[2023-03-16 18:18:12,484] [INFO] DFAST_QC pipeline started.
[2023-03-16 18:18:12,484] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 18:18:12,484] [INFO] DQC Reference Directory: /var/lib/cwl/stg9eb2aa74-d161-4024-a98f-5734837b31bd/dqc_reference
[2023-03-16 18:18:13,586] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 18:18:13,586] [INFO] Task started: Prodigal
[2023-03-16 18:18:13,586] [INFO] Running command: cat /var/lib/cwl/stg4278e781-3caa-47df-b872-c9deec546cea/OceanDNA-b16059.fa | prodigal -d OceanDNA-b16059/cds.fna -a OceanDNA-b16059/protein.faa -g 11 -q > /dev/null
[2023-03-16 18:18:20,838] [INFO] Task succeeded: Prodigal
[2023-03-16 18:18:20,838] [INFO] Task started: HMMsearch
[2023-03-16 18:18:20,838] [INFO] Running command: hmmsearch --tblout OceanDNA-b16059/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9eb2aa74-d161-4024-a98f-5734837b31bd/dqc_reference/reference_markers.hmm OceanDNA-b16059/protein.faa > /dev/null
[2023-03-16 18:18:21,190] [INFO] Task succeeded: HMMsearch
[2023-03-16 18:18:21,191] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4278e781-3caa-47df-b872-c9deec546cea/OceanDNA-b16059.fa]
[2023-03-16 18:18:21,200] [INFO] Query marker FASTA was written to OceanDNA-b16059/markers.fasta
[2023-03-16 18:18:21,200] [INFO] Task started: Blastn
[2023-03-16 18:18:21,200] [INFO] Running command: blastn -query OceanDNA-b16059/markers.fasta -db /var/lib/cwl/stg9eb2aa74-d161-4024-a98f-5734837b31bd/dqc_reference/reference_markers.fasta -out OceanDNA-b16059/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:18:22,387] [INFO] Task succeeded: Blastn
[2023-03-16 18:18:22,388] [INFO] Selected 23 target genomes.
[2023-03-16 18:18:22,388] [INFO] Target genome list was writen to OceanDNA-b16059/target_genomes.txt
[2023-03-16 18:18:22,406] [INFO] Task started: fastANI
[2023-03-16 18:18:22,406] [INFO] Running command: fastANI --query /var/lib/cwl/stg4278e781-3caa-47df-b872-c9deec546cea/OceanDNA-b16059.fa --refList OceanDNA-b16059/target_genomes.txt --output OceanDNA-b16059/fastani_result.tsv --threads 1
[2023-03-16 18:18:42,377] [INFO] Task succeeded: fastANI
[2023-03-16 18:18:42,378] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9eb2aa74-d161-4024-a98f-5734837b31bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 18:18:42,378] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9eb2aa74-d161-4024-a98f-5734837b31bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 18:18:42,382] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 18:18:42,382] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 18:18:42,382] [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
Crocosphaera chwakensis	strain=CCY0110	GCA_000169335.1	2546361	2546361	type	True	75.895	68	475	95	below_threshold
Crocosphaera subtropica	strain=ATCC 51142	GCA_000017845.1	2546360	2546360	type	True	75.6216	67	475	95	below_threshold
Crocosphaera watsonii	strain=WH 8501	GCA_000167195.1	263511	263511	suspected-type	True	75.5518	58	475	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 18:18:42,383] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16059/tc_result.tsv
[2023-03-16 18:18:42,383] [INFO] ===== Taxonomy check completed =====
[2023-03-16 18:18:42,383] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 18:18:42,383] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9eb2aa74-d161-4024-a98f-5734837b31bd/dqc_reference/checkm_data
[2023-03-16 18:18:42,384] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 18:18:42,387] [INFO] Task started: CheckM
[2023-03-16 18:18:42,387] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16059/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16059/checkm_input OceanDNA-b16059/checkm_result
[2023-03-16 18:19:10,544] [INFO] Task succeeded: CheckM
[2023-03-16 18:19:10,544] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 18:19:10,546] [INFO] ===== Completeness check finished =====
[2023-03-16 18:19:10,546] [INFO] ===== Start GTDB Search =====
[2023-03-16 18:19:10,547] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16059/markers.fasta)
[2023-03-16 18:19:10,548] [INFO] Task started: Blastn
[2023-03-16 18:19:10,548] [INFO] Running command: blastn -query OceanDNA-b16059/markers.fasta -db /var/lib/cwl/stg9eb2aa74-d161-4024-a98f-5734837b31bd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16059/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:19:11,709] [INFO] Task succeeded: Blastn
[2023-03-16 18:19:11,710] [INFO] Selected 15 target genomes.
[2023-03-16 18:19:11,710] [INFO] Target genome list was writen to OceanDNA-b16059/target_genomes_gtdb.txt
[2023-03-16 18:19:11,832] [INFO] Task started: fastANI
[2023-03-16 18:19:11,832] [INFO] Running command: fastANI --query /var/lib/cwl/stg4278e781-3caa-47df-b872-c9deec546cea/OceanDNA-b16059.fa --refList OceanDNA-b16059/target_genomes_gtdb.txt --output OceanDNA-b16059/fastani_result_gtdb.tsv --threads 1
[2023-03-16 18:19:27,295] [INFO] Task succeeded: fastANI
[2023-03-16 18:19:27,299] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 18:19:27,300] [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
GCF_000025125.1	s__Atelocyanobacterium thalassa	99.9656	475	475	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae_A;g__Atelocyanobacterium	95.0	99.95	99.95	0.99	0.99	2	conclusive
GCA_000737945.1	s__Atelocyanobacterium thalassa_A	84.3615	429	475	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae_A;g__Atelocyanobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000169335.1	s__Crocosphaera chwakensis	75.895	68	475	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae_A;g__Crocosphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002172675.1	s__Crocosphaera sp002172675	75.6786	73	475	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae_A;g__Crocosphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000017845.1	s__Crocosphaera subtropica	75.6216	67	475	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae_A;g__Crocosphaera	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003013815.1	s__Crocosphaera sp003013815	75.5782	58	475	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae_A;g__Crocosphaera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 18:19:27,300] [INFO] GTDB search result was written to OceanDNA-b16059/result_gtdb.tsv
[2023-03-16 18:19:27,300] [INFO] ===== GTDB Search completed =====
[2023-03-16 18:19:27,301] [INFO] DFAST_QC result json was written to OceanDNA-b16059/dqc_result.json
[2023-03-16 18:19:27,301] [INFO] DFAST_QC completed!
[2023-03-16 18:19:27,301] [INFO] Total running time: 0h1m15s