[2024-01-24 14:14:20,614] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:20,615] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:20,616] [INFO] DQC Reference Directory: /var/lib/cwl/stg7b2a3a61-f8ce-4af5-a5c3-6b50c7905f6a/dqc_reference
[2024-01-24 14:14:21,871] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:21,872] [INFO] Task started: Prodigal
[2024-01-24 14:14:21,873] [INFO] Running command: gunzip -c /var/lib/cwl/stg828b5766-e7c7-4b12-8328-a61c682362f5/GCF_007747995.1_ASM774799v1_genomic.fna.gz | prodigal -d GCF_007747995.1_ASM774799v1_genomic.fna/cds.fna -a GCF_007747995.1_ASM774799v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:52,267] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:52,267] [INFO] Task started: HMMsearch
[2024-01-24 14:14:52,268] [INFO] Running command: hmmsearch --tblout GCF_007747995.1_ASM774799v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7b2a3a61-f8ce-4af5-a5c3-6b50c7905f6a/dqc_reference/reference_markers.hmm GCF_007747995.1_ASM774799v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:52,591] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:52,592] [INFO] Found 6/6 markers.
[2024-01-24 14:14:52,648] [INFO] Query marker FASTA was written to GCF_007747995.1_ASM774799v1_genomic.fna/markers.fasta
[2024-01-24 14:14:52,648] [INFO] Task started: Blastn
[2024-01-24 14:14:52,648] [INFO] Running command: blastn -query GCF_007747995.1_ASM774799v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b2a3a61-f8ce-4af5-a5c3-6b50c7905f6a/dqc_reference/reference_markers.fasta -out GCF_007747995.1_ASM774799v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:53,259] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:53,263] [INFO] Selected 18 target genomes.
[2024-01-24 14:14:53,263] [INFO] Target genome list was writen to GCF_007747995.1_ASM774799v1_genomic.fna/target_genomes.txt
[2024-01-24 14:14:53,273] [INFO] Task started: fastANI
[2024-01-24 14:14:53,274] [INFO] Running command: fastANI --query /var/lib/cwl/stg828b5766-e7c7-4b12-8328-a61c682362f5/GCF_007747995.1_ASM774799v1_genomic.fna.gz --refList GCF_007747995.1_ASM774799v1_genomic.fna/target_genomes.txt --output GCF_007747995.1_ASM774799v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:09,979] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:09,979] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7b2a3a61-f8ce-4af5-a5c3-6b50c7905f6a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:09,979] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7b2a3a61-f8ce-4af5-a5c3-6b50c7905f6a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:09,983] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:15:09,983] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:15:09,983] [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
Symmachiella dynata	strain=Mal52	GCA_007747995.1	2527995	2527995	type	True	100.0	2587	2589	95	conclusive
Symmachiella macrocystis	strain=CA54	GCA_007860075.1	2527985	2527985	type	True	90.9966	2181	2589	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:09,985] [INFO] DFAST Taxonomy check result was written to GCF_007747995.1_ASM774799v1_genomic.fna/tc_result.tsv
[2024-01-24 14:15:09,986] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:09,986] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:09,986] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7b2a3a61-f8ce-4af5-a5c3-6b50c7905f6a/dqc_reference/checkm_data
[2024-01-24 14:15:09,987] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:10,055] [INFO] Task started: CheckM
[2024-01-24 14:15:10,055] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007747995.1_ASM774799v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007747995.1_ASM774799v1_genomic.fna/checkm_input GCF_007747995.1_ASM774799v1_genomic.fna/checkm_result
[2024-01-24 14:16:35,503] [INFO] Task succeeded: CheckM
[2024-01-24 14:16:35,504] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:16:35,520] [INFO] ===== Completeness check finished =====
[2024-01-24 14:16:35,520] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:16:35,521] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007747995.1_ASM774799v1_genomic.fna/markers.fasta)
[2024-01-24 14:16:35,521] [INFO] Task started: Blastn
[2024-01-24 14:16:35,521] [INFO] Running command: blastn -query GCF_007747995.1_ASM774799v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b2a3a61-f8ce-4af5-a5c3-6b50c7905f6a/dqc_reference/reference_markers_gtdb.fasta -out GCF_007747995.1_ASM774799v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:16:36,347] [INFO] Task succeeded: Blastn
[2024-01-24 14:16:36,350] [INFO] Selected 24 target genomes.
[2024-01-24 14:16:36,350] [INFO] Target genome list was writen to GCF_007747995.1_ASM774799v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:16:36,368] [INFO] Task started: fastANI
[2024-01-24 14:16:36,368] [INFO] Running command: fastANI --query /var/lib/cwl/stg828b5766-e7c7-4b12-8328-a61c682362f5/GCF_007747995.1_ASM774799v1_genomic.fna.gz --refList GCF_007747995.1_ASM774799v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007747995.1_ASM774799v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:17:02,919] [INFO] Task succeeded: fastANI
[2024-01-24 14:17:02,927] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:17:02,927] [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_007747995.1	s__Symmachiella dynata	100.0	2588	2589	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Mal52;g__Symmachiella	95.0	96.81	96.81	0.94	0.94	2	conclusive
GCF_007860075.1	s__Symmachiella macrocystis	90.9966	2181	2589	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Mal52;g__Symmachiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002724315.1	s__UBA8437 sp002724315	75.6629	50	2589	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__UBA8437	95.0	97.85	97.85	0.87	0.87	2	-
GCF_000255655.1	s__Schlesneria paludicola	75.616	50	2589	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Schlesneria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007694185.1	s__UBA6163 sp007694185	75.4442	50	2589	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__UBA6163	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005798445.1	s__SXKJ01 sp005798445	75.1285	59	2589	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__SXKJ01	95.0	99.80	99.80	0.90	0.90	2	-
GCA_016124895.1	s__JABMPE01 sp016124895	75.0301	50	2589	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JABMPE01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:17:02,929] [INFO] GTDB search result was written to GCF_007747995.1_ASM774799v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:17:02,929] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:17:02,932] [INFO] DFAST_QC result json was written to GCF_007747995.1_ASM774799v1_genomic.fna/dqc_result.json
[2024-01-24 14:17:02,932] [INFO] DFAST_QC completed!
[2024-01-24 14:17:02,932] [INFO] Total running time: 0h2m42s