[2024-01-24 12:31:33,358] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:33,360] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:33,360] [INFO] DQC Reference Directory: /var/lib/cwl/stg3e49942e-7323-4e07-be8c-cbd47a724b4c/dqc_reference
[2024-01-24 12:31:34,483] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:34,489] [INFO] Task started: Prodigal
[2024-01-24 12:31:34,489] [INFO] Running command: gunzip -c /var/lib/cwl/stgb5aa34df-bdf1-4738-bf73-8863415df3ce/GCF_009846485.1_ASM984648v1_genomic.fna.gz | prodigal -d GCF_009846485.1_ASM984648v1_genomic.fna/cds.fna -a GCF_009846485.1_ASM984648v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:45,276] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:45,276] [INFO] Task started: HMMsearch
[2024-01-24 12:31:45,276] [INFO] Running command: hmmsearch --tblout GCF_009846485.1_ASM984648v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3e49942e-7323-4e07-be8c-cbd47a724b4c/dqc_reference/reference_markers.hmm GCF_009846485.1_ASM984648v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:45,547] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:45,549] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb5aa34df-bdf1-4738-bf73-8863415df3ce/GCF_009846485.1_ASM984648v1_genomic.fna.gz]
[2024-01-24 12:31:45,588] [INFO] Query marker FASTA was written to GCF_009846485.1_ASM984648v1_genomic.fna/markers.fasta
[2024-01-24 12:31:45,589] [INFO] Task started: Blastn
[2024-01-24 12:31:45,589] [INFO] Running command: blastn -query GCF_009846485.1_ASM984648v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e49942e-7323-4e07-be8c-cbd47a724b4c/dqc_reference/reference_markers.fasta -out GCF_009846485.1_ASM984648v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:46,135] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:46,138] [INFO] Selected 21 target genomes.
[2024-01-24 12:31:46,138] [INFO] Target genome list was writen to GCF_009846485.1_ASM984648v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:46,152] [INFO] Task started: fastANI
[2024-01-24 12:31:46,152] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5aa34df-bdf1-4738-bf73-8863415df3ce/GCF_009846485.1_ASM984648v1_genomic.fna.gz --refList GCF_009846485.1_ASM984648v1_genomic.fna/target_genomes.txt --output GCF_009846485.1_ASM984648v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:01,648] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:01,648] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3e49942e-7323-4e07-be8c-cbd47a724b4c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:01,648] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3e49942e-7323-4e07-be8c-cbd47a724b4c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:01,652] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:32:01,652] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:32:01,652] [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
Baaleninema simplex	strain=PCC 7105	GCA_000332355.1	2862350	2862350	type	True	77.4701	260	1622	95	below_threshold
Oscillatoria acuminata	strain=PCC 6304	GCA_000317105.1	118323	118323	type	True	76.2291	134	1622	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:32:01,654] [INFO] DFAST Taxonomy check result was written to GCF_009846485.1_ASM984648v1_genomic.fna/tc_result.tsv
[2024-01-24 12:32:01,654] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:01,654] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:01,654] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3e49942e-7323-4e07-be8c-cbd47a724b4c/dqc_reference/checkm_data
[2024-01-24 12:32:01,655] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:01,702] [INFO] Task started: CheckM
[2024-01-24 12:32:01,702] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009846485.1_ASM984648v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009846485.1_ASM984648v1_genomic.fna/checkm_input GCF_009846485.1_ASM984648v1_genomic.fna/checkm_result
[2024-01-24 12:32:35,763] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:35,764] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:35,780] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:35,780] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:35,780] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009846485.1_ASM984648v1_genomic.fna/markers.fasta)
[2024-01-24 12:32:35,780] [INFO] Task started: Blastn
[2024-01-24 12:32:35,780] [INFO] Running command: blastn -query GCF_009846485.1_ASM984648v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e49942e-7323-4e07-be8c-cbd47a724b4c/dqc_reference/reference_markers_gtdb.fasta -out GCF_009846485.1_ASM984648v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:36,476] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:36,479] [INFO] Selected 6 target genomes.
[2024-01-24 12:32:36,479] [INFO] Target genome list was writen to GCF_009846485.1_ASM984648v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:36,480] [INFO] Task started: fastANI
[2024-01-24 12:32:36,480] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5aa34df-bdf1-4738-bf73-8863415df3ce/GCF_009846485.1_ASM984648v1_genomic.fna.gz --refList GCF_009846485.1_ASM984648v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009846485.1_ASM984648v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:44,269] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:44,275] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:44,275] [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_009846485.1	s__Phormidium_A sp009846485	100.0	1622	1622	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Geitlerinemaceae;g__Phormidium_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_007693465.1	s__Phormidium_A sp007693465	92.4528	928	1622	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Geitlerinemaceae;g__Phormidium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012911965.1	s__Phormidium_A sp007126595	89.3075	1129	1622	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Geitlerinemaceae;g__Phormidium_A	95.0	99.08	98.97	0.85	0.76	4	-
GCA_001314905.1	s__Phormidium_A sp001314905	84.7014	1116	1622	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Geitlerinemaceae;g__Phormidium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004299065.1	s__Phormidium_A sp004299065	84.627	958	1622	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Geitlerinemaceae;g__Phormidium_A	95.0	99.50	99.50	0.89	0.89	2	-
GCF_001637315.1	s__Phormidium_A willei_A	84.3507	1010	1622	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Geitlerinemaceae;g__Phormidium_A	95.0	95.56	95.56	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:44,277] [INFO] GTDB search result was written to GCF_009846485.1_ASM984648v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:44,277] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:44,279] [INFO] DFAST_QC result json was written to GCF_009846485.1_ASM984648v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:44,279] [INFO] DFAST_QC completed!
[2024-01-24 12:32:44,280] [INFO] Total running time: 0h1m11s