[2023-06-29 18:37:32,207] [INFO] DFAST_QC pipeline started.
[2023-06-29 18:37:32,210] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 18:37:32,210] [INFO] DQC Reference Directory: /var/lib/cwl/stgfd1caee1-5ec6-40ba-a79a-18017c6117ed/dqc_reference
[2023-06-29 18:37:34,391] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 18:37:34,392] [INFO] Task started: Prodigal
[2023-06-29 18:37:34,392] [INFO] Running command: gunzip -c /var/lib/cwl/stg2d080c25-62c3-48eb-874a-86755dc35b1b/GCA_021624765.1_ASM2162476v1_genomic.fna.gz | prodigal -d GCA_021624765.1_ASM2162476v1_genomic.fna/cds.fna -a GCA_021624765.1_ASM2162476v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 18:37:37,488] [INFO] Task succeeded: Prodigal
[2023-06-29 18:37:37,489] [INFO] Task started: HMMsearch
[2023-06-29 18:37:37,489] [INFO] Running command: hmmsearch --tblout GCA_021624765.1_ASM2162476v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfd1caee1-5ec6-40ba-a79a-18017c6117ed/dqc_reference/reference_markers.hmm GCA_021624765.1_ASM2162476v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 18:37:37,687] [INFO] Task succeeded: HMMsearch
[2023-06-29 18:37:37,688] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2d080c25-62c3-48eb-874a-86755dc35b1b/GCA_021624765.1_ASM2162476v1_genomic.fna.gz]
[2023-06-29 18:37:37,708] [INFO] Query marker FASTA was written to GCA_021624765.1_ASM2162476v1_genomic.fna/markers.fasta
[2023-06-29 18:37:37,708] [INFO] Task started: Blastn
[2023-06-29 18:37:37,709] [INFO] Running command: blastn -query GCA_021624765.1_ASM2162476v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd1caee1-5ec6-40ba-a79a-18017c6117ed/dqc_reference/reference_markers.fasta -out GCA_021624765.1_ASM2162476v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 18:37:39,389] [INFO] Task succeeded: Blastn
[2023-06-29 18:37:39,395] [INFO] Selected 25 target genomes.
[2023-06-29 18:37:39,396] [INFO] Target genome list was writen to GCA_021624765.1_ASM2162476v1_genomic.fna/target_genomes.txt
[2023-06-29 18:37:39,402] [INFO] Task started: fastANI
[2023-06-29 18:37:39,402] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d080c25-62c3-48eb-874a-86755dc35b1b/GCA_021624765.1_ASM2162476v1_genomic.fna.gz --refList GCA_021624765.1_ASM2162476v1_genomic.fna/target_genomes.txt --output GCA_021624765.1_ASM2162476v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 18:37:53,608] [INFO] Task succeeded: fastANI
[2023-06-29 18:37:53,609] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfd1caee1-5ec6-40ba-a79a-18017c6117ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 18:37:53,609] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfd1caee1-5ec6-40ba-a79a-18017c6117ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 18:37:53,612] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 18:37:53,612] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 18:37:53,612] [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 18:37:53,614] [INFO] DFAST Taxonomy check result was written to GCA_021624765.1_ASM2162476v1_genomic.fna/tc_result.tsv
[2023-06-29 18:37:53,615] [INFO] ===== Taxonomy check completed =====
[2023-06-29 18:37:53,616] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 18:37:53,616] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfd1caee1-5ec6-40ba-a79a-18017c6117ed/dqc_reference/checkm_data
[2023-06-29 18:37:53,620] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 18:37:53,641] [INFO] Task started: CheckM
[2023-06-29 18:37:53,642] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021624765.1_ASM2162476v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021624765.1_ASM2162476v1_genomic.fna/checkm_input GCA_021624765.1_ASM2162476v1_genomic.fna/checkm_result
[2023-06-29 18:38:10,200] [INFO] Task succeeded: CheckM
[2023-06-29 18:38:10,202] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 18:38:10,224] [INFO] ===== Completeness check finished =====
[2023-06-29 18:38:10,224] [INFO] ===== Start GTDB Search =====
[2023-06-29 18:38:10,225] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021624765.1_ASM2162476v1_genomic.fna/markers.fasta)
[2023-06-29 18:38:10,225] [INFO] Task started: Blastn
[2023-06-29 18:38:10,225] [INFO] Running command: blastn -query GCA_021624765.1_ASM2162476v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd1caee1-5ec6-40ba-a79a-18017c6117ed/dqc_reference/reference_markers_gtdb.fasta -out GCA_021624765.1_ASM2162476v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 18:38:11,181] [INFO] Task succeeded: Blastn
[2023-06-29 18:38:11,186] [INFO] Selected 13 target genomes.
[2023-06-29 18:38:11,186] [INFO] Target genome list was writen to GCA_021624765.1_ASM2162476v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 18:38:11,194] [INFO] Task started: fastANI
[2023-06-29 18:38:11,195] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d080c25-62c3-48eb-874a-86755dc35b1b/GCA_021624765.1_ASM2162476v1_genomic.fna.gz --refList GCA_021624765.1_ASM2162476v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021624765.1_ASM2162476v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 18:38:14,971] [INFO] Task succeeded: fastANI
[2023-06-29 18:38:14,979] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 18:38:14,979] [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_905203015.1	s__UBA7597 sp003448195	99.0326	192	212	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__UBA7597	95.0	98.98	98.79	0.94	0.92	4	conclusive
GCA_900542935.1	s__UBA7597 sp900542935	82.1257	112	212	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__UBA7597	95.0	98.09	97.76	0.86	0.81	5	-
GCA_002474405.1	s__UBA7597 sp002474405	81.5762	119	212	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__UBA7597	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900767195.1	s__UBA7597 sp900767195	80.3997	96	212	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__UBA7597	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 18:38:14,981] [INFO] GTDB search result was written to GCA_021624765.1_ASM2162476v1_genomic.fna/result_gtdb.tsv
[2023-06-29 18:38:14,982] [INFO] ===== GTDB Search completed =====
[2023-06-29 18:38:14,984] [INFO] DFAST_QC result json was written to GCA_021624765.1_ASM2162476v1_genomic.fna/dqc_result.json
[2023-06-29 18:38:14,984] [INFO] DFAST_QC completed!
[2023-06-29 18:38:14,984] [INFO] Total running time: 0h0m43s