[2023-03-19 05:19:33,741] [INFO] DFAST_QC pipeline started.
[2023-03-19 05:19:33,741] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 05:19:33,741] [INFO] DQC Reference Directory: /var/lib/cwl/stg18d7f95b-ece9-43ee-b50b-11b527ea13d2/dqc_reference
[2023-03-19 05:19:35,419] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 05:19:35,419] [INFO] Task started: Prodigal
[2023-03-19 05:19:35,420] [INFO] Running command: cat /var/lib/cwl/stg5cdc2b0c-3767-405b-94b5-f811fd23b759/OceanDNA-b25899.fa | prodigal -d OceanDNA-b25899/cds.fna -a OceanDNA-b25899/protein.faa -g 11 -q > /dev/null
[2023-03-19 05:19:37,563] [INFO] Task succeeded: Prodigal
[2023-03-19 05:19:37,563] [INFO] Task started: HMMsearch
[2023-03-19 05:19:37,563] [INFO] Running command: hmmsearch --tblout OceanDNA-b25899/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg18d7f95b-ece9-43ee-b50b-11b527ea13d2/dqc_reference/reference_markers.hmm OceanDNA-b25899/protein.faa > /dev/null
[2023-03-19 05:19:37,696] [INFO] Task succeeded: HMMsearch
[2023-03-19 05:19:37,697] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg5cdc2b0c-3767-405b-94b5-f811fd23b759/OceanDNA-b25899.fa]
[2023-03-19 05:19:37,702] [INFO] Query marker FASTA was written to OceanDNA-b25899/markers.fasta
[2023-03-19 05:19:37,704] [INFO] Task started: Blastn
[2023-03-19 05:19:37,704] [INFO] Running command: blastn -query OceanDNA-b25899/markers.fasta -db /var/lib/cwl/stg18d7f95b-ece9-43ee-b50b-11b527ea13d2/dqc_reference/reference_markers.fasta -out OceanDNA-b25899/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:19:38,470] [INFO] Task succeeded: Blastn
[2023-03-19 05:19:38,470] [INFO] Selected 8 target genomes.
[2023-03-19 05:19:38,471] [INFO] Target genome list was writen to OceanDNA-b25899/target_genomes.txt
[2023-03-19 05:19:38,476] [INFO] Task started: fastANI
[2023-03-19 05:19:38,476] [INFO] Running command: fastANI --query /var/lib/cwl/stg5cdc2b0c-3767-405b-94b5-f811fd23b759/OceanDNA-b25899.fa --refList OceanDNA-b25899/target_genomes.txt --output OceanDNA-b25899/fastani_result.tsv --threads 1
[2023-03-19 05:19:41,979] [INFO] Task succeeded: fastANI
[2023-03-19 05:19:41,979] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg18d7f95b-ece9-43ee-b50b-11b527ea13d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 05:19:41,979] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg18d7f95b-ece9-43ee-b50b-11b527ea13d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 05:19:41,980] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 05:19:41,980] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 05:19:41,980] [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
--------------------------------------------------------------------------------
[2023-03-19 05:19:41,980] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25899/tc_result.tsv
[2023-03-19 05:19:41,980] [INFO] ===== Taxonomy check completed =====
[2023-03-19 05:19:41,980] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 05:19:41,980] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg18d7f95b-ece9-43ee-b50b-11b527ea13d2/dqc_reference/checkm_data
[2023-03-19 05:19:41,983] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 05:19:41,986] [INFO] Task started: CheckM
[2023-03-19 05:19:41,986] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25899/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25899/checkm_input OceanDNA-b25899/checkm_result
[2023-03-19 05:19:55,364] [INFO] Task succeeded: CheckM
[2023-03-19 05:19:55,365] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.51%
Contamintation: 5.15%
Strain heterogeneity: 14.29%
--------------------------------------------------------------------------------
[2023-03-19 05:19:55,366] [INFO] ===== Completeness check finished =====
[2023-03-19 05:19:55,366] [INFO] ===== Start GTDB Search =====
[2023-03-19 05:19:55,367] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25899/markers.fasta)
[2023-03-19 05:19:55,367] [INFO] Task started: Blastn
[2023-03-19 05:19:55,367] [INFO] Running command: blastn -query OceanDNA-b25899/markers.fasta -db /var/lib/cwl/stg18d7f95b-ece9-43ee-b50b-11b527ea13d2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25899/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:19:56,152] [INFO] Task succeeded: Blastn
[2023-03-19 05:19:56,152] [INFO] Selected 16 target genomes.
[2023-03-19 05:19:56,152] [INFO] Target genome list was writen to OceanDNA-b25899/target_genomes_gtdb.txt
[2023-03-19 05:19:56,197] [INFO] Task started: fastANI
[2023-03-19 05:19:56,197] [INFO] Running command: fastANI --query /var/lib/cwl/stg5cdc2b0c-3767-405b-94b5-f811fd23b759/OceanDNA-b25899.fa --refList OceanDNA-b25899/target_genomes_gtdb.txt --output OceanDNA-b25899/fastani_result_gtdb.tsv --threads 1
[2023-03-19 05:19:59,146] [INFO] Task succeeded: fastANI
[2023-03-19 05:19:59,148] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 05:19:59,148] [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_003210095.1	s__Pelagibacter sp003210095	95.6368	56	68	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	97.98	96.68	0.95	0.91	7	conclusive
--------------------------------------------------------------------------------
[2023-03-19 05:19:59,149] [INFO] GTDB search result was written to OceanDNA-b25899/result_gtdb.tsv
[2023-03-19 05:19:59,149] [INFO] ===== GTDB Search completed =====
[2023-03-19 05:19:59,149] [INFO] DFAST_QC result json was written to OceanDNA-b25899/dqc_result.json
[2023-03-19 05:19:59,149] [INFO] DFAST_QC completed!
[2023-03-19 05:19:59,149] [INFO] Total running time: 0h0m25s