[2023-03-18 03:27:00,921] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:27:00,921] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:27:00,921] [INFO] DQC Reference Directory: /var/lib/cwl/stgacfc7c12-45a5-4845-a877-54ca2d761677/dqc_reference
[2023-03-18 03:27:02,636] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:27:02,637] [INFO] Task started: Prodigal
[2023-03-18 03:27:02,637] [INFO] Running command: cat /var/lib/cwl/stg236bb401-f2b8-4195-8f09-ef8267c4a70d/OceanDNA-a4967.fa | prodigal -d OceanDNA-a4967/cds.fna -a OceanDNA-a4967/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:27:09,629] [INFO] Task succeeded: Prodigal
[2023-03-18 03:27:09,629] [INFO] Task started: HMMsearch
[2023-03-18 03:27:09,629] [INFO] Running command: hmmsearch --tblout OceanDNA-a4967/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgacfc7c12-45a5-4845-a877-54ca2d761677/dqc_reference/reference_markers.hmm OceanDNA-a4967/protein.faa > /dev/null
[2023-03-18 03:27:09,789] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:27:09,789] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg236bb401-f2b8-4195-8f09-ef8267c4a70d/OceanDNA-a4967.fa]
[2023-03-18 03:27:09,798] [INFO] Query marker FASTA was written to OceanDNA-a4967/markers.fasta
[2023-03-18 03:27:09,799] [INFO] Task started: Blastn
[2023-03-18 03:27:09,799] [INFO] Running command: blastn -query OceanDNA-a4967/markers.fasta -db /var/lib/cwl/stgacfc7c12-45a5-4845-a877-54ca2d761677/dqc_reference/reference_markers.fasta -out OceanDNA-a4967/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:27:10,227] [INFO] Task succeeded: Blastn
[2023-03-18 03:27:10,228] [INFO] Selected 2 target genomes.
[2023-03-18 03:27:10,228] [INFO] Target genome list was writen to OceanDNA-a4967/target_genomes.txt
[2023-03-18 03:27:10,229] [INFO] Task started: fastANI
[2023-03-18 03:27:10,229] [INFO] Running command: fastANI --query /var/lib/cwl/stg236bb401-f2b8-4195-8f09-ef8267c4a70d/OceanDNA-a4967.fa --refList OceanDNA-a4967/target_genomes.txt --output OceanDNA-a4967/fastani_result.tsv --threads 1
[2023-03-18 03:27:10,789] [INFO] Task succeeded: fastANI
[2023-03-18 03:27:10,789] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgacfc7c12-45a5-4845-a877-54ca2d761677/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:27:10,789] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgacfc7c12-45a5-4845-a877-54ca2d761677/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:27:10,789] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 03:27:10,790] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 03:27:10,790] [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 03:27:10,790] [INFO] DFAST Taxonomy check result was written to OceanDNA-a4967/tc_result.tsv
[2023-03-18 03:27:10,790] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:27:10,790] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:27:10,790] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgacfc7c12-45a5-4845-a877-54ca2d761677/dqc_reference/checkm_data
[2023-03-18 03:27:10,842] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:27:11,195] [INFO] Task started: CheckM
[2023-03-18 03:27:11,195] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4967/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4967/checkm_input OceanDNA-a4967/checkm_result
[2023-03-18 03:27:36,003] [INFO] Task succeeded: CheckM
[2023-03-18 03:27:36,003] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.89%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 03:27:36,005] [INFO] ===== Completeness check finished =====
[2023-03-18 03:27:36,005] [INFO] ===== Start GTDB Search =====
[2023-03-18 03:27:36,005] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4967/markers.fasta)
[2023-03-18 03:27:36,006] [INFO] Task started: Blastn
[2023-03-18 03:27:36,006] [INFO] Running command: blastn -query OceanDNA-a4967/markers.fasta -db /var/lib/cwl/stgacfc7c12-45a5-4845-a877-54ca2d761677/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4967/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:27:36,432] [INFO] Task succeeded: Blastn
[2023-03-18 03:27:36,433] [INFO] Selected 7 target genomes.
[2023-03-18 03:27:36,433] [INFO] Target genome list was writen to OceanDNA-a4967/target_genomes_gtdb.txt
[2023-03-18 03:27:36,444] [INFO] Task started: fastANI
[2023-03-18 03:27:36,444] [INFO] Running command: fastANI --query /var/lib/cwl/stg236bb401-f2b8-4195-8f09-ef8267c4a70d/OceanDNA-a4967.fa --refList OceanDNA-a4967/target_genomes_gtdb.txt --output OceanDNA-a4967/fastani_result_gtdb.tsv --threads 1
[2023-03-18 03:27:38,370] [INFO] Task succeeded: fastANI
[2023-03-18 03:27:38,374] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 03:27:38,375] [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_014240285.1	s__Thalassarchaeum sp014240285	95.5574	312	385	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_004195715.1	s__Thalassarchaeum sp004195715	85.2629	315	385	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	99.87	99.86	0.95	0.94	3	-
GCA_002457605.1	s__Thalassarchaeum sp002457605	84.1563	235	385	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002505325.1	s__Thalassarchaeum sp002505325	84.0988	234	385	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002507125.1	s__Thalassarchaeum sp002507125	79.1032	139	385	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	98.54	98.42	0.77	0.74	3	-
GCA_003193925.1	s__Thalassarchaeum betae	78.6096	180	385	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	99.52	98.11	0.96	0.90	6	-
--------------------------------------------------------------------------------
[2023-03-18 03:27:38,375] [INFO] GTDB search result was written to OceanDNA-a4967/result_gtdb.tsv
[2023-03-18 03:27:38,375] [INFO] ===== GTDB Search completed =====
[2023-03-18 03:27:38,376] [INFO] DFAST_QC result json was written to OceanDNA-a4967/dqc_result.json
[2023-03-18 03:27:38,376] [INFO] DFAST_QC completed!
[2023-03-18 03:27:38,376] [INFO] Total running time: 0h0m37s