[2024-01-24 13:32:34,799] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:34,801] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:34,801] [INFO] DQC Reference Directory: /var/lib/cwl/stgc4815d40-03d4-4146-8217-1eef346e78db/dqc_reference
[2024-01-24 13:32:36,318] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:36,319] [INFO] Task started: Prodigal
[2024-01-24 13:32:36,319] [INFO] Running command: gunzip -c /var/lib/cwl/stg4a440092-3b2b-4e62-9308-d1444ef34897/GCF_000017945.1_ASM1794v1_genomic.fna.gz | prodigal -d GCF_000017945.1_ASM1794v1_genomic.fna/cds.fna -a GCF_000017945.1_ASM1794v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:43,912] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:43,913] [INFO] Task started: HMMsearch
[2024-01-24 13:32:43,913] [INFO] Running command: hmmsearch --tblout GCF_000017945.1_ASM1794v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc4815d40-03d4-4146-8217-1eef346e78db/dqc_reference/reference_markers.hmm GCF_000017945.1_ASM1794v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:44,162] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:44,163] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg4a440092-3b2b-4e62-9308-d1444ef34897/GCF_000017945.1_ASM1794v1_genomic.fna.gz]
[2024-01-24 13:32:44,187] [INFO] Query marker FASTA was written to GCF_000017945.1_ASM1794v1_genomic.fna/markers.fasta
[2024-01-24 13:32:44,187] [INFO] Task started: Blastn
[2024-01-24 13:32:44,188] [INFO] Running command: blastn -query GCF_000017945.1_ASM1794v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc4815d40-03d4-4146-8217-1eef346e78db/dqc_reference/reference_markers.fasta -out GCF_000017945.1_ASM1794v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:44,778] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:44,781] [INFO] Selected 1 target genomes.
[2024-01-24 13:32:44,782] [INFO] Target genome list was writen to GCF_000017945.1_ASM1794v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:44,783] [INFO] Task started: fastANI
[2024-01-24 13:32:44,783] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a440092-3b2b-4e62-9308-d1444ef34897/GCF_000017945.1_ASM1794v1_genomic.fna.gz --refList GCF_000017945.1_ASM1794v1_genomic.fna/target_genomes.txt --output GCF_000017945.1_ASM1794v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:45,330] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:45,331] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc4815d40-03d4-4146-8217-1eef346e78db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:45,331] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc4815d40-03d4-4146-8217-1eef346e78db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:45,334] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:45,334] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:45,334] [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
Ignicoccus hospitalis	strain=KIN4/I	GCA_000017945.1	160233	160233	type	True	100.0	432	432	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:32:45,336] [INFO] DFAST Taxonomy check result was written to GCF_000017945.1_ASM1794v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:45,336] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:45,337] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:45,337] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc4815d40-03d4-4146-8217-1eef346e78db/dqc_reference/checkm_data
[2024-01-24 13:32:45,338] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:45,354] [INFO] Task started: CheckM
[2024-01-24 13:32:45,354] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000017945.1_ASM1794v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000017945.1_ASM1794v1_genomic.fna/checkm_input GCF_000017945.1_ASM1794v1_genomic.fna/checkm_result
[2024-01-24 13:33:12,550] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:12,551] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:12,579] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:12,580] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:12,580] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000017945.1_ASM1794v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:12,580] [INFO] Task started: Blastn
[2024-01-24 13:33:12,580] [INFO] Running command: blastn -query GCF_000017945.1_ASM1794v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc4815d40-03d4-4146-8217-1eef346e78db/dqc_reference/reference_markers_gtdb.fasta -out GCF_000017945.1_ASM1794v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:13,084] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:13,087] [INFO] Selected 5 target genomes.
[2024-01-24 13:33:13,088] [INFO] Target genome list was writen to GCF_000017945.1_ASM1794v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:13,140] [INFO] Task started: fastANI
[2024-01-24 13:33:13,141] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a440092-3b2b-4e62-9308-d1444ef34897/GCF_000017945.1_ASM1794v1_genomic.fna.gz --refList GCF_000017945.1_ASM1794v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000017945.1_ASM1794v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:15,055] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:15,059] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:15,059] [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_000017945.1	s__Ignicoccus_A hospitalis	100.0	432	432	d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Sulfolobales;f__Ignicoccaceae;g__Ignicoccus_A	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCA_013154085.1	s__Ignicoccus_A sp013154085	78.5277	151	432	d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Sulfolobales;f__Ignicoccaceae;g__Ignicoccus_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:15,061] [INFO] GTDB search result was written to GCF_000017945.1_ASM1794v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:15,062] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:15,064] [INFO] DFAST_QC result json was written to GCF_000017945.1_ASM1794v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:15,064] [INFO] DFAST_QC completed!
[2024-01-24 13:33:15,064] [INFO] Total running time: 0h0m40s