[2023-03-19 00:01:03,444] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:01:03,444] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:01:03,444] [INFO] DQC Reference Directory: /var/lib/cwl/stg23805f58-c615-43eb-80f6-16796ad0199e/dqc_reference
[2023-03-19 00:01:04,714] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:01:04,714] [INFO] Task started: Prodigal
[2023-03-19 00:01:04,714] [INFO] Running command: cat /var/lib/cwl/stg04ab9544-1058-4745-abff-b5be7843d9bd/OceanDNA-b35602.fa | prodigal -d OceanDNA-b35602/cds.fna -a OceanDNA-b35602/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:01:09,474] [INFO] Task succeeded: Prodigal
[2023-03-19 00:01:09,474] [INFO] Task started: HMMsearch
[2023-03-19 00:01:09,474] [INFO] Running command: hmmsearch --tblout OceanDNA-b35602/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg23805f58-c615-43eb-80f6-16796ad0199e/dqc_reference/reference_markers.hmm OceanDNA-b35602/protein.faa > /dev/null
[2023-03-19 00:01:09,667] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:01:09,668] [INFO] Found 6/6 markers.
[2023-03-19 00:01:09,676] [INFO] Query marker FASTA was written to OceanDNA-b35602/markers.fasta
[2023-03-19 00:01:09,678] [INFO] Task started: Blastn
[2023-03-19 00:01:09,678] [INFO] Running command: blastn -query OceanDNA-b35602/markers.fasta -db /var/lib/cwl/stg23805f58-c615-43eb-80f6-16796ad0199e/dqc_reference/reference_markers.fasta -out OceanDNA-b35602/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:01:10,330] [INFO] Task succeeded: Blastn
[2023-03-19 00:01:10,331] [INFO] Selected 16 target genomes.
[2023-03-19 00:01:10,331] [INFO] Target genome list was writen to OceanDNA-b35602/target_genomes.txt
[2023-03-19 00:01:10,350] [INFO] Task started: fastANI
[2023-03-19 00:01:10,350] [INFO] Running command: fastANI --query /var/lib/cwl/stg04ab9544-1058-4745-abff-b5be7843d9bd/OceanDNA-b35602.fa --refList OceanDNA-b35602/target_genomes.txt --output OceanDNA-b35602/fastani_result.tsv --threads 1
[2023-03-19 00:01:17,678] [INFO] Task succeeded: fastANI
[2023-03-19 00:01:17,678] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg23805f58-c615-43eb-80f6-16796ad0199e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:01:17,679] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg23805f58-c615-43eb-80f6-16796ad0199e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:01:17,679] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:01:17,679] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 00:01:17,679] [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 00:01:17,679] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35602/tc_result.tsv
[2023-03-19 00:01:17,679] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:01:17,679] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:01:17,679] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg23805f58-c615-43eb-80f6-16796ad0199e/dqc_reference/checkm_data
[2023-03-19 00:01:17,682] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:01:17,685] [INFO] Task started: CheckM
[2023-03-19 00:01:17,685] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35602/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35602/checkm_input OceanDNA-b35602/checkm_result
[2023-03-19 00:01:35,727] [INFO] Task succeeded: CheckM
[2023-03-19 00:01:35,728] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.39%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 00:01:35,729] [INFO] ===== Completeness check finished =====
[2023-03-19 00:01:35,730] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:01:35,730] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35602/markers.fasta)
[2023-03-19 00:01:35,730] [INFO] Task started: Blastn
[2023-03-19 00:01:35,730] [INFO] Running command: blastn -query OceanDNA-b35602/markers.fasta -db /var/lib/cwl/stg23805f58-c615-43eb-80f6-16796ad0199e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35602/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:01:36,638] [INFO] Task succeeded: Blastn
[2023-03-19 00:01:36,639] [INFO] Selected 21 target genomes.
[2023-03-19 00:01:36,639] [INFO] Target genome list was writen to OceanDNA-b35602/target_genomes_gtdb.txt
[2023-03-19 00:01:36,667] [INFO] Task started: fastANI
[2023-03-19 00:01:36,667] [INFO] Running command: fastANI --query /var/lib/cwl/stg04ab9544-1058-4745-abff-b5be7843d9bd/OceanDNA-b35602.fa --refList OceanDNA-b35602/target_genomes_gtdb.txt --output OceanDNA-b35602/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:01:41,493] [INFO] Task succeeded: fastANI
[2023-03-19 00:01:41,498] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 00:01:41,498] [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_905479195.1	s__GCA-2698665 sp905479195	93.0105	288	317	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-002705445;f__GCA-002716945;g__GCA-2698665	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018670435.1	s__GCA-2698665 sp018670435	81.5823	214	317	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-002705445;f__GCA-002716945;g__GCA-2698665	95.0	99.55	99.48	0.85	0.83	5	-
GCA_018667355.1	s__GCA-2698665 sp018667355	80.7452	222	317	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-002705445;f__GCA-002716945;g__GCA-2698665	95.0	99.95	99.92	0.96	0.95	8	-
GCA_002698665.1	s__GCA-2698665 sp002698665	76.9683	69	317	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-002705445;f__GCA-002716945;g__GCA-2698665	95.0	98.38	98.38	0.83	0.83	2	-
GCA_002718845.1	s__GCA-2718845 sp002718845	76.2662	52	317	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-002705445;f__GCA-002716945;g__GCA-2718845	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 00:01:41,498] [INFO] GTDB search result was written to OceanDNA-b35602/result_gtdb.tsv
[2023-03-19 00:01:41,498] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:01:41,499] [INFO] DFAST_QC result json was written to OceanDNA-b35602/dqc_result.json
[2023-03-19 00:01:41,499] [INFO] DFAST_QC completed!
[2023-03-19 00:01:41,499] [INFO] Total running time: 0h0m38s