[2023-03-18 21:40:18,358] [INFO] DFAST_QC pipeline started.
[2023-03-18 21:40:18,358] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 21:40:18,358] [INFO] DQC Reference Directory: /var/lib/cwl/stgfd7b1d66-61a5-479b-a435-4123b08cd391/dqc_reference
[2023-03-18 21:40:19,478] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 21:40:19,478] [INFO] Task started: Prodigal
[2023-03-18 21:40:19,479] [INFO] Running command: cat /var/lib/cwl/stg377d4569-63d9-4ee6-a1f3-c44f0a4f7de2/OceanDNA-b44090.fa | prodigal -d OceanDNA-b44090/cds.fna -a OceanDNA-b44090/protein.faa -g 11 -q > /dev/null
[2023-03-18 21:40:23,704] [INFO] Task succeeded: Prodigal
[2023-03-18 21:40:23,705] [INFO] Task started: HMMsearch
[2023-03-18 21:40:23,705] [INFO] Running command: hmmsearch --tblout OceanDNA-b44090/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfd7b1d66-61a5-479b-a435-4123b08cd391/dqc_reference/reference_markers.hmm OceanDNA-b44090/protein.faa > /dev/null
[2023-03-18 21:40:23,877] [INFO] Task succeeded: HMMsearch
[2023-03-18 21:40:23,877] [INFO] Found 6/6 markers.
[2023-03-18 21:40:23,886] [INFO] Query marker FASTA was written to OceanDNA-b44090/markers.fasta
[2023-03-18 21:40:23,887] [INFO] Task started: Blastn
[2023-03-18 21:40:23,887] [INFO] Running command: blastn -query OceanDNA-b44090/markers.fasta -db /var/lib/cwl/stgfd7b1d66-61a5-479b-a435-4123b08cd391/dqc_reference/reference_markers.fasta -out OceanDNA-b44090/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:40:24,474] [INFO] Task succeeded: Blastn
[2023-03-18 21:40:24,475] [INFO] Selected 20 target genomes.
[2023-03-18 21:40:24,475] [INFO] Target genome list was writen to OceanDNA-b44090/target_genomes.txt
[2023-03-18 21:40:24,488] [INFO] Task started: fastANI
[2023-03-18 21:40:24,488] [INFO] Running command: fastANI --query /var/lib/cwl/stg377d4569-63d9-4ee6-a1f3-c44f0a4f7de2/OceanDNA-b44090.fa --refList OceanDNA-b44090/target_genomes.txt --output OceanDNA-b44090/fastani_result.tsv --threads 1
[2023-03-18 21:40:35,640] [INFO] Task succeeded: fastANI
[2023-03-18 21:40:35,640] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfd7b1d66-61a5-479b-a435-4123b08cd391/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:40:35,640] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfd7b1d66-61a5-479b-a435-4123b08cd391/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:40:35,640] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:40:35,640] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 21:40:35,640] [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 21:40:35,641] [INFO] DFAST Taxonomy check result was written to OceanDNA-b44090/tc_result.tsv
[2023-03-18 21:40:35,641] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:40:35,641] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:40:35,641] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfd7b1d66-61a5-479b-a435-4123b08cd391/dqc_reference/checkm_data
[2023-03-18 21:40:35,651] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:40:35,654] [INFO] Task started: CheckM
[2023-03-18 21:40:35,654] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b44090/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b44090/checkm_input OceanDNA-b44090/checkm_result
[2023-03-18 21:40:52,942] [INFO] Task succeeded: CheckM
[2023-03-18 21:40:52,942] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 2.60%
Strain heterogeneity: 40.00%
--------------------------------------------------------------------------------
[2023-03-18 21:40:52,944] [INFO] ===== Completeness check finished =====
[2023-03-18 21:40:52,944] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:40:52,944] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b44090/markers.fasta)
[2023-03-18 21:40:52,946] [INFO] Task started: Blastn
[2023-03-18 21:40:52,946] [INFO] Running command: blastn -query OceanDNA-b44090/markers.fasta -db /var/lib/cwl/stgfd7b1d66-61a5-479b-a435-4123b08cd391/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b44090/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:40:53,967] [INFO] Task succeeded: Blastn
[2023-03-18 21:40:53,968] [INFO] Selected 29 target genomes.
[2023-03-18 21:40:53,968] [INFO] Target genome list was writen to OceanDNA-b44090/target_genomes_gtdb.txt
[2023-03-18 21:40:54,024] [INFO] Task started: fastANI
[2023-03-18 21:40:54,025] [INFO] Running command: fastANI --query /var/lib/cwl/stg377d4569-63d9-4ee6-a1f3-c44f0a4f7de2/OceanDNA-b44090.fa --refList OceanDNA-b44090/target_genomes_gtdb.txt --output OceanDNA-b44090/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:41:05,183] [INFO] Task succeeded: fastANI
[2023-03-18 21:41:05,185] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 21:41:05,185] [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_002721165.1	s__UBA11869 sp002721165	80.5738	191	267	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA4486;f__UBA4486;g__UBA11869	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014239225.1	s__UBA11869 sp014239225	79.1101	98	267	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA4486;f__UBA4486;g__UBA11869	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 21:41:05,185] [INFO] GTDB search result was written to OceanDNA-b44090/result_gtdb.tsv
[2023-03-18 21:41:05,185] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:41:05,186] [INFO] DFAST_QC result json was written to OceanDNA-b44090/dqc_result.json
[2023-03-18 21:41:05,186] [INFO] DFAST_QC completed!
[2023-03-18 21:41:05,186] [INFO] Total running time: 0h0m47s