[2024-01-24 11:34:42,830] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:42,831] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:42,832] [INFO] DQC Reference Directory: /var/lib/cwl/stg67a66fae-174f-4da2-a067-e001b89a8d03/dqc_reference
[2024-01-24 11:34:44,246] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:44,247] [INFO] Task started: Prodigal
[2024-01-24 11:34:44,247] [INFO] Running command: gunzip -c /var/lib/cwl/stg10632155-34de-46b2-a5d2-d3a20743c043/GCF_015207075.1_ASM1520707v1_genomic.fna.gz | prodigal -d GCF_015207075.1_ASM1520707v1_genomic.fna/cds.fna -a GCF_015207075.1_ASM1520707v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:34:53,189] [INFO] Task succeeded: Prodigal
[2024-01-24 11:34:53,189] [INFO] Task started: HMMsearch
[2024-01-24 11:34:53,189] [INFO] Running command: hmmsearch --tblout GCF_015207075.1_ASM1520707v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg67a66fae-174f-4da2-a067-e001b89a8d03/dqc_reference/reference_markers.hmm GCF_015207075.1_ASM1520707v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:34:53,506] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:34:53,515] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg10632155-34de-46b2-a5d2-d3a20743c043/GCF_015207075.1_ASM1520707v1_genomic.fna.gz]
[2024-01-24 11:34:53,562] [INFO] Query marker FASTA was written to GCF_015207075.1_ASM1520707v1_genomic.fna/markers.fasta
[2024-01-24 11:34:53,563] [INFO] Task started: Blastn
[2024-01-24 11:34:53,563] [INFO] Running command: blastn -query GCF_015207075.1_ASM1520707v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg67a66fae-174f-4da2-a067-e001b89a8d03/dqc_reference/reference_markers.fasta -out GCF_015207075.1_ASM1520707v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:34:54,227] [INFO] Task succeeded: Blastn
[2024-01-24 11:34:54,229] [INFO] Selected 17 target genomes.
[2024-01-24 11:34:54,230] [INFO] Target genome list was writen to GCF_015207075.1_ASM1520707v1_genomic.fna/target_genomes.txt
[2024-01-24 11:34:54,234] [INFO] Task started: fastANI
[2024-01-24 11:34:54,234] [INFO] Running command: fastANI --query /var/lib/cwl/stg10632155-34de-46b2-a5d2-d3a20743c043/GCF_015207075.1_ASM1520707v1_genomic.fna.gz --refList GCF_015207075.1_ASM1520707v1_genomic.fna/target_genomes.txt --output GCF_015207075.1_ASM1520707v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:08,560] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:08,560] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg67a66fae-174f-4da2-a067-e001b89a8d03/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:08,560] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg67a66fae-174f-4da2-a067-e001b89a8d03/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:08,564] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:35:08,564] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:35:08,564] [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	76.128	90	1168	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:08,565] [INFO] DFAST Taxonomy check result was written to GCF_015207075.1_ASM1520707v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:08,566] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:08,566] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:08,566] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg67a66fae-174f-4da2-a067-e001b89a8d03/dqc_reference/checkm_data
[2024-01-24 11:35:08,567] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:08,608] [INFO] Task started: CheckM
[2024-01-24 11:35:08,609] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015207075.1_ASM1520707v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015207075.1_ASM1520707v1_genomic.fna/checkm_input GCF_015207075.1_ASM1520707v1_genomic.fna/checkm_result
[2024-01-24 11:35:40,978] [INFO] Task succeeded: CheckM
[2024-01-24 11:35:40,979] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 44.84%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:35:40,995] [INFO] ===== Completeness check finished =====
[2024-01-24 11:35:40,995] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:35:40,996] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015207075.1_ASM1520707v1_genomic.fna/markers.fasta)
[2024-01-24 11:35:40,996] [INFO] Task started: Blastn
[2024-01-24 11:35:40,996] [INFO] Running command: blastn -query GCF_015207075.1_ASM1520707v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg67a66fae-174f-4da2-a067-e001b89a8d03/dqc_reference/reference_markers_gtdb.fasta -out GCF_015207075.1_ASM1520707v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:41,973] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:41,979] [INFO] Selected 20 target genomes.
[2024-01-24 11:35:41,980] [INFO] Target genome list was writen to GCF_015207075.1_ASM1520707v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:35:42,016] [INFO] Task started: fastANI
[2024-01-24 11:35:42,016] [INFO] Running command: fastANI --query /var/lib/cwl/stg10632155-34de-46b2-a5d2-d3a20743c043/GCF_015207075.1_ASM1520707v1_genomic.fna.gz --refList GCF_015207075.1_ASM1520707v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015207075.1_ASM1520707v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:35:59,546] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:59,556] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:35:59,556] [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
GCA_015207075.1	s__LEGE-11467 sp015207075	100.0	1145	1168	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Geitlerinemaceae;g__LEGE-11467	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_015295945.1	s__DVED01 sp003695795	76.6394	179	1168	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Geitlerinemaceae;g__DVED01	95.0	99.89	99.88	0.96	0.93	3	-
GCF_000332355.1	s__Geitlerinema sp000332355	76.128	90	1168	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Geitlerinemaceae;g__Geitlerinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012911965.1	s__Phormidium_A sp007126595	76.0611	52	1168	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Geitlerinemaceae;g__Phormidium_A	95.0	99.08	98.97	0.85	0.76	4	-
GCF_014696265.1	s__FACHB-1375 sp014696265	75.5843	55	1168	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Phormidiaceae_A;g__FACHB-1375	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:35:59,558] [INFO] GTDB search result was written to GCF_015207075.1_ASM1520707v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:35:59,559] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:35:59,561] [INFO] DFAST_QC result json was written to GCF_015207075.1_ASM1520707v1_genomic.fna/dqc_result.json
[2024-01-24 11:35:59,562] [INFO] DFAST_QC completed!
[2024-01-24 11:35:59,562] [INFO] Total running time: 0h1m17s