[2023-06-29 12:49:24,600] [INFO] DFAST_QC pipeline started.
[2023-06-29 12:49:24,607] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 12:49:24,608] [INFO] DQC Reference Directory: /var/lib/cwl/stg7b6e4474-2a91-429e-98f4-a548f3f20e3a/dqc_reference
[2023-06-29 12:49:25,861] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 12:49:25,862] [INFO] Task started: Prodigal
[2023-06-29 12:49:25,862] [INFO] Running command: gunzip -c /var/lib/cwl/stge254505e-ee4c-46e7-8718-68e17d2aead8/GCA_021828745.1_ASM2182874v1_genomic.fna.gz | prodigal -d GCA_021828745.1_ASM2182874v1_genomic.fna/cds.fna -a GCA_021828745.1_ASM2182874v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 12:49:29,976] [INFO] Task succeeded: Prodigal
[2023-06-29 12:49:29,976] [INFO] Task started: HMMsearch
[2023-06-29 12:49:29,976] [INFO] Running command: hmmsearch --tblout GCA_021828745.1_ASM2182874v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7b6e4474-2a91-429e-98f4-a548f3f20e3a/dqc_reference/reference_markers.hmm GCA_021828745.1_ASM2182874v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 12:49:30,194] [INFO] Task succeeded: HMMsearch
[2023-06-29 12:49:30,195] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge254505e-ee4c-46e7-8718-68e17d2aead8/GCA_021828745.1_ASM2182874v1_genomic.fna.gz]
[2023-06-29 12:49:30,215] [INFO] Query marker FASTA was written to GCA_021828745.1_ASM2182874v1_genomic.fna/markers.fasta
[2023-06-29 12:49:30,216] [INFO] Task started: Blastn
[2023-06-29 12:49:30,216] [INFO] Running command: blastn -query GCA_021828745.1_ASM2182874v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b6e4474-2a91-429e-98f4-a548f3f20e3a/dqc_reference/reference_markers.fasta -out GCA_021828745.1_ASM2182874v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:49:30,803] [INFO] Task succeeded: Blastn
[2023-06-29 12:49:30,808] [INFO] Selected 21 target genomes.
[2023-06-29 12:49:30,808] [INFO] Target genome list was writen to GCA_021828745.1_ASM2182874v1_genomic.fna/target_genomes.txt
[2023-06-29 12:49:30,813] [INFO] Task started: fastANI
[2023-06-29 12:49:30,813] [INFO] Running command: fastANI --query /var/lib/cwl/stge254505e-ee4c-46e7-8718-68e17d2aead8/GCA_021828745.1_ASM2182874v1_genomic.fna.gz --refList GCA_021828745.1_ASM2182874v1_genomic.fna/target_genomes.txt --output GCA_021828745.1_ASM2182874v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 12:49:43,056] [INFO] Task succeeded: fastANI
[2023-06-29 12:49:43,056] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7b6e4474-2a91-429e-98f4-a548f3f20e3a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 12:49:43,057] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7b6e4474-2a91-429e-98f4-a548f3f20e3a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 12:49:43,063] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 12:49:43,063] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 12:49:43,063] [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
Ferrovum myxofaciens	strain=P3G	GCA_000735045.1	416213	416213	type	True	87.412	314	413	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 12:49:43,066] [INFO] DFAST Taxonomy check result was written to GCA_021828745.1_ASM2182874v1_genomic.fna/tc_result.tsv
[2023-06-29 12:49:43,067] [INFO] ===== Taxonomy check completed =====
[2023-06-29 12:49:43,067] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 12:49:43,067] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7b6e4474-2a91-429e-98f4-a548f3f20e3a/dqc_reference/checkm_data
[2023-06-29 12:49:43,069] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 12:49:43,094] [INFO] Task started: CheckM
[2023-06-29 12:49:43,095] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021828745.1_ASM2182874v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021828745.1_ASM2182874v1_genomic.fna/checkm_input GCA_021828745.1_ASM2182874v1_genomic.fna/checkm_result
[2023-06-29 12:50:02,425] [INFO] Task succeeded: CheckM
[2023-06-29 12:50:02,426] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 12:50:02,450] [INFO] ===== Completeness check finished =====
[2023-06-29 12:50:02,450] [INFO] ===== Start GTDB Search =====
[2023-06-29 12:50:02,451] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021828745.1_ASM2182874v1_genomic.fna/markers.fasta)
[2023-06-29 12:50:02,451] [INFO] Task started: Blastn
[2023-06-29 12:50:02,452] [INFO] Running command: blastn -query GCA_021828745.1_ASM2182874v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b6e4474-2a91-429e-98f4-a548f3f20e3a/dqc_reference/reference_markers_gtdb.fasta -out GCA_021828745.1_ASM2182874v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:50:03,266] [INFO] Task succeeded: Blastn
[2023-06-29 12:50:03,272] [INFO] Selected 21 target genomes.
[2023-06-29 12:50:03,272] [INFO] Target genome list was writen to GCA_021828745.1_ASM2182874v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 12:50:03,284] [INFO] Task started: fastANI
[2023-06-29 12:50:03,284] [INFO] Running command: fastANI --query /var/lib/cwl/stge254505e-ee4c-46e7-8718-68e17d2aead8/GCA_021828745.1_ASM2182874v1_genomic.fna.gz --refList GCA_021828745.1_ASM2182874v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021828745.1_ASM2182874v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 12:50:14,562] [INFO] Task succeeded: fastANI
[2023-06-29 12:50:14,567] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 12:50:14,568] [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_000735045.1	s__Ferrovum myxofaciens	87.412	314	413	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Ferrovaceae;g__Ferrovum	95.0	98.82	98.23	0.87	0.85	7	-
GCA_010435995.1	s__Ferrovum sp010435995	78.6817	90	413	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Ferrovaceae;g__Ferrovum	95.0	99.83	99.83	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2023-06-29 12:50:14,570] [INFO] GTDB search result was written to GCA_021828745.1_ASM2182874v1_genomic.fna/result_gtdb.tsv
[2023-06-29 12:50:14,570] [INFO] ===== GTDB Search completed =====
[2023-06-29 12:50:14,573] [INFO] DFAST_QC result json was written to GCA_021828745.1_ASM2182874v1_genomic.fna/dqc_result.json
[2023-06-29 12:50:14,573] [INFO] DFAST_QC completed!
[2023-06-29 12:50:14,573] [INFO] Total running time: 0h0m50s