[2024-01-24 13:21:10,910] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:21:10,915] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:21:10,915] [INFO] DQC Reference Directory: /var/lib/cwl/stg0cbf1fee-42f8-405c-87ad-26cfb3adb2ad/dqc_reference
[2024-01-24 13:21:12,318] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:21:12,319] [INFO] Task started: Prodigal
[2024-01-24 13:21:12,320] [INFO] Running command: gunzip -c /var/lib/cwl/stgdd220e28-05fb-4605-ba45-5ab1de90a072/GCF_007860075.1_ASM786007v1_genomic.fna.gz | prodigal -d GCF_007860075.1_ASM786007v1_genomic.fna/cds.fna -a GCF_007860075.1_ASM786007v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:21:39,334] [INFO] Task succeeded: Prodigal
[2024-01-24 13:21:39,335] [INFO] Task started: HMMsearch
[2024-01-24 13:21:39,335] [INFO] Running command: hmmsearch --tblout GCF_007860075.1_ASM786007v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0cbf1fee-42f8-405c-87ad-26cfb3adb2ad/dqc_reference/reference_markers.hmm GCF_007860075.1_ASM786007v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:21:39,696] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:21:39,697] [INFO] Found 6/6 markers.
[2024-01-24 13:21:39,759] [INFO] Query marker FASTA was written to GCF_007860075.1_ASM786007v1_genomic.fna/markers.fasta
[2024-01-24 13:21:39,760] [INFO] Task started: Blastn
[2024-01-24 13:21:39,760] [INFO] Running command: blastn -query GCF_007860075.1_ASM786007v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0cbf1fee-42f8-405c-87ad-26cfb3adb2ad/dqc_reference/reference_markers.fasta -out GCF_007860075.1_ASM786007v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:21:40,378] [INFO] Task succeeded: Blastn
[2024-01-24 13:21:40,383] [INFO] Selected 16 target genomes.
[2024-01-24 13:21:40,384] [INFO] Target genome list was writen to GCF_007860075.1_ASM786007v1_genomic.fna/target_genomes.txt
[2024-01-24 13:21:40,396] [INFO] Task started: fastANI
[2024-01-24 13:21:40,397] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd220e28-05fb-4605-ba45-5ab1de90a072/GCF_007860075.1_ASM786007v1_genomic.fna.gz --refList GCF_007860075.1_ASM786007v1_genomic.fna/target_genomes.txt --output GCF_007860075.1_ASM786007v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:21:57,225] [INFO] Task succeeded: fastANI
[2024-01-24 13:21:57,226] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0cbf1fee-42f8-405c-87ad-26cfb3adb2ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:21:57,227] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0cbf1fee-42f8-405c-87ad-26cfb3adb2ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:21:57,234] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:21:57,235] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:21:57,235] [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 macrocystis	strain=CA54	GCA_007860075.1	2527985	2527985	type	True	100.0	2520	2521	95	conclusive
Symmachiella dynata	strain=Mal52	GCA_007747995.1	2527995	2527995	type	True	90.998	2175	2521	95	below_threshold
Caulifigura coniformis	strain=Pan44	GCA_007745175.1	2527983	2527983	type	True	75.6348	52	2521	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:21:57,239] [INFO] DFAST Taxonomy check result was written to GCF_007860075.1_ASM786007v1_genomic.fna/tc_result.tsv
[2024-01-24 13:21:57,240] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:21:57,241] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:21:57,241] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0cbf1fee-42f8-405c-87ad-26cfb3adb2ad/dqc_reference/checkm_data
[2024-01-24 13:21:57,243] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:21:57,332] [INFO] Task started: CheckM
[2024-01-24 13:21:57,332] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007860075.1_ASM786007v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007860075.1_ASM786007v1_genomic.fna/checkm_input GCF_007860075.1_ASM786007v1_genomic.fna/checkm_result
[2024-01-24 13:23:12,680] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:12,682] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:12,702] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:12,702] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:12,703] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007860075.1_ASM786007v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:12,703] [INFO] Task started: Blastn
[2024-01-24 13:23:12,703] [INFO] Running command: blastn -query GCF_007860075.1_ASM786007v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0cbf1fee-42f8-405c-87ad-26cfb3adb2ad/dqc_reference/reference_markers_gtdb.fasta -out GCF_007860075.1_ASM786007v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:13,639] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:13,643] [INFO] Selected 24 target genomes.
[2024-01-24 13:23:13,644] [INFO] Target genome list was writen to GCF_007860075.1_ASM786007v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:13,748] [INFO] Task started: fastANI
[2024-01-24 13:23:13,748] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd220e28-05fb-4605-ba45-5ab1de90a072/GCF_007860075.1_ASM786007v1_genomic.fna.gz --refList GCF_007860075.1_ASM786007v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007860075.1_ASM786007v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:38,957] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:38,966] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:38,967] [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_007860075.1	s__Symmachiella macrocystis	100.0	2520	2521	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Mal52;g__Symmachiella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007747995.1	s__Symmachiella dynata	90.9905	2176	2521	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Mal52;g__Symmachiella	95.0	96.81	96.81	0.94	0.94	2	-
GCF_001610835.1	s__Planctomyces_A sp001610835	75.7861	50	2521	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Planctomyces_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009691905.1	s__SIAF01 sp009691905	75.7058	64	2521	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__UBA10511;g__SIAF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007745175.1	s__Caulifigura coniformis	75.6348	52	2521	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Caulifigura	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:38,968] [INFO] GTDB search result was written to GCF_007860075.1_ASM786007v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:38,969] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:38,971] [INFO] DFAST_QC result json was written to GCF_007860075.1_ASM786007v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:38,971] [INFO] DFAST_QC completed!
[2024-01-24 13:23:38,971] [INFO] Total running time: 0h2m28s