[2023-06-13 02:18:14,278] [INFO] DFAST_QC pipeline started.
[2023-06-13 02:18:14,282] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 02:18:14,282] [INFO] DQC Reference Directory: /var/lib/cwl/stg61ea343a-fea7-4316-9c37-0a05e454ccdd/dqc_reference
[2023-06-13 02:18:15,496] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 02:18:15,496] [INFO] Task started: Prodigal
[2023-06-13 02:18:15,497] [INFO] Running command: gunzip -c /var/lib/cwl/stg3ddffbe5-8a52-4da6-b3f4-27f919b17778/GCA_022340485.1_ASM2234048v1_genomic.fna.gz | prodigal -d GCA_022340485.1_ASM2234048v1_genomic.fna/cds.fna -a GCA_022340485.1_ASM2234048v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 02:18:23,315] [INFO] Task succeeded: Prodigal
[2023-06-13 02:18:23,315] [INFO] Task started: HMMsearch
[2023-06-13 02:18:23,315] [INFO] Running command: hmmsearch --tblout GCA_022340485.1_ASM2234048v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg61ea343a-fea7-4316-9c37-0a05e454ccdd/dqc_reference/reference_markers.hmm GCA_022340485.1_ASM2234048v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 02:18:23,587] [INFO] Task succeeded: HMMsearch
[2023-06-13 02:18:23,588] [INFO] Found 6/6 markers.
[2023-06-13 02:18:23,614] [INFO] Query marker FASTA was written to GCA_022340485.1_ASM2234048v1_genomic.fna/markers.fasta
[2023-06-13 02:18:23,615] [INFO] Task started: Blastn
[2023-06-13 02:18:23,615] [INFO] Running command: blastn -query GCA_022340485.1_ASM2234048v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg61ea343a-fea7-4316-9c37-0a05e454ccdd/dqc_reference/reference_markers.fasta -out GCA_022340485.1_ASM2234048v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 02:18:24,350] [INFO] Task succeeded: Blastn
[2023-06-13 02:18:24,355] [INFO] Selected 34 target genomes.
[2023-06-13 02:18:24,356] [INFO] Target genome list was writen to GCA_022340485.1_ASM2234048v1_genomic.fna/target_genomes.txt
[2023-06-13 02:18:24,364] [INFO] Task started: fastANI
[2023-06-13 02:18:24,365] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ddffbe5-8a52-4da6-b3f4-27f919b17778/GCA_022340485.1_ASM2234048v1_genomic.fna.gz --refList GCA_022340485.1_ASM2234048v1_genomic.fna/target_genomes.txt --output GCA_022340485.1_ASM2234048v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 02:18:45,487] [INFO] Task succeeded: fastANI
[2023-06-13 02:18:45,487] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg61ea343a-fea7-4316-9c37-0a05e454ccdd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 02:18:45,488] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg61ea343a-fea7-4316-9c37-0a05e454ccdd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 02:18:45,493] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 02:18:45,494] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 02:18:45,494] [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
Thiogranum longum	strain=DSM 19610	GCA_004339085.1	1537524	1537524	type	True	76.2131	53	848	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 02:18:45,496] [INFO] DFAST Taxonomy check result was written to GCA_022340485.1_ASM2234048v1_genomic.fna/tc_result.tsv
[2023-06-13 02:18:45,497] [INFO] ===== Taxonomy check completed =====
[2023-06-13 02:18:45,497] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 02:18:45,497] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg61ea343a-fea7-4316-9c37-0a05e454ccdd/dqc_reference/checkm_data
[2023-06-13 02:18:45,499] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 02:18:45,528] [INFO] Task started: CheckM
[2023-06-13 02:18:45,528] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022340485.1_ASM2234048v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022340485.1_ASM2234048v1_genomic.fna/checkm_input GCA_022340485.1_ASM2234048v1_genomic.fna/checkm_result
[2023-06-13 02:19:14,632] [INFO] Task succeeded: CheckM
[2023-06-13 02:19:14,634] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 02:19:14,657] [INFO] ===== Completeness check finished =====
[2023-06-13 02:19:14,657] [INFO] ===== Start GTDB Search =====
[2023-06-13 02:19:14,658] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022340485.1_ASM2234048v1_genomic.fna/markers.fasta)
[2023-06-13 02:19:14,658] [INFO] Task started: Blastn
[2023-06-13 02:19:14,658] [INFO] Running command: blastn -query GCA_022340485.1_ASM2234048v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg61ea343a-fea7-4316-9c37-0a05e454ccdd/dqc_reference/reference_markers_gtdb.fasta -out GCA_022340485.1_ASM2234048v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 02:19:15,862] [INFO] Task succeeded: Blastn
[2023-06-13 02:19:15,867] [INFO] Selected 23 target genomes.
[2023-06-13 02:19:15,867] [INFO] Target genome list was writen to GCA_022340485.1_ASM2234048v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 02:19:15,879] [INFO] Task started: fastANI
[2023-06-13 02:19:15,880] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ddffbe5-8a52-4da6-b3f4-27f919b17778/GCA_022340485.1_ASM2234048v1_genomic.fna.gz --refList GCA_022340485.1_ASM2234048v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022340485.1_ASM2234048v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 02:19:28,004] [INFO] Task succeeded: fastANI
[2023-06-13 02:19:28,020] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 02:19:28,020] [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_905479705.1	s__UBA9214 sp905479705	78.1528	246	848	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA9214;f__UBA9214;g__UBA9214	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480305.1	s__UBA9214 sp905480305	77.6838	132	848	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA9214;f__UBA9214;g__UBA9214	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003454335.1	s__UBA9214 sp003454335	77.579	158	848	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA9214;f__UBA9214;g__UBA9214	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480065.1	s__UBA9214 sp905480065	76.9878	116	848	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA9214;f__UBA9214;g__UBA9214	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013041945.1	s__UBA9214 sp013041945	76.9048	112	848	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA9214;f__UBA9214;g__UBA9214	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003230545.1	s__SZUA-186 sp003230545	76.6447	90	848	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA9214;f__UBA9214;g__SZUA-186	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339085.1	s__Thiogranum longum	76.2237	54	848	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-19610;f__DSM-19610;g__Thiogranum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011371465.1	s__Thiogranum sp011371465	76.1977	75	848	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-19610;f__DSM-19610;g__Thiogranum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 02:19:28,023] [INFO] GTDB search result was written to GCA_022340485.1_ASM2234048v1_genomic.fna/result_gtdb.tsv
[2023-06-13 02:19:28,023] [INFO] ===== GTDB Search completed =====
[2023-06-13 02:19:28,027] [INFO] DFAST_QC result json was written to GCA_022340485.1_ASM2234048v1_genomic.fna/dqc_result.json
[2023-06-13 02:19:28,027] [INFO] DFAST_QC completed!
[2023-06-13 02:19:28,028] [INFO] Total running time: 0h1m14s