[2023-03-19 04:29:37,749] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:29:37,749] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:29:37,750] [INFO] DQC Reference Directory: /var/lib/cwl/stg22d5a19f-2d33-4844-be30-2699737903e7/dqc_reference
[2023-03-19 04:29:38,863] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:29:38,863] [INFO] Task started: Prodigal
[2023-03-19 04:29:38,864] [INFO] Running command: cat /var/lib/cwl/stgfe5d2211-5237-4362-9282-967ae1055429/OceanDNA-b16115.fa | prodigal -d OceanDNA-b16115/cds.fna -a OceanDNA-b16115/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:30:09,148] [INFO] Task succeeded: Prodigal
[2023-03-19 04:30:09,148] [INFO] Task started: HMMsearch
[2023-03-19 04:30:09,148] [INFO] Running command: hmmsearch --tblout OceanDNA-b16115/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg22d5a19f-2d33-4844-be30-2699737903e7/dqc_reference/reference_markers.hmm OceanDNA-b16115/protein.faa > /dev/null
[2023-03-19 04:30:09,396] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:30:09,397] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgfe5d2211-5237-4362-9282-967ae1055429/OceanDNA-b16115.fa]
[2023-03-19 04:30:09,427] [INFO] Query marker FASTA was written to OceanDNA-b16115/markers.fasta
[2023-03-19 04:30:09,427] [INFO] Task started: Blastn
[2023-03-19 04:30:09,427] [INFO] Running command: blastn -query OceanDNA-b16115/markers.fasta -db /var/lib/cwl/stg22d5a19f-2d33-4844-be30-2699737903e7/dqc_reference/reference_markers.fasta -out OceanDNA-b16115/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:30:09,947] [INFO] Task succeeded: Blastn
[2023-03-19 04:30:09,948] [INFO] Selected 22 target genomes.
[2023-03-19 04:30:09,948] [INFO] Target genome list was writen to OceanDNA-b16115/target_genomes.txt
[2023-03-19 04:30:09,960] [INFO] Task started: fastANI
[2023-03-19 04:30:09,960] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe5d2211-5237-4362-9282-967ae1055429/OceanDNA-b16115.fa --refList OceanDNA-b16115/target_genomes.txt --output OceanDNA-b16115/fastani_result.tsv --threads 1
[2023-03-19 04:30:23,415] [INFO] Task succeeded: fastANI
[2023-03-19 04:30:23,416] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg22d5a19f-2d33-4844-be30-2699737903e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:30:23,416] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg22d5a19f-2d33-4844-be30-2699737903e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:30:23,419] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:30:23,420] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 04:30:23,420] [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
Rippkaea orientalis	strain=PCC 8801	GCA_000021805.1	2546366	2546366	type	True	75.5668	52	1454	95	below_threshold
Okeania hirsuta	strain=PAB10Feb10-1	GCA_003838195.1	1458930	1458930	type	True	75.3371	58	1454	95	below_threshold
Gloeothece citriformis	strain=PCC 7424	GCA_000021825.1	2546356	2546356	type	True	75.0701	50	1454	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 04:30:23,420] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16115/tc_result.tsv
[2023-03-19 04:30:23,420] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:30:23,420] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:30:23,420] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg22d5a19f-2d33-4844-be30-2699737903e7/dqc_reference/checkm_data
[2023-03-19 04:30:23,421] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:30:23,427] [INFO] Task started: CheckM
[2023-03-19 04:30:23,427] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16115/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16115/checkm_input OceanDNA-b16115/checkm_result
[2023-03-19 04:31:37,515] [INFO] Task succeeded: CheckM
[2023-03-19 04:31:37,516] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.89%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 04:31:37,519] [INFO] ===== Completeness check finished =====
[2023-03-19 04:31:37,519] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:31:37,519] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16115/markers.fasta)
[2023-03-19 04:31:37,520] [INFO] Task started: Blastn
[2023-03-19 04:31:37,520] [INFO] Running command: blastn -query OceanDNA-b16115/markers.fasta -db /var/lib/cwl/stg22d5a19f-2d33-4844-be30-2699737903e7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16115/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:31:38,252] [INFO] Task succeeded: Blastn
[2023-03-19 04:31:38,253] [INFO] Selected 30 target genomes.
[2023-03-19 04:31:38,253] [INFO] Target genome list was writen to OceanDNA-b16115/target_genomes_gtdb.txt
[2023-03-19 04:31:38,421] [INFO] Task started: fastANI
[2023-03-19 04:31:38,421] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe5d2211-5237-4362-9282-967ae1055429/OceanDNA-b16115.fa --refList OceanDNA-b16115/target_genomes_gtdb.txt --output OceanDNA-b16115/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:32:02,704] [INFO] Task succeeded: fastANI
[2023-03-19 04:32:02,707] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 04:32:02,708] [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_000734895.2	s__Calothrix sp000734895	75.4974	53	1454	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Calothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010672865.1	s__SIO1D9 sp010672865	75.4893	59	1454	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__SIO1D9;g__SIO1D9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003448685.1	s__Rippkaea sp003448685	75.3958	64	1454	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae_A;g__Rippkaea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 04:32:02,708] [INFO] GTDB search result was written to OceanDNA-b16115/result_gtdb.tsv
[2023-03-19 04:32:02,708] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:32:02,708] [INFO] DFAST_QC result json was written to OceanDNA-b16115/dqc_result.json
[2023-03-19 04:32:02,709] [INFO] DFAST_QC completed!
[2023-03-19 04:32:02,709] [INFO] Total running time: 0h2m25s