[2023-03-15 07:03:38,857] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:03:38,859] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:03:38,859] [INFO] DQC Reference Directory: /var/lib/cwl/stg583aebe5-fd4a-4f97-8f9e-7f488919a7ad/dqc_reference
[2023-03-15 07:03:40,020] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:03:40,020] [INFO] Task started: Prodigal
[2023-03-15 07:03:40,020] [INFO] Running command: cat /var/lib/cwl/stg858ed207-32cd-40e3-b555-c6fb34dc3370/OceanDNA-a1150.fa | prodigal -d OceanDNA-a1150/cds.fna -a OceanDNA-a1150/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:03:42,407] [INFO] Task succeeded: Prodigal
[2023-03-15 07:03:42,407] [INFO] Task started: HMMsearch
[2023-03-15 07:03:42,407] [INFO] Running command: hmmsearch --tblout OceanDNA-a1150/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg583aebe5-fd4a-4f97-8f9e-7f488919a7ad/dqc_reference/reference_markers.hmm OceanDNA-a1150/protein.faa > /dev/null
[2023-03-15 07:03:42,590] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:03:42,591] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg858ed207-32cd-40e3-b555-c6fb34dc3370/OceanDNA-a1150.fa]
[2023-03-15 07:03:42,650] [INFO] Query marker FASTA was written to OceanDNA-a1150/markers.fasta
[2023-03-15 07:03:42,652] [INFO] Task started: Blastn
[2023-03-15 07:03:42,652] [INFO] Running command: blastn -query OceanDNA-a1150/markers.fasta -db /var/lib/cwl/stg583aebe5-fd4a-4f97-8f9e-7f488919a7ad/dqc_reference/reference_markers.fasta -out OceanDNA-a1150/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:03:43,316] [INFO] Task succeeded: Blastn
[2023-03-15 07:03:43,318] [INFO] Selected 5 target genomes.
[2023-03-15 07:03:43,318] [INFO] Target genome list was writen to OceanDNA-a1150/target_genomes.txt
[2023-03-15 07:03:43,321] [INFO] Task started: fastANI
[2023-03-15 07:03:43,321] [INFO] Running command: fastANI --query /var/lib/cwl/stg858ed207-32cd-40e3-b555-c6fb34dc3370/OceanDNA-a1150.fa --refList OceanDNA-a1150/target_genomes.txt --output OceanDNA-a1150/fastani_result.tsv --threads 1
[2023-03-15 07:03:45,198] [INFO] Task succeeded: fastANI
[2023-03-15 07:03:45,198] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg583aebe5-fd4a-4f97-8f9e-7f488919a7ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:03:45,198] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg583aebe5-fd4a-4f97-8f9e-7f488919a7ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:03:45,198] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 07:03:45,198] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 07:03:45,198] [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 07:03:45,204] [INFO] DFAST Taxonomy check result was written to OceanDNA-a1150/tc_result.tsv
[2023-03-15 07:03:45,205] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:03:45,206] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:03:45,206] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg583aebe5-fd4a-4f97-8f9e-7f488919a7ad/dqc_reference/checkm_data
[2023-03-15 07:03:45,208] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:03:45,232] [INFO] Task started: CheckM
[2023-03-15 07:03:45,232] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1150/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1150/checkm_input OceanDNA-a1150/checkm_result
[2023-03-15 07:04:02,160] [INFO] Task succeeded: CheckM
[2023-03-15 07:04:02,160] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 07:04:02,189] [INFO] ===== Completeness check finished =====
[2023-03-15 07:04:02,190] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:04:02,190] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1150/markers.fasta)
[2023-03-15 07:04:02,191] [INFO] Task started: Blastn
[2023-03-15 07:04:02,191] [INFO] Running command: blastn -query OceanDNA-a1150/markers.fasta -db /var/lib/cwl/stg583aebe5-fd4a-4f97-8f9e-7f488919a7ad/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1150/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:04:03,182] [INFO] Task succeeded: Blastn
[2023-03-15 07:04:03,190] [INFO] Selected 9 target genomes.
[2023-03-15 07:04:03,190] [INFO] Target genome list was writen to OceanDNA-a1150/target_genomes_gtdb.txt
[2023-03-15 07:04:03,253] [INFO] Task started: fastANI
[2023-03-15 07:04:03,253] [INFO] Running command: fastANI --query /var/lib/cwl/stg858ed207-32cd-40e3-b555-c6fb34dc3370/OceanDNA-a1150.fa --refList OceanDNA-a1150/target_genomes_gtdb.txt --output OceanDNA-a1150/fastani_result_gtdb.tsv --threads 1
[2023-03-15 07:04:04,863] [INFO] Task succeeded: fastANI
[2023-03-15 07:04:04,865] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 07:04:04,865] [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_016185615.1	s__JACPNE01 sp016185615	78.0484	54	161	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__SCGC-AAA011-G17;f__JACPNG01;g__JACPNE01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 07:04:04,867] [INFO] GTDB search result was written to OceanDNA-a1150/result_gtdb.tsv
[2023-03-15 07:04:04,872] [INFO] ===== GTDB Search completed =====
[2023-03-15 07:04:04,876] [INFO] DFAST_QC result json was written to OceanDNA-a1150/dqc_result.json
[2023-03-15 07:04:04,876] [INFO] DFAST_QC completed!
[2023-03-15 07:04:04,876] [INFO] Total running time: 0h0m26s