[2023-06-19 09:52:15,119] [INFO] DFAST_QC pipeline started.
[2023-06-19 09:52:15,123] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 09:52:15,123] [INFO] DQC Reference Directory: /var/lib/cwl/stg12fec16e-6d3e-4466-83c1-92abe925f22a/dqc_reference
[2023-06-19 09:52:16,580] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 09:52:16,581] [INFO] Task started: Prodigal
[2023-06-19 09:52:16,581] [INFO] Running command: gunzip -c /var/lib/cwl/stg6c72110c-fa96-4656-a7b7-a3cf1ac7958e/GCA_029262415.1_ASM2926241v1_genomic.fna.gz | prodigal -d GCA_029262415.1_ASM2926241v1_genomic.fna/cds.fna -a GCA_029262415.1_ASM2926241v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 09:52:28,218] [INFO] Task succeeded: Prodigal
[2023-06-19 09:52:28,218] [INFO] Task started: HMMsearch
[2023-06-19 09:52:28,218] [INFO] Running command: hmmsearch --tblout GCA_029262415.1_ASM2926241v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg12fec16e-6d3e-4466-83c1-92abe925f22a/dqc_reference/reference_markers.hmm GCA_029262415.1_ASM2926241v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 09:52:28,541] [INFO] Task succeeded: HMMsearch
[2023-06-19 09:52:28,542] [INFO] Found 6/6 markers.
[2023-06-19 09:52:28,579] [INFO] Query marker FASTA was written to GCA_029262415.1_ASM2926241v1_genomic.fna/markers.fasta
[2023-06-19 09:52:28,580] [INFO] Task started: Blastn
[2023-06-19 09:52:28,580] [INFO] Running command: blastn -query GCA_029262415.1_ASM2926241v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg12fec16e-6d3e-4466-83c1-92abe925f22a/dqc_reference/reference_markers.fasta -out GCA_029262415.1_ASM2926241v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 09:52:29,322] [INFO] Task succeeded: Blastn
[2023-06-19 09:52:29,327] [INFO] Selected 25 target genomes.
[2023-06-19 09:52:29,328] [INFO] Target genome list was writen to GCA_029262415.1_ASM2926241v1_genomic.fna/target_genomes.txt
[2023-06-19 09:52:29,332] [INFO] Task started: fastANI
[2023-06-19 09:52:29,332] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c72110c-fa96-4656-a7b7-a3cf1ac7958e/GCA_029262415.1_ASM2926241v1_genomic.fna.gz --refList GCA_029262415.1_ASM2926241v1_genomic.fna/target_genomes.txt --output GCA_029262415.1_ASM2926241v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 09:52:48,797] [INFO] Task succeeded: fastANI
[2023-06-19 09:52:48,798] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg12fec16e-6d3e-4466-83c1-92abe925f22a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 09:52:48,798] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg12fec16e-6d3e-4466-83c1-92abe925f22a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 09:52:48,803] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 09:52:48,803] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 09:52:48,803] [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
Polyangium fumosum	strain=DSM 14668	GCA_005144585.1	889272	889272	neotype	True	74.8873	60	1265	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 09:52:48,805] [INFO] DFAST Taxonomy check result was written to GCA_029262415.1_ASM2926241v1_genomic.fna/tc_result.tsv
[2023-06-19 09:52:48,806] [INFO] ===== Taxonomy check completed =====
[2023-06-19 09:52:48,806] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 09:52:48,807] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg12fec16e-6d3e-4466-83c1-92abe925f22a/dqc_reference/checkm_data
[2023-06-19 09:52:48,809] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 09:52:48,854] [INFO] Task started: CheckM
[2023-06-19 09:52:48,855] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_029262415.1_ASM2926241v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_029262415.1_ASM2926241v1_genomic.fna/checkm_input GCA_029262415.1_ASM2926241v1_genomic.fna/checkm_result
[2023-06-19 09:53:24,940] [INFO] Task succeeded: CheckM
[2023-06-19 09:53:24,941] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 09:53:24,970] [INFO] ===== Completeness check finished =====
[2023-06-19 09:53:24,970] [INFO] ===== Start GTDB Search =====
[2023-06-19 09:53:24,971] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_029262415.1_ASM2926241v1_genomic.fna/markers.fasta)
[2023-06-19 09:53:24,971] [INFO] Task started: Blastn
[2023-06-19 09:53:24,972] [INFO] Running command: blastn -query GCA_029262415.1_ASM2926241v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg12fec16e-6d3e-4466-83c1-92abe925f22a/dqc_reference/reference_markers_gtdb.fasta -out GCA_029262415.1_ASM2926241v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 09:53:25,975] [INFO] Task succeeded: Blastn
[2023-06-19 09:53:25,983] [INFO] Selected 25 target genomes.
[2023-06-19 09:53:25,984] [INFO] Target genome list was writen to GCA_029262415.1_ASM2926241v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 09:53:26,027] [INFO] Task started: fastANI
[2023-06-19 09:53:26,027] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c72110c-fa96-4656-a7b7-a3cf1ac7958e/GCA_029262415.1_ASM2926241v1_genomic.fna.gz --refList GCA_029262415.1_ASM2926241v1_genomic.fna/target_genomes_gtdb.txt --output GCA_029262415.1_ASM2926241v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 09:53:44,085] [INFO] Task succeeded: fastANI
[2023-06-19 09:53:44,093] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-19 09:53:44,094] [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_903893315.1	s__CAITLU01 sp903893315	75.9208	62	1265	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__UBA1149;f__UBA1149;g__CAITLU01	95.0	99.96	99.95	0.98	0.97	4	-
GCA_016874715.1	s__VGTK01 sp016874715	75.2976	69	1265	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__UBA12015;f__UBA12015;g__VGTK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016874795.1	s__VGTG01 sp016874795	75.1124	51	1265	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__UBA12015;f__UBA12015;g__VGTG01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 09:53:44,096] [INFO] GTDB search result was written to GCA_029262415.1_ASM2926241v1_genomic.fna/result_gtdb.tsv
[2023-06-19 09:53:44,096] [INFO] ===== GTDB Search completed =====
[2023-06-19 09:53:44,099] [INFO] DFAST_QC result json was written to GCA_029262415.1_ASM2926241v1_genomic.fna/dqc_result.json
[2023-06-19 09:53:44,099] [INFO] DFAST_QC completed!
[2023-06-19 09:53:44,099] [INFO] Total running time: 0h1m29s