[2023-06-29 10:49:21,152] [INFO] DFAST_QC pipeline started.
[2023-06-29 10:49:21,155] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 10:49:21,155] [INFO] DQC Reference Directory: /var/lib/cwl/stg2184a599-7a15-4046-a1e5-7ecf9c1079be/dqc_reference
[2023-06-29 10:49:22,452] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 10:49:22,452] [INFO] Task started: Prodigal
[2023-06-29 10:49:22,453] [INFO] Running command: gunzip -c /var/lib/cwl/stg7ce7720d-19b6-429c-adc0-01980e2fd45b/GCA_020057645.1_ASM2005764v1_genomic.fna.gz | prodigal -d GCA_020057645.1_ASM2005764v1_genomic.fna/cds.fna -a GCA_020057645.1_ASM2005764v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 10:49:24,106] [INFO] Task succeeded: Prodigal
[2023-06-29 10:49:24,106] [INFO] Task started: HMMsearch
[2023-06-29 10:49:24,106] [INFO] Running command: hmmsearch --tblout GCA_020057645.1_ASM2005764v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2184a599-7a15-4046-a1e5-7ecf9c1079be/dqc_reference/reference_markers.hmm GCA_020057645.1_ASM2005764v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 10:49:24,312] [INFO] Task succeeded: HMMsearch
[2023-06-29 10:49:24,314] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg7ce7720d-19b6-429c-adc0-01980e2fd45b/GCA_020057645.1_ASM2005764v1_genomic.fna.gz]
[2023-06-29 10:49:24,332] [INFO] Query marker FASTA was written to GCA_020057645.1_ASM2005764v1_genomic.fna/markers.fasta
[2023-06-29 10:49:24,333] [INFO] Task started: Blastn
[2023-06-29 10:49:24,333] [INFO] Running command: blastn -query GCA_020057645.1_ASM2005764v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2184a599-7a15-4046-a1e5-7ecf9c1079be/dqc_reference/reference_markers.fasta -out GCA_020057645.1_ASM2005764v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 10:49:28,016] [INFO] Task succeeded: Blastn
[2023-06-29 10:49:28,048] [INFO] Selected 5 target genomes.
[2023-06-29 10:49:28,049] [INFO] Target genome list was writen to GCA_020057645.1_ASM2005764v1_genomic.fna/target_genomes.txt
[2023-06-29 10:49:28,054] [INFO] Task started: fastANI
[2023-06-29 10:49:28,054] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ce7720d-19b6-429c-adc0-01980e2fd45b/GCA_020057645.1_ASM2005764v1_genomic.fna.gz --refList GCA_020057645.1_ASM2005764v1_genomic.fna/target_genomes.txt --output GCA_020057645.1_ASM2005764v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 10:49:30,556] [INFO] Task succeeded: fastANI
[2023-06-29 10:49:30,556] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2184a599-7a15-4046-a1e5-7ecf9c1079be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 10:49:30,557] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2184a599-7a15-4046-a1e5-7ecf9c1079be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 10:49:30,558] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 10:49:30,559] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 10:49:30,559] [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
--------------------------------------------------------------------------------
[2023-06-29 10:49:30,561] [INFO] DFAST Taxonomy check result was written to GCA_020057645.1_ASM2005764v1_genomic.fna/tc_result.tsv
[2023-06-29 10:49:30,562] [INFO] ===== Taxonomy check completed =====
[2023-06-29 10:49:30,562] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 10:49:30,563] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2184a599-7a15-4046-a1e5-7ecf9c1079be/dqc_reference/checkm_data
[2023-06-29 10:49:30,566] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 10:49:30,581] [INFO] Task started: CheckM
[2023-06-29 10:49:30,581] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020057645.1_ASM2005764v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020057645.1_ASM2005764v1_genomic.fna/checkm_input GCA_020057645.1_ASM2005764v1_genomic.fna/checkm_result
[2023-06-29 10:49:44,882] [INFO] Task succeeded: CheckM
[2023-06-29 10:49:44,883] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 63.89%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 10:49:44,901] [INFO] ===== Completeness check finished =====
[2023-06-29 10:49:44,901] [INFO] ===== Start GTDB Search =====
[2023-06-29 10:49:44,901] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020057645.1_ASM2005764v1_genomic.fna/markers.fasta)
[2023-06-29 10:49:44,902] [INFO] Task started: Blastn
[2023-06-29 10:49:44,902] [INFO] Running command: blastn -query GCA_020057645.1_ASM2005764v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2184a599-7a15-4046-a1e5-7ecf9c1079be/dqc_reference/reference_markers_gtdb.fasta -out GCA_020057645.1_ASM2005764v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 10:49:45,638] [INFO] Task succeeded: Blastn
[2023-06-29 10:49:45,642] [INFO] Selected 7 target genomes.
[2023-06-29 10:49:45,643] [INFO] Target genome list was writen to GCA_020057645.1_ASM2005764v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 10:49:45,648] [INFO] Task started: fastANI
[2023-06-29 10:49:45,649] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ce7720d-19b6-429c-adc0-01980e2fd45b/GCA_020057645.1_ASM2005764v1_genomic.fna.gz --refList GCA_020057645.1_ASM2005764v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020057645.1_ASM2005764v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 10:49:47,525] [INFO] Task succeeded: fastANI
[2023-06-29 10:49:47,533] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 10:49:47,533] [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_002780805.1	s__UBA10183 sp002780805	85.5379	108	215	d__Bacteria;p__Omnitrophota;c__Koll11;o__UBA10183;f__UBA10183;g__UBA10183	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003485765.1	s__UBA10183 sp003485765	81.6217	169	215	d__Bacteria;p__Omnitrophota;c__Koll11;o__UBA10183;f__UBA10183;g__UBA10183	95.0	99.85	99.85	0.81	0.81	2	-
GCA_001871815.1	s__UBA10183 sp001871815	81.1261	118	215	d__Bacteria;p__Omnitrophota;c__Koll11;o__UBA10183;f__UBA10183;g__UBA10183	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018819285.1	s__UBA10183 sp018819285	80.8561	154	215	d__Bacteria;p__Omnitrophota;c__Koll11;o__UBA10183;f__UBA10183;g__UBA10183	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018824725.1	s__UBA10183 sp018824725	80.8319	147	215	d__Bacteria;p__Omnitrophota;c__Koll11;o__UBA10183;f__UBA10183;g__UBA10183	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002771475.1	s__UBA10183 sp002771475	80.079	140	215	d__Bacteria;p__Omnitrophota;c__Koll11;o__UBA10183;f__UBA10183;g__UBA10183	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 10:49:47,535] [INFO] GTDB search result was written to GCA_020057645.1_ASM2005764v1_genomic.fna/result_gtdb.tsv
[2023-06-29 10:49:47,536] [INFO] ===== GTDB Search completed =====
[2023-06-29 10:49:47,539] [INFO] DFAST_QC result json was written to GCA_020057645.1_ASM2005764v1_genomic.fna/dqc_result.json
[2023-06-29 10:49:47,539] [INFO] DFAST_QC completed!
[2023-06-29 10:49:47,540] [INFO] Total running time: 0h0m26s