[2023-06-28 17:50:17,700] [INFO] DFAST_QC pipeline started.
[2023-06-28 17:50:17,703] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 17:50:17,703] [INFO] DQC Reference Directory: /var/lib/cwl/stgb381b6ee-8928-4a49-bf42-c46e7335eeaf/dqc_reference
[2023-06-28 17:50:18,917] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 17:50:18,918] [INFO] Task started: Prodigal
[2023-06-28 17:50:18,918] [INFO] Running command: gunzip -c /var/lib/cwl/stg4b225f4d-7cc3-471e-b777-66c2e40d718a/GCA_027442155.1_ASM2744215v1_genomic.fna.gz | prodigal -d GCA_027442155.1_ASM2744215v1_genomic.fna/cds.fna -a GCA_027442155.1_ASM2744215v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 17:50:24,932] [INFO] Task succeeded: Prodigal
[2023-06-28 17:50:24,932] [INFO] Task started: HMMsearch
[2023-06-28 17:50:24,932] [INFO] Running command: hmmsearch --tblout GCA_027442155.1_ASM2744215v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb381b6ee-8928-4a49-bf42-c46e7335eeaf/dqc_reference/reference_markers.hmm GCA_027442155.1_ASM2744215v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 17:50:25,184] [INFO] Task succeeded: HMMsearch
[2023-06-28 17:50:25,185] [INFO] Found 6/6 markers.
[2023-06-28 17:50:25,215] [INFO] Query marker FASTA was written to GCA_027442155.1_ASM2744215v1_genomic.fna/markers.fasta
[2023-06-28 17:50:25,215] [INFO] Task started: Blastn
[2023-06-28 17:50:25,216] [INFO] Running command: blastn -query GCA_027442155.1_ASM2744215v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb381b6ee-8928-4a49-bf42-c46e7335eeaf/dqc_reference/reference_markers.fasta -out GCA_027442155.1_ASM2744215v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 17:50:25,858] [INFO] Task succeeded: Blastn
[2023-06-28 17:50:25,863] [INFO] Selected 32 target genomes.
[2023-06-28 17:50:25,863] [INFO] Target genome list was writen to GCA_027442155.1_ASM2744215v1_genomic.fna/target_genomes.txt
[2023-06-28 17:50:25,876] [INFO] Task started: fastANI
[2023-06-28 17:50:25,877] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b225f4d-7cc3-471e-b777-66c2e40d718a/GCA_027442155.1_ASM2744215v1_genomic.fna.gz --refList GCA_027442155.1_ASM2744215v1_genomic.fna/target_genomes.txt --output GCA_027442155.1_ASM2744215v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 17:50:43,148] [INFO] Task succeeded: fastANI
[2023-06-28 17:50:43,149] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb381b6ee-8928-4a49-bf42-c46e7335eeaf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 17:50:43,149] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb381b6ee-8928-4a49-bf42-c46e7335eeaf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 17:50:43,154] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 17:50:43,154] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 17:50:43,154] [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	76.7039	101	606	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 17:50:43,156] [INFO] DFAST Taxonomy check result was written to GCA_027442155.1_ASM2744215v1_genomic.fna/tc_result.tsv
[2023-06-28 17:50:43,156] [INFO] ===== Taxonomy check completed =====
[2023-06-28 17:50:43,156] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 17:50:43,157] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb381b6ee-8928-4a49-bf42-c46e7335eeaf/dqc_reference/checkm_data
[2023-06-28 17:50:43,158] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 17:50:43,184] [INFO] Task started: CheckM
[2023-06-28 17:50:43,184] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027442155.1_ASM2744215v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027442155.1_ASM2744215v1_genomic.fna/checkm_input GCA_027442155.1_ASM2744215v1_genomic.fna/checkm_result
[2023-06-28 17:51:07,577] [INFO] Task succeeded: CheckM
[2023-06-28 17:51:07,579] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 17:51:07,602] [INFO] ===== Completeness check finished =====
[2023-06-28 17:51:07,602] [INFO] ===== Start GTDB Search =====
[2023-06-28 17:51:07,602] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027442155.1_ASM2744215v1_genomic.fna/markers.fasta)
[2023-06-28 17:51:07,603] [INFO] Task started: Blastn
[2023-06-28 17:51:07,603] [INFO] Running command: blastn -query GCA_027442155.1_ASM2744215v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb381b6ee-8928-4a49-bf42-c46e7335eeaf/dqc_reference/reference_markers_gtdb.fasta -out GCA_027442155.1_ASM2744215v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 17:51:08,625] [INFO] Task succeeded: Blastn
[2023-06-28 17:51:08,629] [INFO] Selected 32 target genomes.
[2023-06-28 17:51:08,630] [INFO] Target genome list was writen to GCA_027442155.1_ASM2744215v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 17:51:08,656] [INFO] Task started: fastANI
[2023-06-28 17:51:08,657] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b225f4d-7cc3-471e-b777-66c2e40d718a/GCA_027442155.1_ASM2744215v1_genomic.fna.gz --refList GCA_027442155.1_ASM2744215v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027442155.1_ASM2744215v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 17:51:24,620] [INFO] Task succeeded: fastANI
[2023-06-28 17:51:24,626] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 17:51:24,626] [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	76.6854	102	606	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Ferrovaceae;g__Ferrovum	95.0	98.82	98.23	0.87	0.85	7	-
--------------------------------------------------------------------------------
[2023-06-28 17:51:24,628] [INFO] GTDB search result was written to GCA_027442155.1_ASM2744215v1_genomic.fna/result_gtdb.tsv
[2023-06-28 17:51:24,629] [INFO] ===== GTDB Search completed =====
[2023-06-28 17:51:24,632] [INFO] DFAST_QC result json was written to GCA_027442155.1_ASM2744215v1_genomic.fna/dqc_result.json
[2023-06-28 17:51:24,632] [INFO] DFAST_QC completed!
[2023-06-28 17:51:24,632] [INFO] Total running time: 0h1m7s