/cwl/stg1d18b895-9239-471f-93f5-df5de94bfec1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a5205/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:44:46,055] [INFO] Task succeeded: Blastn
[2023-03-15 12:44:46,056] [INFO] Selected 5 target genomes.
[2023-03-15 12:44:46,056] [INFO] Target genome list was writen to OceanDNA-a5205/target_genomes_gtdb.txt
[2023-03-15 12:44:46,099] [INFO] Task started: fastANI
[2023-03-15 12:44:46,100] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d5813b6-a6bd-43d6-8d67-45811374cd85/OceanDNA-a5205.fa --refList OceanDNA-a5205/target_genomes_gtdb.txt --output OceanDNA-a5205/fastani_result_gtdb.tsv --threads 1
[2023-03-15 12:44:47,347] [INFO] Task succeeded: fastANI
[2023-03-15 12:44:47,350] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 12:44:47,350] [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_002687935.1	s__Undinarchaeum sp002687935	99.8769	95	95	d__Archaea;p__Undinarchaeota;c__Undinarchaeia;o__Undinarchaeales;f__Undinarchaeaceae;g__Undinarchaeum	95.0	99.93	99.89	0.99	0.98	4	conclusive
GCA_002495465.1	s__Undinarchaeum marinum	85.2325	82	95	d__Archaea;p__Undinarchaeota;c__Undinarchaeia;o__Undinarchaeales;f__Undinarchaeaceae;g__Undinarchaeum	95.0	96.77	96.77	0.92	0.92	2	-
GCA_014189675.1	s__Undinarchaeum sp014189675	85.085	85	95	d__Archaea;p__Undinarchaeota;c__Undinarchaeia;o__Undinarchaeales;f__Undinarchaeaceae;g__Undinarchaeum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 12:44:47,351] [INFO] GTDB search result was written to OceanDNA-a5205/result_gtdb.tsv
[2023-03-15 12:44:47,351] [INFO] ===== GTDB Search completed =====
[2023-03-15 12:44:47,351] [INFO] DFAST_QC result json was written to OceanDNA-a5205/dqc_result.json
[2023-03-15 12:44:47,351] [INFO] DFAST_QC completed!
[2023-03-15 12:44:47,351] [INFO] Total running time: 0h0m23s