[2024-01-24 15:27:21,550] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:27:21,552] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:27:21,552] [INFO] DQC Reference Directory: /var/lib/cwl/stg8369ac0b-e7d0-4ff5-a3f2-1c7c1cd12cbc/dqc_reference
[2024-01-24 15:27:23,024] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:27:23,025] [INFO] Task started: Prodigal
[2024-01-24 15:27:23,026] [INFO] Running command: gunzip -c /var/lib/cwl/stg2e92eb44-cbbc-4e15-80b7-d8bc63670bee/GCF_007744255.1_ASM774425v1_genomic.fna.gz | prodigal -d GCF_007744255.1_ASM774425v1_genomic.fna/cds.fna -a GCF_007744255.1_ASM774425v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:43,924] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:43,925] [INFO] Task started: HMMsearch
[2024-01-24 15:27:43,925] [INFO] Running command: hmmsearch --tblout GCF_007744255.1_ASM774425v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8369ac0b-e7d0-4ff5-a3f2-1c7c1cd12cbc/dqc_reference/reference_markers.hmm GCF_007744255.1_ASM774425v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:44,262] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:44,263] [INFO] Found 6/6 markers.
[2024-01-24 15:27:44,318] [INFO] Query marker FASTA was written to GCF_007744255.1_ASM774425v1_genomic.fna/markers.fasta
[2024-01-24 15:27:44,319] [INFO] Task started: Blastn
[2024-01-24 15:27:44,319] [INFO] Running command: blastn -query GCF_007744255.1_ASM774425v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8369ac0b-e7d0-4ff5-a3f2-1c7c1cd12cbc/dqc_reference/reference_markers.fasta -out GCF_007744255.1_ASM774425v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:44,895] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:44,898] [INFO] Selected 17 target genomes.
[2024-01-24 15:27:44,899] [INFO] Target genome list was writen to GCF_007744255.1_ASM774425v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:44,906] [INFO] Task started: fastANI
[2024-01-24 15:27:44,906] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e92eb44-cbbc-4e15-80b7-d8bc63670bee/GCF_007744255.1_ASM774425v1_genomic.fna.gz --refList GCF_007744255.1_ASM774425v1_genomic.fna/target_genomes.txt --output GCF_007744255.1_ASM774425v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:28:00,225] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:00,226] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8369ac0b-e7d0-4ff5-a3f2-1c7c1cd12cbc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:28:00,227] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8369ac0b-e7d0-4ff5-a3f2-1c7c1cd12cbc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:28:00,235] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:28:00,235] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:28:00,235] [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
Thalassoglobus polymorphus	strain=Mal48	GCA_007744255.1	2527994	2527994	type	True	100.0	2116	2119	95	conclusive
Thalassoglobus neptunius	strain=KOR42	GCA_007859735.1	1938619	1938619	type	True	76.7654	123	2119	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:28:00,237] [INFO] DFAST Taxonomy check result was written to GCF_007744255.1_ASM774425v1_genomic.fna/tc_result.tsv
[2024-01-24 15:28:00,238] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:28:00,238] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:28:00,238] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8369ac0b-e7d0-4ff5-a3f2-1c7c1cd12cbc/dqc_reference/checkm_data
[2024-01-24 15:28:00,240] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:28:00,302] [INFO] Task started: CheckM
[2024-01-24 15:28:00,302] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007744255.1_ASM774425v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007744255.1_ASM774425v1_genomic.fna/checkm_input GCF_007744255.1_ASM774425v1_genomic.fna/checkm_result
[2024-01-24 15:29:02,975] [INFO] Task succeeded: CheckM
[2024-01-24 15:29:02,976] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:29:02,998] [INFO] ===== Completeness check finished =====
[2024-01-24 15:29:02,998] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:29:02,999] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007744255.1_ASM774425v1_genomic.fna/markers.fasta)
[2024-01-24 15:29:03,000] [INFO] Task started: Blastn
[2024-01-24 15:29:03,000] [INFO] Running command: blastn -query GCF_007744255.1_ASM774425v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8369ac0b-e7d0-4ff5-a3f2-1c7c1cd12cbc/dqc_reference/reference_markers_gtdb.fasta -out GCF_007744255.1_ASM774425v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:29:03,769] [INFO] Task succeeded: Blastn
[2024-01-24 15:29:03,773] [INFO] Selected 25 target genomes.
[2024-01-24 15:29:03,773] [INFO] Target genome list was writen to GCF_007744255.1_ASM774425v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:29:03,796] [INFO] Task started: fastANI
[2024-01-24 15:29:03,796] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e92eb44-cbbc-4e15-80b7-d8bc63670bee/GCF_007744255.1_ASM774425v1_genomic.fna.gz --refList GCF_007744255.1_ASM774425v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007744255.1_ASM774425v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:29:26,504] [INFO] Task succeeded: fastANI
[2024-01-24 15:29:26,511] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:29:26,511] [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_007744255.1	s__Thalassoglobus polymorphus	100.0	2113	2119	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Thalassoglobus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007859735.1	s__Thalassoglobus neptunius	76.7654	123	2119	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Thalassoglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018659505.1	s__Thalassoglobus sp018659505	76.7265	140	2119	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Thalassoglobus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:29:26,513] [INFO] GTDB search result was written to GCF_007744255.1_ASM774425v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:29:26,513] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:29:26,515] [INFO] DFAST_QC result json was written to GCF_007744255.1_ASM774425v1_genomic.fna/dqc_result.json
[2024-01-24 15:29:26,516] [INFO] DFAST_QC completed!
[2024-01-24 15:29:26,516] [INFO] Total running time: 0h2m5s