[2023-03-17 04:15:15,032] [INFO] DFAST_QC pipeline started.
[2023-03-17 04:15:15,032] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 04:15:15,032] [INFO] DQC Reference Directory: /var/lib/cwl/stg09e301cb-9f27-4c35-8f36-f5afd820224b/dqc_reference
[2023-03-17 04:15:16,760] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 04:15:16,760] [INFO] Task started: Prodigal
[2023-03-17 04:15:16,760] [INFO] Running command: cat /var/lib/cwl/stga66d2e7b-8a29-4a2f-bff2-7e7d5dc1ef49/OceanDNA-b16091.fa | prodigal -d OceanDNA-b16091/cds.fna -a OceanDNA-b16091/protein.faa -g 11 -q > /dev/null
[2023-03-17 04:15:37,903] [INFO] Task succeeded: Prodigal
[2023-03-17 04:15:37,903] [INFO] Task started: HMMsearch
[2023-03-17 04:15:37,903] [INFO] Running command: hmmsearch --tblout OceanDNA-b16091/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg09e301cb-9f27-4c35-8f36-f5afd820224b/dqc_reference/reference_markers.hmm OceanDNA-b16091/protein.faa > /dev/null
[2023-03-17 04:15:38,137] [INFO] Task succeeded: HMMsearch
[2023-03-17 04:15:38,137] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga66d2e7b-8a29-4a2f-bff2-7e7d5dc1ef49/OceanDNA-b16091.fa]
[2023-03-17 04:15:38,165] [INFO] Query marker FASTA was written to OceanDNA-b16091/markers.fasta
[2023-03-17 04:15:38,166] [INFO] Task started: Blastn
[2023-03-17 04:15:38,166] [INFO] Running command: blastn -query OceanDNA-b16091/markers.fasta -db /var/lib/cwl/stg09e301cb-9f27-4c35-8f36-f5afd820224b/dqc_reference/reference_markers.fasta -out OceanDNA-b16091/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:15:38,674] [INFO] Task succeeded: Blastn
[2023-03-17 04:15:38,674] [INFO] Selected 10 target genomes.
[2023-03-17 04:15:38,675] [INFO] Target genome list was writen to OceanDNA-b16091/target_genomes.txt
[2023-03-17 04:15:38,681] [INFO] Task started: fastANI
[2023-03-17 04:15:38,681] [INFO] Running command: fastANI --query /var/lib/cwl/stga66d2e7b-8a29-4a2f-bff2-7e7d5dc1ef49/OceanDNA-b16091.fa --refList OceanDNA-b16091/target_genomes.txt --output OceanDNA-b16091/fastani_result.tsv --threads 1
[2023-03-17 04:15:50,764] [INFO] Task succeeded: fastANI
[2023-03-17 04:15:50,764] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg09e301cb-9f27-4c35-8f36-f5afd820224b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 04:15:50,764] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg09e301cb-9f27-4c35-8f36-f5afd820224b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 04:15:50,770] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2023-03-17 04:15:50,770] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-17 04:15:50,770] [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 watsonii	strain=WH 8501	GCA_000167195.1	263511	263511	suspected-type	True	98.6584	1235	1398	95	conclusive
Crocosphaera subtropica	strain=ATCC 51142	GCA_000017845.1	2546360	2546360	type	True	81.585	949	1398	95	below_threshold
Crocosphaera chwakensis	strain=CCY0110	GCA_000169335.1	2546361	2546361	type	True	81.2616	925	1398	95	below_threshold
Rippkaea orientalis	strain=PCC 8801	GCA_000021805.1	2546366	2546366	type	True	76.8365	293	1398	95	below_threshold
Microcystis aeruginosa	strain=NIES-843	GCA_000010625.1	1126	1126	suspected-type	True	76.2076	92	1398	95	below_threshold
Gloeothece citriformis	strain=PCC 7424	GCA_000021825.1	2546356	2546356	type	True	76.1483	160	1398	95	below_threshold
Stanieria cyanosphaera	strain=PCC 7437	GCA_000317575.1	102116	102116	type	True	75.8148	109	1398	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 04:15:50,770] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16091/tc_result.tsv
[2023-03-17 04:15:50,770] [INFO] ===== Taxonomy check completed =====
[2023-03-17 04:15:50,770] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 04:15:50,770] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg09e301cb-9f27-4c35-8f36-f5afd820224b/dqc_reference/checkm_data
[2023-03-17 04:15:50,771] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 04:15:50,777] [INFO] Task started: CheckM
[2023-03-17 04:15:50,777] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16091/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16091/checkm_input OceanDNA-b16091/checkm_result
[2023-03-17 04:16:44,071] [INFO] Task succeeded: CheckM
[2023-03-17 04:16:44,071] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 04:16:44,075] [INFO] ===== Completeness check finished =====
[2023-03-17 04:16:44,075] [INFO] ===== Start GTDB Search =====
[2023-03-17 04:16:44,075] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16091/markers.fasta)
[2023-03-17 04:16:44,075] [INFO] Task started: Blastn
[2023-03-17 04:16:44,075] [INFO] Running command: blastn -query OceanDNA-b16091/markers.fasta -db /var/lib/cwl/stg09e301cb-9f27-4c35-8f36-f5afd820224b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16091/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:16:44,755] [INFO] Task succeeded: Blastn
[2023-03-17 04:16:44,756] [INFO] Selected 7 target genomes.
[2023-03-17 04:16:44,756] [INFO] Target genome list was writen to OceanDNA-b16091/target_genomes_gtdb.txt
[2023-03-17 04:16:44,861] [INFO] Task started: fastANI
[2023-03-17 04:16:44,861] [INFO] Running command: fastANI --query /var/lib/cwl/stga66d2e7b-8a29-4a2f-bff2-7e7d5dc1ef49/OceanDNA-b16091.fa --refList OceanDNA-b16091/target_genomes_gtdb.txt --output OceanDNA-b16091/fastani_result_gtdb.tsv --threads 1
[2023-03-17 04:16:54,871] [INFO] Task succeeded: fastANI
[2023-03-17 04:16:54,876] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 04:16:54,876] [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_000167195.1	s__Crocosphaera watsonii	98.6451	1236	1398	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae_A;g__Crocosphaera	95.0	99.01	98.50	0.92	0.88	4	conclusive
GCF_000017845.1	s__Crocosphaera subtropica	81.5976	946	1398	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	81.4909	905	1398	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	81.3534	929	1398	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_000169335.1	s__Crocosphaera chwakensis	81.3072	920	1398	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_003574135.1	s__Rippkaea sp003574135	76.3982	121	1398	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae_A;g__Rippkaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000829235.1	s__Rippkaea sp000829235	76.2975	111	1398	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae_A;g__Rippkaea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 04:16:54,876] [INFO] GTDB search result was written to OceanDNA-b16091/result_gtdb.tsv
[2023-03-17 04:16:54,876] [INFO] ===== GTDB Search completed =====
[2023-03-17 04:16:54,877] [INFO] DFAST_QC result json was written to OceanDNA-b16091/dqc_result.json
[2023-03-17 04:16:54,878] [INFO] DFAST_QC completed!
[2023-03-17 04:16:54,878] [INFO] Total running time: 0h1m40s