[2023-06-29 22:48:44,383] [INFO] DFAST_QC pipeline started.
[2023-06-29 22:48:44,385] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 22:48:44,385] [INFO] DQC Reference Directory: /var/lib/cwl/stg43234fab-bf97-41a1-8490-f94d7abc1271/dqc_reference
[2023-06-29 22:48:45,652] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 22:48:45,653] [INFO] Task started: Prodigal
[2023-06-29 22:48:45,653] [INFO] Running command: gunzip -c /var/lib/cwl/stga8087400-a8ab-45a4-a994-ead6d32f8577/GCA_016285515.1_ASM1628551v1_genomic.fna.gz | prodigal -d GCA_016285515.1_ASM1628551v1_genomic.fna/cds.fna -a GCA_016285515.1_ASM1628551v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 22:48:59,436] [INFO] Task succeeded: Prodigal
[2023-06-29 22:48:59,437] [INFO] Task started: HMMsearch
[2023-06-29 22:48:59,437] [INFO] Running command: hmmsearch --tblout GCA_016285515.1_ASM1628551v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg43234fab-bf97-41a1-8490-f94d7abc1271/dqc_reference/reference_markers.hmm GCA_016285515.1_ASM1628551v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 22:48:59,733] [INFO] Task succeeded: HMMsearch
[2023-06-29 22:48:59,735] [INFO] Found 6/6 markers.
[2023-06-29 22:48:59,760] [INFO] Query marker FASTA was written to GCA_016285515.1_ASM1628551v1_genomic.fna/markers.fasta
[2023-06-29 22:48:59,761] [INFO] Task started: Blastn
[2023-06-29 22:48:59,761] [INFO] Running command: blastn -query GCA_016285515.1_ASM1628551v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg43234fab-bf97-41a1-8490-f94d7abc1271/dqc_reference/reference_markers.fasta -out GCA_016285515.1_ASM1628551v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 22:49:00,370] [INFO] Task succeeded: Blastn
[2023-06-29 22:49:00,375] [INFO] Selected 30 target genomes.
[2023-06-29 22:49:00,375] [INFO] Target genome list was writen to GCA_016285515.1_ASM1628551v1_genomic.fna/target_genomes.txt
[2023-06-29 22:49:00,382] [INFO] Task started: fastANI
[2023-06-29 22:49:00,382] [INFO] Running command: fastANI --query /var/lib/cwl/stga8087400-a8ab-45a4-a994-ead6d32f8577/GCA_016285515.1_ASM1628551v1_genomic.fna.gz --refList GCA_016285515.1_ASM1628551v1_genomic.fna/target_genomes.txt --output GCA_016285515.1_ASM1628551v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 22:49:17,769] [INFO] Task succeeded: fastANI
[2023-06-29 22:49:17,769] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg43234fab-bf97-41a1-8490-f94d7abc1271/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 22:49:17,770] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg43234fab-bf97-41a1-8490-f94d7abc1271/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 22:49:17,772] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 22:49:17,772] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 22:49:17,772] [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 22:49:17,794] [INFO] DFAST Taxonomy check result was written to GCA_016285515.1_ASM1628551v1_genomic.fna/tc_result.tsv
[2023-06-29 22:49:17,795] [INFO] ===== Taxonomy check completed =====
[2023-06-29 22:49:17,795] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 22:49:17,796] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg43234fab-bf97-41a1-8490-f94d7abc1271/dqc_reference/checkm_data
[2023-06-29 22:49:17,800] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 22:49:17,831] [INFO] Task started: CheckM
[2023-06-29 22:49:17,831] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016285515.1_ASM1628551v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016285515.1_ASM1628551v1_genomic.fna/checkm_input GCA_016285515.1_ASM1628551v1_genomic.fna/checkm_result
[2023-06-29 22:50:01,928] [INFO] Task succeeded: CheckM
[2023-06-29 22:50:01,930] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 22:50:01,950] [INFO] ===== Completeness check finished =====
[2023-06-29 22:50:01,951] [INFO] ===== Start GTDB Search =====
[2023-06-29 22:50:01,951] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016285515.1_ASM1628551v1_genomic.fna/markers.fasta)
[2023-06-29 22:50:01,951] [INFO] Task started: Blastn
[2023-06-29 22:50:01,952] [INFO] Running command: blastn -query GCA_016285515.1_ASM1628551v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg43234fab-bf97-41a1-8490-f94d7abc1271/dqc_reference/reference_markers_gtdb.fasta -out GCA_016285515.1_ASM1628551v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 22:50:02,697] [INFO] Task succeeded: Blastn
[2023-06-29 22:50:02,703] [INFO] Selected 23 target genomes.
[2023-06-29 22:50:02,703] [INFO] Target genome list was writen to GCA_016285515.1_ASM1628551v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 22:50:02,720] [INFO] Task started: fastANI
[2023-06-29 22:50:02,721] [INFO] Running command: fastANI --query /var/lib/cwl/stga8087400-a8ab-45a4-a994-ead6d32f8577/GCA_016285515.1_ASM1628551v1_genomic.fna.gz --refList GCA_016285515.1_ASM1628551v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016285515.1_ASM1628551v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 22:50:14,980] [INFO] Task succeeded: fastANI
[2023-06-29 22:50:14,986] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 22:50:14,986] [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_016285515.1	s__RGIG7150 sp016285515	100.0	827	831	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__BM520;g__RGIG7150	95.0	98.38	98.38	0.96	0.96	2	conclusive
GCA_017538085.1	s__RGIG7150 sp017538085	94.557	464	831	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__BM520;g__RGIG7150	95.0	96.14	95.79	0.83	0.75	4	-
--------------------------------------------------------------------------------
[2023-06-29 22:50:14,989] [INFO] GTDB search result was written to GCA_016285515.1_ASM1628551v1_genomic.fna/result_gtdb.tsv
[2023-06-29 22:50:14,990] [INFO] ===== GTDB Search completed =====
[2023-06-29 22:50:14,993] [INFO] DFAST_QC result json was written to GCA_016285515.1_ASM1628551v1_genomic.fna/dqc_result.json
[2023-06-29 22:50:14,993] [INFO] DFAST_QC completed!
[2023-06-29 22:50:14,993] [INFO] Total running time: 0h1m31s