[2023-03-19 03:22:59,845] [INFO] DFAST_QC pipeline started.
[2023-03-19 03:22:59,852] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 03:22:59,852] [INFO] DQC Reference Directory: /var/lib/cwl/stg5182c2a4-b4ce-476b-9263-2e8df762da48/dqc_reference
[2023-03-19 03:23:01,003] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 03:23:01,003] [INFO] Task started: Prodigal
[2023-03-19 03:23:01,004] [INFO] Running command: cat /var/lib/cwl/stg28a9619c-1ad4-45ff-b192-ed1a9565c118/OceanDNA-b25378.fa | prodigal -d OceanDNA-b25378/cds.fna -a OceanDNA-b25378/protein.faa -g 11 -q > /dev/null
[2023-03-19 03:23:04,202] [INFO] Task succeeded: Prodigal
[2023-03-19 03:23:04,203] [INFO] Task started: HMMsearch
[2023-03-19 03:23:04,203] [INFO] Running command: hmmsearch --tblout OceanDNA-b25378/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5182c2a4-b4ce-476b-9263-2e8df762da48/dqc_reference/reference_markers.hmm OceanDNA-b25378/protein.faa > /dev/null
[2023-03-19 03:23:04,348] [INFO] Task succeeded: HMMsearch
[2023-03-19 03:23:04,349] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg28a9619c-1ad4-45ff-b192-ed1a9565c118/OceanDNA-b25378.fa]
[2023-03-19 03:23:04,387] [INFO] Query marker FASTA was written to OceanDNA-b25378/markers.fasta
[2023-03-19 03:23:04,387] [INFO] Task started: Blastn
[2023-03-19 03:23:04,387] [INFO] Running command: blastn -query OceanDNA-b25378/markers.fasta -db /var/lib/cwl/stg5182c2a4-b4ce-476b-9263-2e8df762da48/dqc_reference/reference_markers.fasta -out OceanDNA-b25378/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:23:04,867] [INFO] Task succeeded: Blastn
[2023-03-19 03:23:04,874] [INFO] Selected 15 target genomes.
[2023-03-19 03:23:04,874] [INFO] Target genome list was writen to OceanDNA-b25378/target_genomes.txt
[2023-03-19 03:23:04,883] [INFO] Task started: fastANI
[2023-03-19 03:23:04,883] [INFO] Running command: fastANI --query /var/lib/cwl/stg28a9619c-1ad4-45ff-b192-ed1a9565c118/OceanDNA-b25378.fa --refList OceanDNA-b25378/target_genomes.txt --output OceanDNA-b25378/fastani_result.tsv --threads 1
[2023-03-19 03:23:11,333] [INFO] Task succeeded: fastANI
[2023-03-19 03:23:11,333] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5182c2a4-b4ce-476b-9263-2e8df762da48/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 03:23:11,333] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5182c2a4-b4ce-476b-9263-2e8df762da48/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 03:23:11,334] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 03:23:11,334] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 03:23:11,334] [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 03:23:11,341] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25378/tc_result.tsv
[2023-03-19 03:23:11,354] [INFO] ===== Taxonomy check completed =====
[2023-03-19 03:23:11,355] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 03:23:11,355] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5182c2a4-b4ce-476b-9263-2e8df762da48/dqc_reference/checkm_data
[2023-03-19 03:23:11,365] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 03:23:11,380] [INFO] Task started: CheckM
[2023-03-19 03:23:11,380] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25378/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25378/checkm_input OceanDNA-b25378/checkm_result
[2023-03-19 03:23:26,885] [INFO] Task succeeded: CheckM
[2023-03-19 03:23:26,885] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 03:23:27,025] [INFO] ===== Completeness check finished =====
[2023-03-19 03:23:27,025] [INFO] ===== Start GTDB Search =====
[2023-03-19 03:23:27,025] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25378/markers.fasta)
[2023-03-19 03:23:27,026] [INFO] Task started: Blastn
[2023-03-19 03:23:27,027] [INFO] Running command: blastn -query OceanDNA-b25378/markers.fasta -db /var/lib/cwl/stg5182c2a4-b4ce-476b-9263-2e8df762da48/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25378/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:23:27,867] [INFO] Task succeeded: Blastn
[2023-03-19 03:23:27,891] [INFO] Selected 14 target genomes.
[2023-03-19 03:23:27,891] [INFO] Target genome list was writen to OceanDNA-b25378/target_genomes_gtdb.txt
[2023-03-19 03:23:27,930] [INFO] Task started: fastANI
[2023-03-19 03:23:27,930] [INFO] Running command: fastANI --query /var/lib/cwl/stg28a9619c-1ad4-45ff-b192-ed1a9565c118/OceanDNA-b25378.fa --refList OceanDNA-b25378/target_genomes_gtdb.txt --output OceanDNA-b25378/fastani_result_gtdb.tsv --threads 1
[2023-03-19 03:23:30,671] [INFO] Task succeeded: fastANI
[2023-03-19 03:23:30,677] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 03:23:30,678] [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_905616445.1	s__SYDM01 sp905616445	86.1809	105	208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__SYDM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905620505.1	s__SYDM01 sp905620505	83.9082	105	208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__SYDM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905618885.1	s__SYDM01 sp905618885	82.6654	87	208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__SYDM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016777565.1	s__SYDM01 sp016777565	80.2209	119	208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__SYDM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005801485.1	s__SYDM01 sp005801485	80.006	77	208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__SYDM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008638125.1	s__SYDM01 sp008638125	78.5815	100	208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__SYDM01	95.0	98.84	98.46	0.87	0.80	9	-
GCA_902590625.1	s__Pelagibacter_A sp902590625	76.9882	50	208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902609855.1	s__Pelagibacter_A sp902609855	76.9501	64	208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902597875.1	s__MED-G40 sp902597875	76.4145	55	208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__MED-G40	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 03:23:30,685] [INFO] GTDB search result was written to OceanDNA-b25378/result_gtdb.tsv
[2023-03-19 03:23:30,702] [INFO] ===== GTDB Search completed =====
[2023-03-19 03:23:30,709] [INFO] DFAST_QC result json was written to OceanDNA-b25378/dqc_result.json
[2023-03-19 03:23:30,710] [INFO] DFAST_QC completed!
[2023-03-19 03:23:30,710] [INFO] Total running time: 0h0m31s