[2023-06-17 12:24:33,241] [INFO] DFAST_QC pipeline started.
[2023-06-17 12:24:33,243] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 12:24:33,243] [INFO] DQC Reference Directory: /var/lib/cwl/stge98cce72-326e-45e4-bc94-fbc47e762620/dqc_reference
[2023-06-17 12:24:34,518] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 12:24:34,519] [INFO] Task started: Prodigal
[2023-06-17 12:24:34,519] [INFO] Running command: gunzip -c /var/lib/cwl/stg514300c4-d06e-4918-b39a-a4e8e5f8ed6c/GCA_028720665.1_ASM2872066v1_genomic.fna.gz | prodigal -d GCA_028720665.1_ASM2872066v1_genomic.fna/cds.fna -a GCA_028720665.1_ASM2872066v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 12:24:38,996] [INFO] Task succeeded: Prodigal
[2023-06-17 12:24:38,996] [INFO] Task started: HMMsearch
[2023-06-17 12:24:38,996] [INFO] Running command: hmmsearch --tblout GCA_028720665.1_ASM2872066v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge98cce72-326e-45e4-bc94-fbc47e762620/dqc_reference/reference_markers.hmm GCA_028720665.1_ASM2872066v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 12:24:39,250] [INFO] Task succeeded: HMMsearch
[2023-06-17 12:24:39,251] [INFO] Found 6/6 markers.
[2023-06-17 12:24:39,274] [INFO] Query marker FASTA was written to GCA_028720665.1_ASM2872066v1_genomic.fna/markers.fasta
[2023-06-17 12:24:39,275] [INFO] Task started: Blastn
[2023-06-17 12:24:39,275] [INFO] Running command: blastn -query GCA_028720665.1_ASM2872066v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge98cce72-326e-45e4-bc94-fbc47e762620/dqc_reference/reference_markers.fasta -out GCA_028720665.1_ASM2872066v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 12:24:39,885] [INFO] Task succeeded: Blastn
[2023-06-17 12:24:39,889] [INFO] Selected 17 target genomes.
[2023-06-17 12:24:39,890] [INFO] Target genome list was writen to GCA_028720665.1_ASM2872066v1_genomic.fna/target_genomes.txt
[2023-06-17 12:24:39,924] [INFO] Task started: fastANI
[2023-06-17 12:24:39,925] [INFO] Running command: fastANI --query /var/lib/cwl/stg514300c4-d06e-4918-b39a-a4e8e5f8ed6c/GCA_028720665.1_ASM2872066v1_genomic.fna.gz --refList GCA_028720665.1_ASM2872066v1_genomic.fna/target_genomes.txt --output GCA_028720665.1_ASM2872066v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 12:24:50,670] [INFO] Task succeeded: fastANI
[2023-06-17 12:24:50,670] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge98cce72-326e-45e4-bc94-fbc47e762620/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 12:24:50,671] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge98cce72-326e-45e4-bc94-fbc47e762620/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 12:24:50,672] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 12:24:50,673] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 12:24:50,673] [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
--------------------------------------------------------------------------------
[2023-06-17 12:24:50,675] [INFO] DFAST Taxonomy check result was written to GCA_028720665.1_ASM2872066v1_genomic.fna/tc_result.tsv
[2023-06-17 12:24:50,675] [INFO] ===== Taxonomy check completed =====
[2023-06-17 12:24:50,675] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 12:24:50,676] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge98cce72-326e-45e4-bc94-fbc47e762620/dqc_reference/checkm_data
[2023-06-17 12:24:50,678] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 12:24:50,712] [INFO] Task started: CheckM
[2023-06-17 12:24:50,712] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028720665.1_ASM2872066v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028720665.1_ASM2872066v1_genomic.fna/checkm_input GCA_028720665.1_ASM2872066v1_genomic.fna/checkm_result
[2023-06-17 12:25:11,629] [INFO] Task succeeded: CheckM
[2023-06-17 12:25:11,630] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 12:25:11,653] [INFO] ===== Completeness check finished =====
[2023-06-17 12:25:11,653] [INFO] ===== Start GTDB Search =====
[2023-06-17 12:25:11,653] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028720665.1_ASM2872066v1_genomic.fna/markers.fasta)
[2023-06-17 12:25:11,654] [INFO] Task started: Blastn
[2023-06-17 12:25:11,654] [INFO] Running command: blastn -query GCA_028720665.1_ASM2872066v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge98cce72-326e-45e4-bc94-fbc47e762620/dqc_reference/reference_markers_gtdb.fasta -out GCA_028720665.1_ASM2872066v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 12:25:12,495] [INFO] Task succeeded: Blastn
[2023-06-17 12:25:12,507] [INFO] Selected 22 target genomes.
[2023-06-17 12:25:12,508] [INFO] Target genome list was writen to GCA_028720665.1_ASM2872066v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 12:25:12,523] [INFO] Task started: fastANI
[2023-06-17 12:25:12,523] [INFO] Running command: fastANI --query /var/lib/cwl/stg514300c4-d06e-4918-b39a-a4e8e5f8ed6c/GCA_028720665.1_ASM2872066v1_genomic.fna.gz --refList GCA_028720665.1_ASM2872066v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028720665.1_ASM2872066v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 12:25:20,222] [INFO] Task succeeded: fastANI
[2023-06-17 12:25:20,243] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-17 12:25:20,244] [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_017404365.1	s__Copromorpha sp017404365	78.5488	87	571	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__Copromorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902362435.1	s__Copromorpha sp900066305	78.5324	70	571	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__Copromorpha	95.0	99.11	98.22	0.97	0.95	3	-
GCA_017438285.1	s__Copromorpha sp017438285	78.4823	86	571	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__Copromorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902795135.1	s__Copromorpha sp902795135	78.4722	71	571	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__Copromorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902787725.1	s__Copromorpha sp902787725	78.0823	86	571	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__Copromorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002310095.1	s__Copromorpha sp002310095	77.9828	92	571	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__Copromorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017416795.1	s__Copromorpha sp017416795	77.8897	70	571	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__Copromorpha	95.0	95.76	95.76	0.88	0.88	2	-
GCA_900543485.1	s__Copromorpha excrementipullorum	77.4968	58	571	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__Copromorpha	95.0	99.13	99.09	0.94	0.94	3	-
GCA_017459895.1	s__Copromorpha sp017459895	76.6389	70	571	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__Copromorpha	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 12:25:20,247] [INFO] GTDB search result was written to GCA_028720665.1_ASM2872066v1_genomic.fna/result_gtdb.tsv
[2023-06-17 12:25:20,248] [INFO] ===== GTDB Search completed =====
[2023-06-17 12:25:20,252] [INFO] DFAST_QC result json was written to GCA_028720665.1_ASM2872066v1_genomic.fna/dqc_result.json
[2023-06-17 12:25:20,253] [INFO] DFAST_QC completed!
[2023-06-17 12:25:20,253] [INFO] Total running time: 0h0m47s