[2024-01-25 19:13:05,698] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:13:05,702] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:13:05,702] [INFO] DQC Reference Directory: /var/lib/cwl/stgafa6a6fd-d85f-4752-9e62-7f091b17a386/dqc_reference
[2024-01-25 19:13:06,878] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:13:06,879] [INFO] Task started: Prodigal
[2024-01-25 19:13:06,880] [INFO] Running command: gunzip -c /var/lib/cwl/stg9ad8bc43-c2aa-45c0-9e29-54116c8461b0/GCF_014982745.1_ASM1498274v1_genomic.fna.gz | prodigal -d GCF_014982745.1_ASM1498274v1_genomic.fna/cds.fna -a GCF_014982745.1_ASM1498274v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:13:10,116] [INFO] Task succeeded: Prodigal
[2024-01-25 19:13:10,116] [INFO] Task started: HMMsearch
[2024-01-25 19:13:10,116] [INFO] Running command: hmmsearch --tblout GCF_014982745.1_ASM1498274v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgafa6a6fd-d85f-4752-9e62-7f091b17a386/dqc_reference/reference_markers.hmm GCF_014982745.1_ASM1498274v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:13:10,325] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:13:10,328] [INFO] Found 6/6 markers.
[2024-01-25 19:13:10,346] [INFO] Query marker FASTA was written to GCF_014982745.1_ASM1498274v1_genomic.fna/markers.fasta
[2024-01-25 19:13:10,346] [INFO] Task started: Blastn
[2024-01-25 19:13:10,346] [INFO] Running command: blastn -query GCF_014982745.1_ASM1498274v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgafa6a6fd-d85f-4752-9e62-7f091b17a386/dqc_reference/reference_markers.fasta -out GCF_014982745.1_ASM1498274v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:13:10,878] [INFO] Task succeeded: Blastn
[2024-01-25 19:13:10,882] [INFO] Selected 17 target genomes.
[2024-01-25 19:13:10,883] [INFO] Target genome list was writen to GCF_014982745.1_ASM1498274v1_genomic.fna/target_genomes.txt
[2024-01-25 19:13:10,897] [INFO] Task started: fastANI
[2024-01-25 19:13:10,898] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ad8bc43-c2aa-45c0-9e29-54116c8461b0/GCF_014982745.1_ASM1498274v1_genomic.fna.gz --refList GCF_014982745.1_ASM1498274v1_genomic.fna/target_genomes.txt --output GCF_014982745.1_ASM1498274v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:13:18,055] [INFO] Task succeeded: fastANI
[2024-01-25 19:13:18,055] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgafa6a6fd-d85f-4752-9e62-7f091b17a386/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:13:18,055] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgafa6a6fd-d85f-4752-9e62-7f091b17a386/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:13:18,058] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:13:18,059] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:13:18,059] [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
Gallibacter intestinalis	strain=DSM 108706	GCA_014982745.1	2779356	2779356	type	True	100.0	522	523	95	conclusive
--------------------------------------------------------------------------------
[2024-01-25 19:13:18,061] [INFO] DFAST Taxonomy check result was written to GCF_014982745.1_ASM1498274v1_genomic.fna/tc_result.tsv
[2024-01-25 19:13:18,061] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:13:18,061] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:13:18,061] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgafa6a6fd-d85f-4752-9e62-7f091b17a386/dqc_reference/checkm_data
[2024-01-25 19:13:18,062] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:13:18,080] [INFO] Task started: CheckM
[2024-01-25 19:13:18,081] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014982745.1_ASM1498274v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014982745.1_ASM1498274v1_genomic.fna/checkm_input GCF_014982745.1_ASM1498274v1_genomic.fna/checkm_result
[2024-01-25 19:13:34,223] [INFO] Task succeeded: CheckM
[2024-01-25 19:13:34,224] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:13:34,260] [INFO] ===== Completeness check finished =====
[2024-01-25 19:13:34,261] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:13:34,261] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014982745.1_ASM1498274v1_genomic.fna/markers.fasta)
[2024-01-25 19:13:34,261] [INFO] Task started: Blastn
[2024-01-25 19:13:34,261] [INFO] Running command: blastn -query GCF_014982745.1_ASM1498274v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgafa6a6fd-d85f-4752-9e62-7f091b17a386/dqc_reference/reference_markers_gtdb.fasta -out GCF_014982745.1_ASM1498274v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:13:35,038] [INFO] Task succeeded: Blastn
[2024-01-25 19:13:35,044] [INFO] Selected 21 target genomes.
[2024-01-25 19:13:35,044] [INFO] Target genome list was writen to GCF_014982745.1_ASM1498274v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:13:35,086] [INFO] Task started: fastANI
[2024-01-25 19:13:35,086] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ad8bc43-c2aa-45c0-9e29-54116c8461b0/GCF_014982745.1_ASM1498274v1_genomic.fna.gz --refList GCF_014982745.1_ASM1498274v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014982745.1_ASM1498274v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:13:42,313] [INFO] Task succeeded: fastANI
[2024-01-25 19:13:42,315] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:13:42,315] [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_014982745.1	s__Eubacterium_M pullicola	100.0	522	523	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__Eubacterium_M	95.0	96.83	96.11	0.88	0.87	4	conclusive
--------------------------------------------------------------------------------
[2024-01-25 19:13:42,319] [INFO] GTDB search result was written to GCF_014982745.1_ASM1498274v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:13:42,319] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:13:42,321] [INFO] DFAST_QC result json was written to GCF_014982745.1_ASM1498274v1_genomic.fna/dqc_result.json
[2024-01-25 19:13:42,321] [INFO] DFAST_QC completed!
[2024-01-25 19:13:42,321] [INFO] Total running time: 0h0m37s