[2023-03-15 10:52:57,305] [INFO] DFAST_QC pipeline started.
[2023-03-15 10:52:57,305] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 10:52:57,306] [INFO] DQC Reference Directory: /var/lib/cwl/stg3ac1784e-7a1f-41df-8a83-9f2e3a18caba/dqc_reference
[2023-03-15 10:52:58,862] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 10:52:58,862] [INFO] Task started: Prodigal
[2023-03-15 10:52:58,862] [INFO] Running command: cat /var/lib/cwl/stg1eed3004-bef5-4d87-90ad-b7273ce899a7/OceanDNA-b6212.fa | prodigal -d OceanDNA-b6212/cds.fna -a OceanDNA-b6212/protein.faa -g 11 -q > /dev/null
[2023-03-15 10:53:16,802] [INFO] Task succeeded: Prodigal
[2023-03-15 10:53:16,803] [INFO] Task started: HMMsearch
[2023-03-15 10:53:16,803] [INFO] Running command: hmmsearch --tblout OceanDNA-b6212/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3ac1784e-7a1f-41df-8a83-9f2e3a18caba/dqc_reference/reference_markers.hmm OceanDNA-b6212/protein.faa > /dev/null
[2023-03-15 10:53:17,037] [INFO] Task succeeded: HMMsearch
[2023-03-15 10:53:17,038] [INFO] Found 6/6 markers.
[2023-03-15 10:53:17,064] [INFO] Query marker FASTA was written to OceanDNA-b6212/markers.fasta
[2023-03-15 10:53:17,066] [INFO] Task started: Blastn
[2023-03-15 10:53:17,066] [INFO] Running command: blastn -query OceanDNA-b6212/markers.fasta -db /var/lib/cwl/stg3ac1784e-7a1f-41df-8a83-9f2e3a18caba/dqc_reference/reference_markers.fasta -out OceanDNA-b6212/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:53:17,665] [INFO] Task succeeded: Blastn
[2023-03-15 10:53:17,666] [INFO] Selected 31 target genomes.
[2023-03-15 10:53:17,666] [INFO] Target genome list was writen to OceanDNA-b6212/target_genomes.txt
[2023-03-15 10:53:17,688] [INFO] Task started: fastANI
[2023-03-15 10:53:17,689] [INFO] Running command: fastANI --query /var/lib/cwl/stg1eed3004-bef5-4d87-90ad-b7273ce899a7/OceanDNA-b6212.fa --refList OceanDNA-b6212/target_genomes.txt --output OceanDNA-b6212/fastani_result.tsv --threads 1
[2023-03-15 10:53:36,373] [INFO] Task succeeded: fastANI
[2023-03-15 10:53:36,374] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3ac1784e-7a1f-41df-8a83-9f2e3a18caba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 10:53:36,374] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3ac1784e-7a1f-41df-8a83-9f2e3a18caba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 10:53:36,378] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 10:53:36,378] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 10:53:36,379] [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
Leptobacterium flavescens	strain=KCTC 22160	GCA_010671605.1	472055	472055	type	True	76.6475	119	800	95	below_threshold
Joostella marina	strain=DSM 19592	GCA_000260115.1	453852	453852	type	True	75.806	58	800	95	below_threshold
Abyssalbus ytuae	strain=MT3330	GCA_022807975.1	2926907	2926907	type	True	75.3887	59	800	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 10:53:36,379] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6212/tc_result.tsv
[2023-03-15 10:53:36,379] [INFO] ===== Taxonomy check completed =====
[2023-03-15 10:53:36,379] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 10:53:36,379] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3ac1784e-7a1f-41df-8a83-9f2e3a18caba/dqc_reference/checkm_data
[2023-03-15 10:53:36,380] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 10:53:36,385] [INFO] Task started: CheckM
[2023-03-15 10:53:36,385] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6212/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6212/checkm_input OceanDNA-b6212/checkm_result
[2023-03-15 10:54:24,042] [INFO] Task succeeded: CheckM
[2023-03-15 10:54:24,043] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 10:54:24,076] [INFO] ===== Completeness check finished =====
[2023-03-15 10:54:24,076] [INFO] ===== Start GTDB Search =====
[2023-03-15 10:54:24,076] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6212/markers.fasta)
[2023-03-15 10:54:24,077] [INFO] Task started: Blastn
[2023-03-15 10:54:24,077] [INFO] Running command: blastn -query OceanDNA-b6212/markers.fasta -db /var/lib/cwl/stg3ac1784e-7a1f-41df-8a83-9f2e3a18caba/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6212/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:54:24,883] [INFO] Task succeeded: Blastn
[2023-03-15 10:54:24,884] [INFO] Selected 27 target genomes.
[2023-03-15 10:54:24,885] [INFO] Target genome list was writen to OceanDNA-b6212/target_genomes_gtdb.txt
[2023-03-15 10:54:25,228] [INFO] Task started: fastANI
[2023-03-15 10:54:25,229] [INFO] Running command: fastANI --query /var/lib/cwl/stg1eed3004-bef5-4d87-90ad-b7273ce899a7/OceanDNA-b6212.fa --refList OceanDNA-b6212/target_genomes_gtdb.txt --output OceanDNA-b6212/fastani_result_gtdb.tsv --threads 1
[2023-03-15 10:54:41,819] [INFO] Task succeeded: fastANI
[2023-03-15 10:54:41,823] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 10:54:41,823] [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_009901575.1	s__Leptobacterium sp009901575	77.488	216	800	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leptobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010671605.1	s__Leptobacterium flavescens	76.6475	119	800	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leptobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000260115.1	s__Joostella marina	75.806	58	800	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Joostella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 10:54:41,823] [INFO] GTDB search result was written to OceanDNA-b6212/result_gtdb.tsv
[2023-03-15 10:54:41,823] [INFO] ===== GTDB Search completed =====
[2023-03-15 10:54:41,824] [INFO] DFAST_QC result json was written to OceanDNA-b6212/dqc_result.json
[2023-03-15 10:54:41,824] [INFO] DFAST_QC completed!
[2023-03-15 10:54:41,824] [INFO] Total running time: 0h1m45s