[2023-06-19 07:30:04,375] [INFO] DFAST_QC pipeline started.
[2023-06-19 07:30:04,376] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 07:30:04,377] [INFO] DQC Reference Directory: /var/lib/cwl/stg96b6da59-62c6-4366-ba11-159b06f8beb3/dqc_reference
[2023-06-19 07:30:05,673] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 07:30:05,674] [INFO] Task started: Prodigal
[2023-06-19 07:30:05,674] [INFO] Running command: gunzip -c /var/lib/cwl/stg4333afb6-ebad-4804-9954-f6e9eab8fecb/GCA_014381295.1_ASM1438129v1_genomic.fna.gz | prodigal -d GCA_014381295.1_ASM1438129v1_genomic.fna/cds.fna -a GCA_014381295.1_ASM1438129v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 07:30:16,078] [INFO] Task succeeded: Prodigal
[2023-06-19 07:30:16,078] [INFO] Task started: HMMsearch
[2023-06-19 07:30:16,079] [INFO] Running command: hmmsearch --tblout GCA_014381295.1_ASM1438129v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg96b6da59-62c6-4366-ba11-159b06f8beb3/dqc_reference/reference_markers.hmm GCA_014381295.1_ASM1438129v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 07:30:16,286] [INFO] Task succeeded: HMMsearch
[2023-06-19 07:30:16,288] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4333afb6-ebad-4804-9954-f6e9eab8fecb/GCA_014381295.1_ASM1438129v1_genomic.fna.gz]
[2023-06-19 07:30:16,311] [INFO] Query marker FASTA was written to GCA_014381295.1_ASM1438129v1_genomic.fna/markers.fasta
[2023-06-19 07:30:16,312] [INFO] Task started: Blastn
[2023-06-19 07:30:16,312] [INFO] Running command: blastn -query GCA_014381295.1_ASM1438129v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg96b6da59-62c6-4366-ba11-159b06f8beb3/dqc_reference/reference_markers.fasta -out GCA_014381295.1_ASM1438129v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 07:30:16,918] [INFO] Task succeeded: Blastn
[2023-06-19 07:30:16,941] [INFO] Selected 24 target genomes.
[2023-06-19 07:30:16,942] [INFO] Target genome list was writen to GCA_014381295.1_ASM1438129v1_genomic.fna/target_genomes.txt
[2023-06-19 07:30:16,946] [INFO] Task started: fastANI
[2023-06-19 07:30:16,947] [INFO] Running command: fastANI --query /var/lib/cwl/stg4333afb6-ebad-4804-9954-f6e9eab8fecb/GCA_014381295.1_ASM1438129v1_genomic.fna.gz --refList GCA_014381295.1_ASM1438129v1_genomic.fna/target_genomes.txt --output GCA_014381295.1_ASM1438129v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 07:30:32,353] [INFO] Task succeeded: fastANI
[2023-06-19 07:30:32,354] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg96b6da59-62c6-4366-ba11-159b06f8beb3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 07:30:32,354] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg96b6da59-62c6-4366-ba11-159b06f8beb3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 07:30:32,358] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 07:30:32,359] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 07:30:32,359] [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
Parasynechococcus marenigrum	strain=WH 8102	GCA_000195975.1	2881428	2881428	type	True	77.1724	104	501	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 07:30:32,361] [INFO] DFAST Taxonomy check result was written to GCA_014381295.1_ASM1438129v1_genomic.fna/tc_result.tsv
[2023-06-19 07:30:32,361] [INFO] ===== Taxonomy check completed =====
[2023-06-19 07:30:32,362] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 07:30:32,362] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg96b6da59-62c6-4366-ba11-159b06f8beb3/dqc_reference/checkm_data
[2023-06-19 07:30:32,363] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 07:30:32,391] [INFO] Task started: CheckM
[2023-06-19 07:30:32,392] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_014381295.1_ASM1438129v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_014381295.1_ASM1438129v1_genomic.fna/checkm_input GCA_014381295.1_ASM1438129v1_genomic.fna/checkm_result
[2023-06-19 07:31:08,238] [INFO] Task succeeded: CheckM
[2023-06-19 07:31:08,240] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 07:31:08,262] [INFO] ===== Completeness check finished =====
[2023-06-19 07:31:08,262] [INFO] ===== Start GTDB Search =====
[2023-06-19 07:31:08,262] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_014381295.1_ASM1438129v1_genomic.fna/markers.fasta)
[2023-06-19 07:31:08,263] [INFO] Task started: Blastn
[2023-06-19 07:31:08,263] [INFO] Running command: blastn -query GCA_014381295.1_ASM1438129v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg96b6da59-62c6-4366-ba11-159b06f8beb3/dqc_reference/reference_markers_gtdb.fasta -out GCA_014381295.1_ASM1438129v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 07:31:08,989] [INFO] Task succeeded: Blastn
[2023-06-19 07:31:08,994] [INFO] Selected 6 target genomes.
[2023-06-19 07:31:08,994] [INFO] Target genome list was writen to GCA_014381295.1_ASM1438129v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 07:31:08,998] [INFO] Task started: fastANI
[2023-06-19 07:31:08,998] [INFO] Running command: fastANI --query /var/lib/cwl/stg4333afb6-ebad-4804-9954-f6e9eab8fecb/GCA_014381295.1_ASM1438129v1_genomic.fna.gz --refList GCA_014381295.1_ASM1438129v1_genomic.fna/target_genomes_gtdb.txt --output GCA_014381295.1_ASM1438129v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 07:31:11,915] [INFO] Task succeeded: fastANI
[2023-06-19 07:31:11,922] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 07:31:11,923] [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_014279775.1	s__Synechococcus_C sp002500205	98.7825	479	501	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	99.03	97.76	0.95	0.86	9	conclusive
GCF_014279835.1	s__Synechococcus_C sp014279835	91.6304	485	501	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	96.93	96.36	0.92	0.87	4	-
GCF_000014585.1	s__Synechococcus_C sp000014585	88.8002	467	501	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001040845.1	s__Synechococcus_C sp001040845	88.5464	469	501	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003210315.1	s__Synechococcus_C sp003210315	88.2176	292	501	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	96.13	96.13	0.52	0.52	2	-
GCF_000230675.1	s__Synechococcus_C sp000230675	88.1903	473	501	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	96.29	95.09	0.90	0.84	8	-
--------------------------------------------------------------------------------
[2023-06-19 07:31:11,925] [INFO] GTDB search result was written to GCA_014381295.1_ASM1438129v1_genomic.fna/result_gtdb.tsv
[2023-06-19 07:31:11,925] [INFO] ===== GTDB Search completed =====
[2023-06-19 07:31:11,928] [INFO] DFAST_QC result json was written to GCA_014381295.1_ASM1438129v1_genomic.fna/dqc_result.json
[2023-06-19 07:31:11,928] [INFO] DFAST_QC completed!
[2023-06-19 07:31:11,928] [INFO] Total running time: 0h1m8s