[2023-03-18 20:59:43,924] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:59:43,924] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:59:43,924] [INFO] DQC Reference Directory: /var/lib/cwl/stg0dda64d6-701a-4ca1-81d2-d942f47f0e12/dqc_reference
[2023-03-18 20:59:45,685] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:59:45,685] [INFO] Task started: Prodigal
[2023-03-18 20:59:45,685] [INFO] Running command: cat /var/lib/cwl/stg96566905-ffda-4764-8f81-04a58fe96ae6/OceanDNA-b24353.fa | prodigal -d OceanDNA-b24353/cds.fna -a OceanDNA-b24353/protein.faa -g 11 -q > /dev/null
[2023-03-18 20:59:52,534] [INFO] Task succeeded: Prodigal
[2023-03-18 20:59:52,534] [INFO] Task started: HMMsearch
[2023-03-18 20:59:52,534] [INFO] Running command: hmmsearch --tblout OceanDNA-b24353/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0dda64d6-701a-4ca1-81d2-d942f47f0e12/dqc_reference/reference_markers.hmm OceanDNA-b24353/protein.faa > /dev/null
[2023-03-18 20:59:52,721] [INFO] Task succeeded: HMMsearch
[2023-03-18 20:59:52,721] [INFO] Found 6/6 markers.
[2023-03-18 20:59:52,730] [INFO] Query marker FASTA was written to OceanDNA-b24353/markers.fasta
[2023-03-18 20:59:52,730] [INFO] Task started: Blastn
[2023-03-18 20:59:52,730] [INFO] Running command: blastn -query OceanDNA-b24353/markers.fasta -db /var/lib/cwl/stg0dda64d6-701a-4ca1-81d2-d942f47f0e12/dqc_reference/reference_markers.fasta -out OceanDNA-b24353/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:59:53,284] [INFO] Task succeeded: Blastn
[2023-03-18 20:59:53,285] [INFO] Selected 17 target genomes.
[2023-03-18 20:59:53,285] [INFO] Target genome list was writen to OceanDNA-b24353/target_genomes.txt
[2023-03-18 20:59:53,295] [INFO] Task started: fastANI
[2023-03-18 20:59:53,295] [INFO] Running command: fastANI --query /var/lib/cwl/stg96566905-ffda-4764-8f81-04a58fe96ae6/OceanDNA-b24353.fa --refList OceanDNA-b24353/target_genomes.txt --output OceanDNA-b24353/fastani_result.tsv --threads 1
[2023-03-18 21:00:01,181] [INFO] Task succeeded: fastANI
[2023-03-18 21:00:01,182] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0dda64d6-701a-4ca1-81d2-d942f47f0e12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:00:01,182] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0dda64d6-701a-4ca1-81d2-d942f47f0e12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:00:01,182] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:00:01,182] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 21:00:01,182] [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 21:00:01,182] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24353/tc_result.tsv
[2023-03-18 21:00:01,183] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:00:01,183] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:00:01,183] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0dda64d6-701a-4ca1-81d2-d942f47f0e12/dqc_reference/checkm_data
[2023-03-18 21:00:01,186] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:00:01,280] [INFO] Task started: CheckM
[2023-03-18 21:00:01,280] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24353/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24353/checkm_input OceanDNA-b24353/checkm_result
[2023-03-18 21:00:23,902] [INFO] Task succeeded: CheckM
[2023-03-18 21:00:23,902] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.89%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 21:00:23,904] [INFO] ===== Completeness check finished =====
[2023-03-18 21:00:23,904] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:00:23,904] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24353/markers.fasta)
[2023-03-18 21:00:23,906] [INFO] Task started: Blastn
[2023-03-18 21:00:23,907] [INFO] Running command: blastn -query OceanDNA-b24353/markers.fasta -db /var/lib/cwl/stg0dda64d6-701a-4ca1-81d2-d942f47f0e12/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24353/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:00:24,814] [INFO] Task succeeded: Blastn
[2023-03-18 21:00:24,816] [INFO] Selected 25 target genomes.
[2023-03-18 21:00:24,816] [INFO] Target genome list was writen to OceanDNA-b24353/target_genomes_gtdb.txt
[2023-03-18 21:00:24,843] [INFO] Task started: fastANI
[2023-03-18 21:00:24,843] [INFO] Running command: fastANI --query /var/lib/cwl/stg96566905-ffda-4764-8f81-04a58fe96ae6/OceanDNA-b24353.fa --refList OceanDNA-b24353/target_genomes_gtdb.txt --output OceanDNA-b24353/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:00:30,126] [INFO] Task succeeded: fastANI
[2023-03-18 21:00:30,129] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 21:00:30,129] [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_002717485.1	s__GCA-2717485 sp002717485	99.7639	329	378	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__GCA-2717485	95.0	99.83	99.82	0.92	0.91	3	conclusive
GCA_002938195.1	s__MarineAlpha5-Bin7 sp002938195	75.9552	52	378	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__MarineAlpha5-Bin7	95.0	99.81	99.67	0.81	0.76	3	-
GCA_902577425.1	s__MarineAlpha5-Bin3 sp902577425	75.6289	59	378	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__MarineAlpha5-Bin3	95.0	95.54	95.54	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2023-03-18 21:00:30,131] [INFO] GTDB search result was written to OceanDNA-b24353/result_gtdb.tsv
[2023-03-18 21:00:30,131] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:00:30,132] [INFO] DFAST_QC result json was written to OceanDNA-b24353/dqc_result.json
[2023-03-18 21:00:30,132] [INFO] DFAST_QC completed!
[2023-03-18 21:00:30,132] [INFO] Total running time: 0h0m46s