[2023-03-18 02:48:49,267] [INFO] DFAST_QC pipeline started.
[2023-03-18 02:48:49,267] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 02:48:49,267] [INFO] DQC Reference Directory: /var/lib/cwl/stg52707fc3-3f70-4fc2-8702-374960adf17b/dqc_reference
[2023-03-18 02:48:50,487] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 02:48:50,487] [INFO] Task started: Prodigal
[2023-03-18 02:48:50,487] [INFO] Running command: cat /var/lib/cwl/stg8c521e5b-77bc-4275-83c3-211d82f50ad8/OceanDNA-a1143.fa | prodigal -d OceanDNA-a1143/cds.fna -a OceanDNA-a1143/protein.faa -g 11 -q > /dev/null
[2023-03-18 02:48:53,327] [INFO] Task succeeded: Prodigal
[2023-03-18 02:48:53,328] [INFO] Task started: HMMsearch
[2023-03-18 02:48:53,328] [INFO] Running command: hmmsearch --tblout OceanDNA-a1143/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg52707fc3-3f70-4fc2-8702-374960adf17b/dqc_reference/reference_markers.hmm OceanDNA-a1143/protein.faa > /dev/null
[2023-03-18 02:48:53,498] [INFO] Task succeeded: HMMsearch
[2023-03-18 02:48:53,498] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg8c521e5b-77bc-4275-83c3-211d82f50ad8/OceanDNA-a1143.fa]
[2023-03-18 02:48:53,503] [INFO] Query marker FASTA was written to OceanDNA-a1143/markers.fasta
[2023-03-18 02:48:53,504] [INFO] Task started: Blastn
[2023-03-18 02:48:53,504] [INFO] Running command: blastn -query OceanDNA-a1143/markers.fasta -db /var/lib/cwl/stg52707fc3-3f70-4fc2-8702-374960adf17b/dqc_reference/reference_markers.fasta -out OceanDNA-a1143/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:48:55,494] [INFO] Task succeeded: Blastn
[2023-03-18 02:48:55,494] [INFO] Selected 5 target genomes.
[2023-03-18 02:48:55,495] [INFO] Target genome list was writen to OceanDNA-a1143/target_genomes.txt
[2023-03-18 02:48:55,501] [INFO] Task started: fastANI
[2023-03-18 02:48:55,501] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c521e5b-77bc-4275-83c3-211d82f50ad8/OceanDNA-a1143.fa --refList OceanDNA-a1143/target_genomes.txt --output OceanDNA-a1143/fastani_result.tsv --threads 1
[2023-03-18 02:48:57,648] [INFO] Task succeeded: fastANI
[2023-03-18 02:48:57,649] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg52707fc3-3f70-4fc2-8702-374960adf17b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 02:48:57,649] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg52707fc3-3f70-4fc2-8702-374960adf17b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 02:48:57,649] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 02:48:57,649] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 02:48:57,649] [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 02:48:57,649] [INFO] DFAST Taxonomy check result was written to OceanDNA-a1143/tc_result.tsv
[2023-03-18 02:48:57,650] [INFO] ===== Taxonomy check completed =====
[2023-03-18 02:48:57,650] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 02:48:57,650] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg52707fc3-3f70-4fc2-8702-374960adf17b/dqc_reference/checkm_data
[2023-03-18 02:48:57,654] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 02:48:57,656] [INFO] Task started: CheckM
[2023-03-18 02:48:57,656] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1143/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1143/checkm_input OceanDNA-a1143/checkm_result
[2023-03-18 02:49:14,023] [INFO] Task succeeded: CheckM
[2023-03-18 02:49:14,024] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 02:49:14,025] [INFO] ===== Completeness check finished =====
[2023-03-18 02:49:14,025] [INFO] ===== Start GTDB Search =====
[2023-03-18 02:49:14,025] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1143/markers.fasta)
[2023-03-18 02:49:14,027] [INFO] Task started: Blastn
[2023-03-18 02:49:14,028] [INFO] Running command: blastn -query OceanDNA-a1143/markers.fasta -db /var/lib/cwl/stg52707fc3-3f70-4fc2-8702-374960adf17b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1143/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:49:14,914] [INFO] Task succeeded: Blastn
[2023-03-18 02:49:14,915] [INFO] Selected 6 target genomes.
[2023-03-18 02:49:14,915] [INFO] Target genome list was writen to OceanDNA-a1143/target_genomes_gtdb.txt
[2023-03-18 02:49:14,941] [INFO] Task started: fastANI
[2023-03-18 02:49:14,941] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c521e5b-77bc-4275-83c3-211d82f50ad8/OceanDNA-a1143.fa --refList OceanDNA-a1143/target_genomes_gtdb.txt --output OceanDNA-a1143/fastani_result_gtdb.tsv --threads 1
[2023-03-18 02:49:16,086] [INFO] Task succeeded: fastANI
[2023-03-18 02:49:16,088] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 02:49:16,088] [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_018671245.1	s__JABHIB01 sp018671245	99.9535	178	183	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__SCGC-AAA011-G17;f__PNOQ01;g__JABHIB01	95.0	99.97	99.97	0.97	0.95	4	conclusive
--------------------------------------------------------------------------------
[2023-03-18 02:49:16,088] [INFO] GTDB search result was written to OceanDNA-a1143/result_gtdb.tsv
[2023-03-18 02:49:16,088] [INFO] ===== GTDB Search completed =====
[2023-03-18 02:49:16,089] [INFO] DFAST_QC result json was written to OceanDNA-a1143/dqc_result.json
[2023-03-18 02:49:16,089] [INFO] DFAST_QC completed!
[2023-03-18 02:49:16,089] [INFO] Total running time: 0h0m27s