[2023-03-15 15:55:17,978] [INFO] DFAST_QC pipeline started.
[2023-03-15 15:55:17,978] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 15:55:17,978] [INFO] DQC Reference Directory: /var/lib/cwl/stge8f75544-3122-49b5-9998-032efefd3867/dqc_reference
[2023-03-15 15:55:19,065] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 15:55:19,066] [INFO] Task started: Prodigal
[2023-03-15 15:55:19,066] [INFO] Running command: cat /var/lib/cwl/stg1588a854-c654-48eb-bfac-f1a6121d1f5b/OceanDNA-b11525.fa | prodigal -d OceanDNA-b11525/cds.fna -a OceanDNA-b11525/protein.faa -g 11 -q > /dev/null
[2023-03-15 15:55:38,393] [INFO] Task succeeded: Prodigal
[2023-03-15 15:55:38,393] [INFO] Task started: HMMsearch
[2023-03-15 15:55:38,393] [INFO] Running command: hmmsearch --tblout OceanDNA-b11525/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge8f75544-3122-49b5-9998-032efefd3867/dqc_reference/reference_markers.hmm OceanDNA-b11525/protein.faa > /dev/null
[2023-03-15 15:55:38,614] [INFO] Task succeeded: HMMsearch
[2023-03-15 15:55:38,615] [INFO] Found 6/6 markers.
[2023-03-15 15:55:38,634] [INFO] Query marker FASTA was written to OceanDNA-b11525/markers.fasta
[2023-03-15 15:55:38,635] [INFO] Task started: Blastn
[2023-03-15 15:55:38,635] [INFO] Running command: blastn -query OceanDNA-b11525/markers.fasta -db /var/lib/cwl/stge8f75544-3122-49b5-9998-032efefd3867/dqc_reference/reference_markers.fasta -out OceanDNA-b11525/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:55:39,189] [INFO] Task succeeded: Blastn
[2023-03-15 15:55:39,190] [INFO] Selected 25 target genomes.
[2023-03-15 15:55:39,190] [INFO] Target genome list was writen to OceanDNA-b11525/target_genomes.txt
[2023-03-15 15:55:39,207] [INFO] Task started: fastANI
[2023-03-15 15:55:39,207] [INFO] Running command: fastANI --query /var/lib/cwl/stg1588a854-c654-48eb-bfac-f1a6121d1f5b/OceanDNA-b11525.fa --refList OceanDNA-b11525/target_genomes.txt --output OceanDNA-b11525/fastani_result.tsv --threads 1
[2023-03-15 15:55:54,208] [INFO] Task succeeded: fastANI
[2023-03-15 15:55:54,208] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge8f75544-3122-49b5-9998-032efefd3867/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 15:55:54,209] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge8f75544-3122-49b5-9998-032efefd3867/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 15:55:54,209] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 15:55:54,209] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 15:55:54,209] [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
--------------------------------------------------------------------------------
[2023-03-15 15:55:54,209] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11525/tc_result.tsv
[2023-03-15 15:55:54,209] [INFO] ===== Taxonomy check completed =====
[2023-03-15 15:55:54,209] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 15:55:54,209] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge8f75544-3122-49b5-9998-032efefd3867/dqc_reference/checkm_data
[2023-03-15 15:55:54,212] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 15:55:54,216] [INFO] Task started: CheckM
[2023-03-15 15:55:54,216] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11525/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11525/checkm_input OceanDNA-b11525/checkm_result
[2023-03-15 15:56:44,593] [INFO] Task succeeded: CheckM
[2023-03-15 15:56:44,593] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.20%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 15:56:44,595] [INFO] ===== Completeness check finished =====
[2023-03-15 15:56:44,596] [INFO] ===== Start GTDB Search =====
[2023-03-15 15:56:44,596] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11525/markers.fasta)
[2023-03-15 15:56:44,596] [INFO] Task started: Blastn
[2023-03-15 15:56:44,596] [INFO] Running command: blastn -query OceanDNA-b11525/markers.fasta -db /var/lib/cwl/stge8f75544-3122-49b5-9998-032efefd3867/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11525/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:56:45,301] [INFO] Task succeeded: Blastn
[2023-03-15 15:56:45,302] [INFO] Selected 28 target genomes.
[2023-03-15 15:56:45,302] [INFO] Target genome list was writen to OceanDNA-b11525/target_genomes_gtdb.txt
[2023-03-15 15:56:45,355] [INFO] Task started: fastANI
[2023-03-15 15:56:45,355] [INFO] Running command: fastANI --query /var/lib/cwl/stg1588a854-c654-48eb-bfac-f1a6121d1f5b/OceanDNA-b11525.fa --refList OceanDNA-b11525/target_genomes_gtdb.txt --output OceanDNA-b11525/fastani_result_gtdb.tsv --threads 1
[2023-03-15 15:56:59,055] [INFO] Task succeeded: fastANI
[2023-03-15 15:56:59,058] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 15:56:59,058] [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_002722245.1	s__GCA-002722245 sp002722245	99.8475	926	973	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__GCA-002722245;g__GCA-002722245	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002717515.1	s__GCA-002722245 sp002717515	78.8979	177	973	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__GCA-002722245;g__GCA-002722245	95.0	99.42	99.42	0.83	0.83	2	-
GCA_002720635.1	s__GCA-002722245 sp002720635	77.7026	131	973	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__GCA-002722245;g__GCA-002722245	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 15:56:59,059] [INFO] GTDB search result was written to OceanDNA-b11525/result_gtdb.tsv
[2023-03-15 15:56:59,059] [INFO] ===== GTDB Search completed =====
[2023-03-15 15:56:59,059] [INFO] DFAST_QC result json was written to OceanDNA-b11525/dqc_result.json
[2023-03-15 15:56:59,059] [INFO] DFAST_QC completed!
[2023-03-15 15:56:59,059] [INFO] Total running time: 0h1m41s