[2024-01-24 10:57:22,726] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:22,728] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:22,728] [INFO] DQC Reference Directory: /var/lib/cwl/stg0c99cc3a-6322-4a2d-b661-8ccbee93d4c6/dqc_reference
[2024-01-24 10:57:23,985] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:23,986] [INFO] Task started: Prodigal
[2024-01-24 10:57:23,986] [INFO] Running command: gunzip -c /var/lib/cwl/stgc4cb698d-b4e5-4d35-866b-4ab95566f325/GCF_003123745.1_ASM312374v1_genomic.fna.gz | prodigal -d GCF_003123745.1_ASM312374v1_genomic.fna/cds.fna -a GCF_003123745.1_ASM312374v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:32,005] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:32,005] [INFO] Task started: HMMsearch
[2024-01-24 10:57:32,006] [INFO] Running command: hmmsearch --tblout GCF_003123745.1_ASM312374v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0c99cc3a-6322-4a2d-b661-8ccbee93d4c6/dqc_reference/reference_markers.hmm GCF_003123745.1_ASM312374v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:32,293] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:32,294] [INFO] Found 6/6 markers.
[2024-01-24 10:57:32,327] [INFO] Query marker FASTA was written to GCF_003123745.1_ASM312374v1_genomic.fna/markers.fasta
[2024-01-24 10:57:32,328] [INFO] Task started: Blastn
[2024-01-24 10:57:32,328] [INFO] Running command: blastn -query GCF_003123745.1_ASM312374v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c99cc3a-6322-4a2d-b661-8ccbee93d4c6/dqc_reference/reference_markers.fasta -out GCF_003123745.1_ASM312374v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:33,061] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:33,064] [INFO] Selected 23 target genomes.
[2024-01-24 10:57:33,064] [INFO] Target genome list was writen to GCF_003123745.1_ASM312374v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:33,073] [INFO] Task started: fastANI
[2024-01-24 10:57:33,073] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4cb698d-b4e5-4d35-866b-4ab95566f325/GCF_003123745.1_ASM312374v1_genomic.fna.gz --refList GCF_003123745.1_ASM312374v1_genomic.fna/target_genomes.txt --output GCF_003123745.1_ASM312374v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:47,099] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:47,100] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0c99cc3a-6322-4a2d-b661-8ccbee93d4c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:47,100] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0c99cc3a-6322-4a2d-b661-8ccbee93d4c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:47,105] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:57:47,105] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:57:47,106] [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
Ancrocorticia populi	strain=sk1b4	GCA_003123745.1	2175228	2175228	type	True	100.0	878	879	95	conclusive
Changpingibacter yushuensis	strain=JY-X040	GCA_014041995.1	2758440	2758440	type	True	77.3736	79	879	95	below_threshold
Peptidiphaga gingivicola	strain=BA112	GCA_001652275.1	2741497	2741497	type	True	76.5892	59	879	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:47,107] [INFO] DFAST Taxonomy check result was written to GCF_003123745.1_ASM312374v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:47,107] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:47,108] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:47,108] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0c99cc3a-6322-4a2d-b661-8ccbee93d4c6/dqc_reference/checkm_data
[2024-01-24 10:57:47,109] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:47,141] [INFO] Task started: CheckM
[2024-01-24 10:57:47,141] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003123745.1_ASM312374v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003123745.1_ASM312374v1_genomic.fna/checkm_input GCF_003123745.1_ASM312374v1_genomic.fna/checkm_result
[2024-01-24 10:58:15,765] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:15,767] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:15,785] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:15,785] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:15,786] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003123745.1_ASM312374v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:15,786] [INFO] Task started: Blastn
[2024-01-24 10:58:15,786] [INFO] Running command: blastn -query GCF_003123745.1_ASM312374v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c99cc3a-6322-4a2d-b661-8ccbee93d4c6/dqc_reference/reference_markers_gtdb.fasta -out GCF_003123745.1_ASM312374v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:16,840] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:16,844] [INFO] Selected 28 target genomes.
[2024-01-24 10:58:16,844] [INFO] Target genome list was writen to GCF_003123745.1_ASM312374v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:16,883] [INFO] Task started: fastANI
[2024-01-24 10:58:16,883] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4cb698d-b4e5-4d35-866b-4ab95566f325/GCF_003123745.1_ASM312374v1_genomic.fna.gz --refList GCF_003123745.1_ASM312374v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003123745.1_ASM312374v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:34,657] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:34,662] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:58:34,662] [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_003123745.1	s__Ancrocorticia populi	100.0	878	879	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Ancrocorticia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014041995.1	s__Ancrocorticia sp014041995	77.3736	79	879	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Ancrocorticia	95.0	98.59	98.59	0.89	0.89	2	-
GCA_015062745.1	s__Asp313 sp015062745	76.9468	61	879	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Asp313	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:58:34,664] [INFO] GTDB search result was written to GCF_003123745.1_ASM312374v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:34,664] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:34,666] [INFO] DFAST_QC result json was written to GCF_003123745.1_ASM312374v1_genomic.fna/dqc_result.json
[2024-01-24 10:58:34,667] [INFO] DFAST_QC completed!
[2024-01-24 10:58:34,667] [INFO] Total running time: 0h1m12s