[2023-03-14 12:49:51,276] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:49:51,277] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:49:51,277] [INFO] DQC Reference Directory: /var/lib/cwl/stgeca0fccb-b7f9-4941-a459-21fdd5a1126d/dqc_reference
[2023-03-14 12:49:52,730] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:49:52,732] [INFO] Task started: Prodigal
[2023-03-14 12:49:52,733] [INFO] Running command: cat /var/lib/cwl/stg85b5da93-e935-4480-a265-375fc3581306/OceanDNA-b32609.fa | prodigal -d OceanDNA-b32609/cds.fna -a OceanDNA-b32609/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:50:12,413] [INFO] Task succeeded: Prodigal
[2023-03-14 12:50:12,413] [INFO] Task started: HMMsearch
[2023-03-14 12:50:12,414] [INFO] Running command: hmmsearch --tblout OceanDNA-b32609/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeca0fccb-b7f9-4941-a459-21fdd5a1126d/dqc_reference/reference_markers.hmm OceanDNA-b32609/protein.faa > /dev/null
[2023-03-14 12:50:12,589] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:50:12,590] [INFO] Found 6/6 markers.
[2023-03-14 12:50:12,604] [INFO] Query marker FASTA was written to OceanDNA-b32609/markers.fasta
[2023-03-14 12:50:12,606] [INFO] Task started: Blastn
[2023-03-14 12:50:12,606] [INFO] Running command: blastn -query OceanDNA-b32609/markers.fasta -db /var/lib/cwl/stgeca0fccb-b7f9-4941-a459-21fdd5a1126d/dqc_reference/reference_markers.fasta -out OceanDNA-b32609/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:50:13,281] [INFO] Task succeeded: Blastn
[2023-03-14 12:50:13,282] [INFO] Selected 31 target genomes.
[2023-03-14 12:50:13,283] [INFO] Target genome list was writen to OceanDNA-b32609/target_genomes.txt
[2023-03-14 12:50:13,304] [INFO] Task started: fastANI
[2023-03-14 12:50:13,305] [INFO] Running command: fastANI --query /var/lib/cwl/stg85b5da93-e935-4480-a265-375fc3581306/OceanDNA-b32609.fa --refList OceanDNA-b32609/target_genomes.txt --output OceanDNA-b32609/fastani_result.tsv --threads 1
[2023-03-14 12:50:32,028] [INFO] Task succeeded: fastANI
[2023-03-14 12:50:32,028] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeca0fccb-b7f9-4941-a459-21fdd5a1126d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:50:32,028] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeca0fccb-b7f9-4941-a459-21fdd5a1126d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:50:32,028] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:50:32,029] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 12:50:32,029] [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
--------------------------------------------------------------------------------
[2023-03-14 12:50:32,029] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32609/tc_result.tsv
[2023-03-14 12:50:32,029] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:50:32,029] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:50:32,030] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeca0fccb-b7f9-4941-a459-21fdd5a1126d/dqc_reference/checkm_data
[2023-03-14 12:50:32,040] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:50:32,043] [INFO] Task started: CheckM
[2023-03-14 12:50:32,043] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32609/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32609/checkm_input OceanDNA-b32609/checkm_result
[2023-03-14 12:51:24,817] [INFO] Task succeeded: CheckM
[2023-03-14 12:51:24,817] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-14 12:51:24,826] [INFO] ===== Completeness check finished =====
[2023-03-14 12:51:24,826] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:51:24,826] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32609/markers.fasta)
[2023-03-14 12:51:24,832] [INFO] Task started: Blastn
[2023-03-14 12:51:24,832] [INFO] Running command: blastn -query OceanDNA-b32609/markers.fasta -db /var/lib/cwl/stgeca0fccb-b7f9-4941-a459-21fdd5a1126d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32609/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:51:26,156] [INFO] Task succeeded: Blastn
[2023-03-14 12:51:26,157] [INFO] Selected 26 target genomes.
[2023-03-14 12:51:26,157] [INFO] Target genome list was writen to OceanDNA-b32609/target_genomes_gtdb.txt
[2023-03-14 12:51:26,179] [INFO] Task started: fastANI
[2023-03-14 12:51:26,179] [INFO] Running command: fastANI --query /var/lib/cwl/stg85b5da93-e935-4480-a265-375fc3581306/OceanDNA-b32609.fa --refList OceanDNA-b32609/target_genomes_gtdb.txt --output OceanDNA-b32609/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:51:46,944] [INFO] Task succeeded: fastANI
[2023-03-14 12:51:46,948] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 12:51:46,948] [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_018666775.1	s__SMXQ01 sp018666775	99.984	658	660	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SMXQ01;f__SMXQ01;g__SMXQ01	95.0	99.98	99.96	1.00	0.99	11	conclusive
GCA_004356985.1	s__SMXQ01 sp004356985	75.5834	66	660	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SMXQ01;f__SMXQ01;g__SMXQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009380075.1	s__WHSO01 sp009380075	75.5406	52	660	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SMXQ01;f__SMXQ01;g__WHSO01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 12:51:46,948] [INFO] GTDB search result was written to OceanDNA-b32609/result_gtdb.tsv
[2023-03-14 12:51:46,948] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:51:46,949] [INFO] DFAST_QC result json was written to OceanDNA-b32609/dqc_result.json
[2023-03-14 12:51:46,949] [INFO] DFAST_QC completed!
[2023-03-14 12:51:46,949] [INFO] Total running time: 0h1m56s