[2023-03-16 16:16:25,432] [INFO] DFAST_QC pipeline started.
[2023-03-16 16:16:25,432] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 16:16:25,432] [INFO] DQC Reference Directory: /var/lib/cwl/stg92ea157f-020f-4e0d-986b-2965a308d2e2/dqc_reference
[2023-03-16 16:16:26,610] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 16:16:26,610] [INFO] Task started: Prodigal
[2023-03-16 16:16:26,610] [INFO] Running command: cat /var/lib/cwl/stg743f3c2c-ec9d-4261-9d4b-7137ce39c6f4/OceanDNA-b26918.fa | prodigal -d OceanDNA-b26918/cds.fna -a OceanDNA-b26918/protein.faa -g 11 -q > /dev/null
[2023-03-16 16:16:46,665] [INFO] Task succeeded: Prodigal
[2023-03-16 16:16:46,665] [INFO] Task started: HMMsearch
[2023-03-16 16:16:46,665] [INFO] Running command: hmmsearch --tblout OceanDNA-b26918/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg92ea157f-020f-4e0d-986b-2965a308d2e2/dqc_reference/reference_markers.hmm OceanDNA-b26918/protein.faa > /dev/null
[2023-03-16 16:16:46,879] [INFO] Task succeeded: HMMsearch
[2023-03-16 16:16:46,880] [INFO] Found 6/6 markers.
[2023-03-16 16:16:46,908] [INFO] Query marker FASTA was written to OceanDNA-b26918/markers.fasta
[2023-03-16 16:16:46,910] [INFO] Task started: Blastn
[2023-03-16 16:16:46,910] [INFO] Running command: blastn -query OceanDNA-b26918/markers.fasta -db /var/lib/cwl/stg92ea157f-020f-4e0d-986b-2965a308d2e2/dqc_reference/reference_markers.fasta -out OceanDNA-b26918/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:16:47,549] [INFO] Task succeeded: Blastn
[2023-03-16 16:16:47,550] [INFO] Selected 39 target genomes.
[2023-03-16 16:16:47,551] [INFO] Target genome list was writen to OceanDNA-b26918/target_genomes.txt
[2023-03-16 16:16:47,572] [INFO] Task started: fastANI
[2023-03-16 16:16:47,572] [INFO] Running command: fastANI --query /var/lib/cwl/stg743f3c2c-ec9d-4261-9d4b-7137ce39c6f4/OceanDNA-b26918.fa --refList OceanDNA-b26918/target_genomes.txt --output OceanDNA-b26918/fastani_result.tsv --threads 1
[2023-03-16 16:17:17,123] [INFO] Task succeeded: fastANI
[2023-03-16 16:17:17,123] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg92ea157f-020f-4e0d-986b-2965a308d2e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 16:17:17,123] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg92ea157f-020f-4e0d-986b-2965a308d2e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 16:17:17,124] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 16:17:17,124] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 16:17:17,124] [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
--------------------------------------------------------------------------------
[2023-03-16 16:17:17,124] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26918/tc_result.tsv
[2023-03-16 16:17:17,124] [INFO] ===== Taxonomy check completed =====
[2023-03-16 16:17:17,124] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 16:17:17,124] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg92ea157f-020f-4e0d-986b-2965a308d2e2/dqc_reference/checkm_data
[2023-03-16 16:17:17,127] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 16:17:17,132] [INFO] Task started: CheckM
[2023-03-16 16:17:17,132] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26918/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26918/checkm_input OceanDNA-b26918/checkm_result
[2023-03-16 16:17:54,978] [INFO] Task succeeded: CheckM
[2023-03-16 16:17:54,979] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.77%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 16:17:54,981] [INFO] ===== Completeness check finished =====
[2023-03-16 16:17:54,981] [INFO] ===== Start GTDB Search =====
[2023-03-16 16:17:54,981] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26918/markers.fasta)
[2023-03-16 16:17:54,983] [INFO] Task started: Blastn
[2023-03-16 16:17:54,983] [INFO] Running command: blastn -query OceanDNA-b26918/markers.fasta -db /var/lib/cwl/stg92ea157f-020f-4e0d-986b-2965a308d2e2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26918/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:17:56,033] [INFO] Task succeeded: Blastn
[2023-03-16 16:17:56,034] [INFO] Selected 36 target genomes.
[2023-03-16 16:17:56,034] [INFO] Target genome list was writen to OceanDNA-b26918/target_genomes_gtdb.txt
[2023-03-16 16:17:57,020] [INFO] Task started: fastANI
[2023-03-16 16:17:57,020] [INFO] Running command: fastANI --query /var/lib/cwl/stg743f3c2c-ec9d-4261-9d4b-7137ce39c6f4/OceanDNA-b26918.fa --refList OceanDNA-b26918/target_genomes_gtdb.txt --output OceanDNA-b26918/fastani_result_gtdb.tsv --threads 1
[2023-03-16 16:18:34,848] [INFO] Task succeeded: fastANI
[2023-03-16 16:18:34,851] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 16:18:34,851] [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_905480295.1	s__R2A130 sp905480295	98.931	472	512	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__R2A130	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_011087605.1	s__R2A130 sp011087605	77.4369	113	512	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__R2A130	95.0	99.98	99.97	0.98	0.98	3	-
GCA_014238155.1	s__R2A130 sp014238155	77.3985	114	512	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__R2A130	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013214695.1	s__R2A130 sp013214695	76.8547	121	512	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__R2A130	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 16:18:34,852] [INFO] GTDB search result was written to OceanDNA-b26918/result_gtdb.tsv
[2023-03-16 16:18:34,852] [INFO] ===== GTDB Search completed =====
[2023-03-16 16:18:34,852] [INFO] DFAST_QC result json was written to OceanDNA-b26918/dqc_result.json
[2023-03-16 16:18:34,853] [INFO] DFAST_QC completed!
[2023-03-16 16:18:34,853] [INFO] Total running time: 0h2m9s