[2023-03-14 11:14:12,743] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:14:12,743] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:14:12,743] [INFO] DQC Reference Directory: /var/lib/cwl/stga6805a88-0eae-4d06-a3d0-0420c508e962/dqc_reference
[2023-03-14 11:14:14,203] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:14:14,203] [INFO] Task started: Prodigal
[2023-03-14 11:14:14,204] [INFO] Running command: cat /var/lib/cwl/stga0f3e4ba-f2f2-442f-9b03-5da31d0ac075/OceanDNA-b32507.fa | prodigal -d OceanDNA-b32507/cds.fna -a OceanDNA-b32507/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:14:17,543] [INFO] Task succeeded: Prodigal
[2023-03-14 11:14:17,543] [INFO] Task started: HMMsearch
[2023-03-14 11:14:17,544] [INFO] Running command: hmmsearch --tblout OceanDNA-b32507/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga6805a88-0eae-4d06-a3d0-0420c508e962/dqc_reference/reference_markers.hmm OceanDNA-b32507/protein.faa > /dev/null
[2023-03-14 11:14:17,729] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:14:17,730] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga0f3e4ba-f2f2-442f-9b03-5da31d0ac075/OceanDNA-b32507.fa]
[2023-03-14 11:14:17,740] [INFO] Query marker FASTA was written to OceanDNA-b32507/markers.fasta
[2023-03-14 11:14:17,740] [INFO] Task started: Blastn
[2023-03-14 11:14:17,740] [INFO] Running command: blastn -query OceanDNA-b32507/markers.fasta -db /var/lib/cwl/stga6805a88-0eae-4d06-a3d0-0420c508e962/dqc_reference/reference_markers.fasta -out OceanDNA-b32507/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:14:18,228] [INFO] Task succeeded: Blastn
[2023-03-14 11:14:18,229] [INFO] Selected 19 target genomes.
[2023-03-14 11:14:18,229] [INFO] Target genome list was writen to OceanDNA-b32507/target_genomes.txt
[2023-03-14 11:14:18,242] [INFO] Task started: fastANI
[2023-03-14 11:14:18,242] [INFO] Running command: fastANI --query /var/lib/cwl/stga0f3e4ba-f2f2-442f-9b03-5da31d0ac075/OceanDNA-b32507.fa --refList OceanDNA-b32507/target_genomes.txt --output OceanDNA-b32507/fastani_result.tsv --threads 1
[2023-03-14 11:14:26,799] [INFO] Task succeeded: fastANI
[2023-03-14 11:14:26,800] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga6805a88-0eae-4d06-a3d0-0420c508e962/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:14:26,800] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga6805a88-0eae-4d06-a3d0-0420c508e962/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:14:26,800] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:14:26,800] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 11:14:26,800] [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
--------------------------------------------------------------------------------
[2023-03-14 11:14:26,800] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32507/tc_result.tsv
[2023-03-14 11:14:26,800] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:14:26,801] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:14:26,801] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga6805a88-0eae-4d06-a3d0-0420c508e962/dqc_reference/checkm_data
[2023-03-14 11:14:26,804] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:14:26,807] [INFO] Task started: CheckM
[2023-03-14 11:14:26,807] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32507/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32507/checkm_input OceanDNA-b32507/checkm_result
[2023-03-14 11:14:42,920] [INFO] Task succeeded: CheckM
[2023-03-14 11:14:42,920] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.29%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:14:42,922] [INFO] ===== Completeness check finished =====
[2023-03-14 11:14:42,922] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:14:42,922] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32507/markers.fasta)
[2023-03-14 11:14:42,923] [INFO] Task started: Blastn
[2023-03-14 11:14:42,923] [INFO] Running command: blastn -query OceanDNA-b32507/markers.fasta -db /var/lib/cwl/stga6805a88-0eae-4d06-a3d0-0420c508e962/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32507/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:14:43,647] [INFO] Task succeeded: Blastn
[2023-03-14 11:14:43,648] [INFO] Selected 18 target genomes.
[2023-03-14 11:14:43,648] [INFO] Target genome list was writen to OceanDNA-b32507/target_genomes_gtdb.txt
[2023-03-14 11:14:43,670] [INFO] Task started: fastANI
[2023-03-14 11:14:43,670] [INFO] Running command: fastANI --query /var/lib/cwl/stga0f3e4ba-f2f2-442f-9b03-5da31d0ac075/OceanDNA-b32507.fa --refList OceanDNA-b32507/target_genomes_gtdb.txt --output OceanDNA-b32507/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:14:47,564] [INFO] Task succeeded: fastANI
[2023-03-14 11:14:47,567] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 11:14:47,567] [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_002710765.1	s__GCA-2710765 sp002710765	95.1397	147	198	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__GCA-2710765	95.0	95.05	95.05	0.69	0.69	2	conclusive
GCA_902524895.1	s__SP4073 sp902524895	76.2423	51	198	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__SP4073	95.0	96.76	96.76	0.88	0.88	2	-
GCA_002691145.1	s__GCA-2691145 sp002691145	75.8792	50	198	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__GCA-2691145	95.0	99.68	99.51	0.96	0.92	4	-
--------------------------------------------------------------------------------
[2023-03-14 11:14:47,568] [INFO] GTDB search result was written to OceanDNA-b32507/result_gtdb.tsv
[2023-03-14 11:14:47,568] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:14:47,568] [INFO] DFAST_QC result json was written to OceanDNA-b32507/dqc_result.json
[2023-03-14 11:14:47,568] [INFO] DFAST_QC completed!
[2023-03-14 11:14:47,568] [INFO] Total running time: 0h0m35s