[2023-03-15 12:33:51,692] [INFO] DFAST_QC pipeline started.
[2023-03-15 12:33:51,692] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 12:33:51,692] [INFO] DQC Reference Directory: /var/lib/cwl/stgf5e26e67-9765-4ed5-9874-c21d5247d088/dqc_reference
[2023-03-15 12:33:52,795] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 12:33:52,796] [INFO] Task started: Prodigal
[2023-03-15 12:33:52,796] [INFO] Running command: cat /var/lib/cwl/stg9b254bc7-a0c7-47e4-a2e1-7ba50a20c4ab/OceanDNA-b27118.fa | prodigal -d OceanDNA-b27118/cds.fna -a OceanDNA-b27118/protein.faa -g 11 -q > /dev/null
[2023-03-15 12:33:56,757] [INFO] Task succeeded: Prodigal
[2023-03-15 12:33:56,758] [INFO] Task started: HMMsearch
[2023-03-15 12:33:56,758] [INFO] Running command: hmmsearch --tblout OceanDNA-b27118/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf5e26e67-9765-4ed5-9874-c21d5247d088/dqc_reference/reference_markers.hmm OceanDNA-b27118/protein.faa > /dev/null
[2023-03-15 12:33:56,910] [INFO] Task succeeded: HMMsearch
[2023-03-15 12:33:56,910] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9b254bc7-a0c7-47e4-a2e1-7ba50a20c4ab/OceanDNA-b27118.fa]
[2023-03-15 12:33:56,920] [INFO] Query marker FASTA was written to OceanDNA-b27118/markers.fasta
[2023-03-15 12:33:56,920] [INFO] Task started: Blastn
[2023-03-15 12:33:56,920] [INFO] Running command: blastn -query OceanDNA-b27118/markers.fasta -db /var/lib/cwl/stgf5e26e67-9765-4ed5-9874-c21d5247d088/dqc_reference/reference_markers.fasta -out OceanDNA-b27118/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:33:57,406] [INFO] Task succeeded: Blastn
[2023-03-15 12:33:57,408] [INFO] Selected 16 target genomes.
[2023-03-15 12:33:57,408] [INFO] Target genome list was writen to OceanDNA-b27118/target_genomes.txt
[2023-03-15 12:33:57,417] [INFO] Task started: fastANI
[2023-03-15 12:33:57,417] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b254bc7-a0c7-47e4-a2e1-7ba50a20c4ab/OceanDNA-b27118.fa --refList OceanDNA-b27118/target_genomes.txt --output OceanDNA-b27118/fastani_result.tsv --threads 1
[2023-03-15 12:34:02,814] [INFO] Task succeeded: fastANI
[2023-03-15 12:34:02,814] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf5e26e67-9765-4ed5-9874-c21d5247d088/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 12:34:02,814] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf5e26e67-9765-4ed5-9874-c21d5247d088/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 12:34:02,815] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 12:34:02,815] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 12:34:02,815] [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 12:34:02,818] [INFO] DFAST Taxonomy check result was written to OceanDNA-b27118/tc_result.tsv
[2023-03-15 12:34:02,819] [INFO] ===== Taxonomy check completed =====
[2023-03-15 12:34:02,820] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 12:34:02,820] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf5e26e67-9765-4ed5-9874-c21d5247d088/dqc_reference/checkm_data
[2023-03-15 12:34:02,822] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 12:34:02,825] [INFO] Task started: CheckM
[2023-03-15 12:34:02,825] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b27118/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b27118/checkm_input OceanDNA-b27118/checkm_result
[2023-03-15 12:34:19,576] [INFO] Task succeeded: CheckM
[2023-03-15 12:34:19,577] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 61.65%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 12:34:19,579] [INFO] ===== Completeness check finished =====
[2023-03-15 12:34:19,579] [INFO] ===== Start GTDB Search =====
[2023-03-15 12:34:19,579] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b27118/markers.fasta)
[2023-03-15 12:34:19,581] [INFO] Task started: Blastn
[2023-03-15 12:34:19,581] [INFO] Running command: blastn -query OceanDNA-b27118/markers.fasta -db /var/lib/cwl/stgf5e26e67-9765-4ed5-9874-c21d5247d088/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b27118/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:34:20,723] [INFO] Task succeeded: Blastn
[2023-03-15 12:34:20,725] [INFO] Selected 24 target genomes.
[2023-03-15 12:34:20,725] [INFO] Target genome list was writen to OceanDNA-b27118/target_genomes_gtdb.txt
[2023-03-15 12:34:20,984] [INFO] Task started: fastANI
[2023-03-15 12:34:20,984] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b254bc7-a0c7-47e4-a2e1-7ba50a20c4ab/OceanDNA-b27118.fa --refList OceanDNA-b27118/target_genomes_gtdb.txt --output OceanDNA-b27118/fastani_result_gtdb.tsv --threads 1
[2023-03-15 12:34:26,305] [INFO] Task succeeded: fastANI
[2023-03-15 12:34:26,307] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 12:34:26,307] [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_002731945.1	s__GCA-002731945 sp002731945	92.6305	190	238	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__GCA-002731945	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 12:34:26,309] [INFO] GTDB search result was written to OceanDNA-b27118/result_gtdb.tsv
[2023-03-15 12:34:26,309] [INFO] ===== GTDB Search completed =====
[2023-03-15 12:34:26,310] [INFO] DFAST_QC result json was written to OceanDNA-b27118/dqc_result.json
[2023-03-15 12:34:26,310] [INFO] DFAST_QC completed!
[2023-03-15 12:34:26,310] [INFO] Total running time: 0h0m35s