[2023-06-27 06:48:50,395] [INFO] DFAST_QC pipeline started.
[2023-06-27 06:48:50,407] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 06:48:50,407] [INFO] DQC Reference Directory: /var/lib/cwl/stg126c91aa-af06-4ef3-9713-14b65f9876cc/dqc_reference
[2023-06-27 06:48:51,651] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 06:48:51,652] [INFO] Task started: Prodigal
[2023-06-27 06:48:51,652] [INFO] Running command: gunzip -c /var/lib/cwl/stge6cc1475-5afb-4d1d-a311-a5a02f236c0a/GCA_002310095.1_ASM231009v1_genomic.fna.gz | prodigal -d GCA_002310095.1_ASM231009v1_genomic.fna/cds.fna -a GCA_002310095.1_ASM231009v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 06:48:55,268] [INFO] Task succeeded: Prodigal
[2023-06-27 06:48:55,268] [INFO] Task started: HMMsearch
[2023-06-27 06:48:55,268] [INFO] Running command: hmmsearch --tblout GCA_002310095.1_ASM231009v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg126c91aa-af06-4ef3-9713-14b65f9876cc/dqc_reference/reference_markers.hmm GCA_002310095.1_ASM231009v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 06:48:55,485] [INFO] Task succeeded: HMMsearch
[2023-06-27 06:48:55,486] [INFO] Found 6/6 markers.
[2023-06-27 06:48:55,509] [INFO] Query marker FASTA was written to GCA_002310095.1_ASM231009v1_genomic.fna/markers.fasta
[2023-06-27 06:48:55,509] [INFO] Task started: Blastn
[2023-06-27 06:48:55,509] [INFO] Running command: blastn -query GCA_002310095.1_ASM231009v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg126c91aa-af06-4ef3-9713-14b65f9876cc/dqc_reference/reference_markers.fasta -out GCA_002310095.1_ASM231009v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 06:48:56,118] [INFO] Task succeeded: Blastn
[2023-06-27 06:48:56,123] [INFO] Selected 15 target genomes.
[2023-06-27 06:48:56,124] [INFO] Target genome list was writen to GCA_002310095.1_ASM231009v1_genomic.fna/target_genomes.txt
[2023-06-27 06:48:56,138] [INFO] Task started: fastANI
[2023-06-27 06:48:56,138] [INFO] Running command: fastANI --query /var/lib/cwl/stge6cc1475-5afb-4d1d-a311-a5a02f236c0a/GCA_002310095.1_ASM231009v1_genomic.fna.gz --refList GCA_002310095.1_ASM231009v1_genomic.fna/target_genomes.txt --output GCA_002310095.1_ASM231009v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 06:49:05,744] [INFO] Task succeeded: fastANI
[2023-06-27 06:49:05,744] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg126c91aa-af06-4ef3-9713-14b65f9876cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 06:49:05,745] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg126c91aa-af06-4ef3-9713-14b65f9876cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 06:49:05,747] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 06:49:05,748] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 06:49:05,748] [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
--------------------------------------------------------------------------------
[2023-06-27 06:49:05,750] [INFO] DFAST Taxonomy check result was written to GCA_002310095.1_ASM231009v1_genomic.fna/tc_result.tsv
[2023-06-27 06:49:05,751] [INFO] ===== Taxonomy check completed =====
[2023-06-27 06:49:05,751] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 06:49:05,751] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg126c91aa-af06-4ef3-9713-14b65f9876cc/dqc_reference/checkm_data
[2023-06-27 06:49:05,755] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 06:49:05,798] [INFO] Task started: CheckM
[2023-06-27 06:49:05,799] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002310095.1_ASM231009v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002310095.1_ASM231009v1_genomic.fna/checkm_input GCA_002310095.1_ASM231009v1_genomic.fna/checkm_result
[2023-06-27 06:49:23,998] [INFO] Task succeeded: CheckM
[2023-06-27 06:49:24,008] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.49%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 06:49:24,033] [INFO] ===== Completeness check finished =====
[2023-06-27 06:49:24,033] [INFO] ===== Start GTDB Search =====
[2023-06-27 06:49:24,034] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002310095.1_ASM231009v1_genomic.fna/markers.fasta)
[2023-06-27 06:49:24,034] [INFO] Task started: Blastn
[2023-06-27 06:49:24,034] [INFO] Running command: blastn -query GCA_002310095.1_ASM231009v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg126c91aa-af06-4ef3-9713-14b65f9876cc/dqc_reference/reference_markers_gtdb.fasta -out GCA_002310095.1_ASM231009v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 06:49:24,877] [INFO] Task succeeded: Blastn
[2023-06-27 06:49:24,882] [INFO] Selected 12 target genomes.
[2023-06-27 06:49:24,882] [INFO] Target genome list was writen to GCA_002310095.1_ASM231009v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 06:49:24,890] [INFO] Task started: fastANI
[2023-06-27 06:49:24,890] [INFO] Running command: fastANI --query /var/lib/cwl/stge6cc1475-5afb-4d1d-a311-a5a02f236c0a/GCA_002310095.1_ASM231009v1_genomic.fna.gz --refList GCA_002310095.1_ASM231009v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002310095.1_ASM231009v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 06:49:29,460] [INFO] Task succeeded: fastANI
[2023-06-27 06:49:29,473] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 06:49:29,474] [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_002310095.1	s__Copromorpha sp002310095	100.0	464	466	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__Copromorpha	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902787725.1	s__Copromorpha sp902787725	83.3374	251	466	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_017404365.1	s__Copromorpha sp017404365	82.8729	274	466	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_015058145.1	s__Copromorpha sp015058145	81.1584	242	466	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_902786815.1	s__Copromorpha sp902786815	80.6493	236	466	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_017431785.1	s__Copromorpha sp017431785	80.2131	236	466	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_902763505.1	s__Copromorpha sp902763505	80.2115	253	466	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_015058205.1	s__Copromorpha sp015058205	79.7668	198	466	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_017432345.1	s__Copromorpha sp017432345	78.316	131	466	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_017459895.1	s__Copromorpha sp017459895	76.8044	94	466	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__Copromorpha	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 06:49:29,476] [INFO] GTDB search result was written to GCA_002310095.1_ASM231009v1_genomic.fna/result_gtdb.tsv
[2023-06-27 06:49:29,476] [INFO] ===== GTDB Search completed =====
[2023-06-27 06:49:29,479] [INFO] DFAST_QC result json was written to GCA_002310095.1_ASM231009v1_genomic.fna/dqc_result.json
[2023-06-27 06:49:29,479] [INFO] DFAST_QC completed!
[2023-06-27 06:49:29,479] [INFO] Total running time: 0h0m39s