[2023-06-17 10:14:06,007] [INFO] DFAST_QC pipeline started.
[2023-06-17 10:14:06,010] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 10:14:06,010] [INFO] DQC Reference Directory: /var/lib/cwl/stgc312f4fd-bf99-406b-9b28-6d28d7a1e2b1/dqc_reference
[2023-06-17 10:14:07,372] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 10:14:07,375] [INFO] Task started: Prodigal
[2023-06-17 10:14:07,375] [INFO] Running command: gunzip -c /var/lib/cwl/stg528b60f1-7eac-46f7-8426-82fb09252136/GCA_028982645.1_ASM2898264v1_genomic.fna.gz | prodigal -d GCA_028982645.1_ASM2898264v1_genomic.fna/cds.fna -a GCA_028982645.1_ASM2898264v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 10:14:15,140] [INFO] Task succeeded: Prodigal
[2023-06-17 10:14:15,140] [INFO] Task started: HMMsearch
[2023-06-17 10:14:15,140] [INFO] Running command: hmmsearch --tblout GCA_028982645.1_ASM2898264v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc312f4fd-bf99-406b-9b28-6d28d7a1e2b1/dqc_reference/reference_markers.hmm GCA_028982645.1_ASM2898264v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 10:14:15,469] [INFO] Task succeeded: HMMsearch
[2023-06-17 10:14:15,470] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg528b60f1-7eac-46f7-8426-82fb09252136/GCA_028982645.1_ASM2898264v1_genomic.fna.gz]
[2023-06-17 10:14:15,514] [INFO] Query marker FASTA was written to GCA_028982645.1_ASM2898264v1_genomic.fna/markers.fasta
[2023-06-17 10:14:15,515] [INFO] Task started: Blastn
[2023-06-17 10:14:15,515] [INFO] Running command: blastn -query GCA_028982645.1_ASM2898264v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc312f4fd-bf99-406b-9b28-6d28d7a1e2b1/dqc_reference/reference_markers.fasta -out GCA_028982645.1_ASM2898264v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 10:14:16,120] [INFO] Task succeeded: Blastn
[2023-06-17 10:14:16,125] [INFO] Selected 14 target genomes.
[2023-06-17 10:14:16,125] [INFO] Target genome list was writen to GCA_028982645.1_ASM2898264v1_genomic.fna/target_genomes.txt
[2023-06-17 10:14:16,127] [INFO] Task started: fastANI
[2023-06-17 10:14:16,127] [INFO] Running command: fastANI --query /var/lib/cwl/stg528b60f1-7eac-46f7-8426-82fb09252136/GCA_028982645.1_ASM2898264v1_genomic.fna.gz --refList GCA_028982645.1_ASM2898264v1_genomic.fna/target_genomes.txt --output GCA_028982645.1_ASM2898264v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 10:14:29,164] [INFO] Task succeeded: fastANI
[2023-06-17 10:14:29,165] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc312f4fd-bf99-406b-9b28-6d28d7a1e2b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 10:14:29,165] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc312f4fd-bf99-406b-9b28-6d28d7a1e2b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 10:14:29,170] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 10:14:29,170] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 10:14:29,170] [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
Okeania hirsuta	strain=PAB10Feb10-1	GCA_003838195.1	1458930	1458930	type	True	80.4305	996	1518	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 10:14:29,172] [INFO] DFAST Taxonomy check result was written to GCA_028982645.1_ASM2898264v1_genomic.fna/tc_result.tsv
[2023-06-17 10:14:29,173] [INFO] ===== Taxonomy check completed =====
[2023-06-17 10:14:29,173] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 10:14:29,173] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc312f4fd-bf99-406b-9b28-6d28d7a1e2b1/dqc_reference/checkm_data
[2023-06-17 10:14:29,175] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 10:14:29,235] [INFO] Task started: CheckM
[2023-06-17 10:14:29,235] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028982645.1_ASM2898264v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028982645.1_ASM2898264v1_genomic.fna/checkm_input GCA_028982645.1_ASM2898264v1_genomic.fna/checkm_result
[2023-06-17 10:14:57,832] [INFO] Task succeeded: CheckM
[2023-06-17 10:14:57,834] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.57%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 10:14:57,860] [INFO] ===== Completeness check finished =====
[2023-06-17 10:14:57,860] [INFO] ===== Start GTDB Search =====
[2023-06-17 10:14:57,860] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028982645.1_ASM2898264v1_genomic.fna/markers.fasta)
[2023-06-17 10:14:57,861] [INFO] Task started: Blastn
[2023-06-17 10:14:57,861] [INFO] Running command: blastn -query GCA_028982645.1_ASM2898264v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc312f4fd-bf99-406b-9b28-6d28d7a1e2b1/dqc_reference/reference_markers_gtdb.fasta -out GCA_028982645.1_ASM2898264v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 10:14:58,657] [INFO] Task succeeded: Blastn
[2023-06-17 10:14:58,661] [INFO] Selected 8 target genomes.
[2023-06-17 10:14:58,661] [INFO] Target genome list was writen to GCA_028982645.1_ASM2898264v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 10:14:58,662] [INFO] Task started: fastANI
[2023-06-17 10:14:58,662] [INFO] Running command: fastANI --query /var/lib/cwl/stg528b60f1-7eac-46f7-8426-82fb09252136/GCA_028982645.1_ASM2898264v1_genomic.fna.gz --refList GCA_028982645.1_ASM2898264v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028982645.1_ASM2898264v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 10:15:14,305] [INFO] Task succeeded: fastANI
[2023-06-17 10:15:14,315] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 10:15:14,316] [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_000014265.1	s__Trichodesmium erythraeum	97.7788	1489	1518	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Trichodesmium	95.0	99.96	99.96	0.99	0.99	2	conclusive
GCA_010672085.1	s__Trichodesmium sp010672085	83.7193	1207	1518	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Trichodesmium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003838195.1	s__Okeania hirsuta	80.4132	999	1518	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Okeania	95.0	98.05	95.33	0.88	0.84	10	-
GCA_010672525.1	s__Okeania sp010672525	80.3219	1046	1518	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Okeania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010672585.1	s__Okeania sp010672585	80.2087	1068	1518	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Okeania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010672455.1	s__Okeania sp010672455	80.2039	1075	1518	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Okeania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014132355.1	s__Okeania sp014132355	80.1293	1027	1518	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Okeania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010692555.1	s__Okeania sp010692555	80.0999	1030	1518	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Okeania	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 10:15:14,318] [INFO] GTDB search result was written to GCA_028982645.1_ASM2898264v1_genomic.fna/result_gtdb.tsv
[2023-06-17 10:15:14,319] [INFO] ===== GTDB Search completed =====
[2023-06-17 10:15:14,322] [INFO] DFAST_QC result json was written to GCA_028982645.1_ASM2898264v1_genomic.fna/dqc_result.json
[2023-06-17 10:15:14,323] [INFO] DFAST_QC completed!
[2023-06-17 10:15:14,323] [INFO] Total running time: 0h1m8s