[2023-06-13 17:01:48,528] [INFO] DFAST_QC pipeline started.
[2023-06-13 17:01:48,530] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 17:01:48,530] [INFO] DQC Reference Directory: /var/lib/cwl/stg4bfac46f-ccf1-4371-8312-45d659fd04e4/dqc_reference
[2023-06-13 17:01:50,221] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 17:01:50,222] [INFO] Task started: Prodigal
[2023-06-13 17:01:50,222] [INFO] Running command: gunzip -c /var/lib/cwl/stg3d537ca6-a5e3-499c-93de-8695db8f0814/GCA_022824565.1_ASM2282456v1_genomic.fna.gz | prodigal -d GCA_022824565.1_ASM2282456v1_genomic.fna/cds.fna -a GCA_022824565.1_ASM2282456v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 17:02:00,735] [INFO] Task succeeded: Prodigal
[2023-06-13 17:02:00,736] [INFO] Task started: HMMsearch
[2023-06-13 17:02:00,736] [INFO] Running command: hmmsearch --tblout GCA_022824565.1_ASM2282456v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4bfac46f-ccf1-4371-8312-45d659fd04e4/dqc_reference/reference_markers.hmm GCA_022824565.1_ASM2282456v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 17:02:00,947] [INFO] Task succeeded: HMMsearch
[2023-06-13 17:02:00,948] [INFO] Found 6/6 markers.
[2023-06-13 17:02:00,976] [INFO] Query marker FASTA was written to GCA_022824565.1_ASM2282456v1_genomic.fna/markers.fasta
[2023-06-13 17:02:00,977] [INFO] Task started: Blastn
[2023-06-13 17:02:00,977] [INFO] Running command: blastn -query GCA_022824565.1_ASM2282456v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4bfac46f-ccf1-4371-8312-45d659fd04e4/dqc_reference/reference_markers.fasta -out GCA_022824565.1_ASM2282456v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 17:02:01,517] [INFO] Task succeeded: Blastn
[2023-06-13 17:02:01,520] [INFO] Selected 22 target genomes.
[2023-06-13 17:02:01,521] [INFO] Target genome list was writen to GCA_022824565.1_ASM2282456v1_genomic.fna/target_genomes.txt
[2023-06-13 17:02:01,527] [INFO] Task started: fastANI
[2023-06-13 17:02:01,527] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d537ca6-a5e3-499c-93de-8695db8f0814/GCA_022824565.1_ASM2282456v1_genomic.fna.gz --refList GCA_022824565.1_ASM2282456v1_genomic.fna/target_genomes.txt --output GCA_022824565.1_ASM2282456v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 17:02:19,579] [INFO] Task succeeded: fastANI
[2023-06-13 17:02:19,579] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4bfac46f-ccf1-4371-8312-45d659fd04e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 17:02:19,579] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4bfac46f-ccf1-4371-8312-45d659fd04e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 17:02:19,581] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 17:02:19,581] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 17:02:19,581] [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
--------------------------------------------------------------------------------
[2023-06-13 17:02:19,583] [INFO] DFAST Taxonomy check result was written to GCA_022824565.1_ASM2282456v1_genomic.fna/tc_result.tsv
[2023-06-13 17:02:19,583] [INFO] ===== Taxonomy check completed =====
[2023-06-13 17:02:19,583] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 17:02:19,584] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4bfac46f-ccf1-4371-8312-45d659fd04e4/dqc_reference/checkm_data
[2023-06-13 17:02:19,586] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 17:02:19,619] [INFO] Task started: CheckM
[2023-06-13 17:02:19,619] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022824565.1_ASM2282456v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022824565.1_ASM2282456v1_genomic.fna/checkm_input GCA_022824565.1_ASM2282456v1_genomic.fna/checkm_result
[2023-06-13 17:02:52,830] [INFO] Task succeeded: CheckM
[2023-06-13 17:02:52,832] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-13 17:02:52,850] [INFO] ===== Completeness check finished =====
[2023-06-13 17:02:52,850] [INFO] ===== Start GTDB Search =====
[2023-06-13 17:02:52,850] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022824565.1_ASM2282456v1_genomic.fna/markers.fasta)
[2023-06-13 17:02:52,850] [INFO] Task started: Blastn
[2023-06-13 17:02:52,851] [INFO] Running command: blastn -query GCA_022824565.1_ASM2282456v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4bfac46f-ccf1-4371-8312-45d659fd04e4/dqc_reference/reference_markers_gtdb.fasta -out GCA_022824565.1_ASM2282456v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 17:02:53,607] [INFO] Task succeeded: Blastn
[2023-06-13 17:02:53,611] [INFO] Selected 12 target genomes.
[2023-06-13 17:02:53,611] [INFO] Target genome list was writen to GCA_022824565.1_ASM2282456v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 17:02:53,629] [INFO] Task started: fastANI
[2023-06-13 17:02:53,629] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d537ca6-a5e3-499c-93de-8695db8f0814/GCA_022824565.1_ASM2282456v1_genomic.fna.gz --refList GCA_022824565.1_ASM2282456v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022824565.1_ASM2282456v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 17:03:02,845] [INFO] Task succeeded: fastANI
[2023-06-13 17:03:02,853] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 17:03:02,853] [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_002238485.1	s__UBA6055 sp002238485	88.0363	948	1056	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__UBA6055	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009840575.1	s__UBA6055 sp009840575	84.4717	850	1056	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__UBA6055	95.0	99.83	99.79	0.96	0.95	8	-
GCA_011523705.1	s__UBA6055 sp011523705	77.6368	376	1056	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__UBA6055	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009841405.1	s__UBA6055 sp009841405	77.6033	411	1056	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__UBA6055	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011523545.1	s__UBA6055 sp011523545	77.553	415	1056	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__UBA6055	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011523515.1	s__UBA6055 sp011523515	77.5143	375	1056	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__UBA6055	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011523735.1	s__UBA6055 sp011523735	77.5005	349	1056	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__UBA6055	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012270545.1	s__UBA6055 sp012270545	77.4692	328	1056	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__UBA6055	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 17:03:02,855] [INFO] GTDB search result was written to GCA_022824565.1_ASM2282456v1_genomic.fna/result_gtdb.tsv
[2023-06-13 17:03:02,856] [INFO] ===== GTDB Search completed =====
[2023-06-13 17:03:02,858] [INFO] DFAST_QC result json was written to GCA_022824565.1_ASM2282456v1_genomic.fna/dqc_result.json
[2023-06-13 17:03:02,858] [INFO] DFAST_QC completed!
[2023-06-13 17:03:02,859] [INFO] Total running time: 0h1m14s