[2023-06-28 18:41:33,151] [INFO] DFAST_QC pipeline started.
[2023-06-28 18:41:33,156] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 18:41:33,156] [INFO] DQC Reference Directory: /var/lib/cwl/stga6ba63a5-4810-447d-abe8-9b047dac6a38/dqc_reference
[2023-06-28 18:41:35,639] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 18:41:35,640] [INFO] Task started: Prodigal
[2023-06-28 18:41:35,641] [INFO] Running command: gunzip -c /var/lib/cwl/stga74b96bc-e1ff-4523-ba68-2675d05cf238/GCA_017447775.1_ASM1744777v1_genomic.fna.gz | prodigal -d GCA_017447775.1_ASM1744777v1_genomic.fna/cds.fna -a GCA_017447775.1_ASM1744777v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 18:41:40,102] [INFO] Task succeeded: Prodigal
[2023-06-28 18:41:40,103] [INFO] Task started: HMMsearch
[2023-06-28 18:41:40,103] [INFO] Running command: hmmsearch --tblout GCA_017447775.1_ASM1744777v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga6ba63a5-4810-447d-abe8-9b047dac6a38/dqc_reference/reference_markers.hmm GCA_017447775.1_ASM1744777v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 18:41:40,341] [INFO] Task succeeded: HMMsearch
[2023-06-28 18:41:40,342] [INFO] Found 6/6 markers.
[2023-06-28 18:41:40,362] [INFO] Query marker FASTA was written to GCA_017447775.1_ASM1744777v1_genomic.fna/markers.fasta
[2023-06-28 18:41:40,362] [INFO] Task started: Blastn
[2023-06-28 18:41:40,362] [INFO] Running command: blastn -query GCA_017447775.1_ASM1744777v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga6ba63a5-4810-447d-abe8-9b047dac6a38/dqc_reference/reference_markers.fasta -out GCA_017447775.1_ASM1744777v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:41:41,025] [INFO] Task succeeded: Blastn
[2023-06-28 18:41:41,030] [INFO] Selected 19 target genomes.
[2023-06-28 18:41:41,030] [INFO] Target genome list was writen to GCA_017447775.1_ASM1744777v1_genomic.fna/target_genomes.txt
[2023-06-28 18:41:41,037] [INFO] Task started: fastANI
[2023-06-28 18:41:41,037] [INFO] Running command: fastANI --query /var/lib/cwl/stga74b96bc-e1ff-4523-ba68-2675d05cf238/GCA_017447775.1_ASM1744777v1_genomic.fna.gz --refList GCA_017447775.1_ASM1744777v1_genomic.fna/target_genomes.txt --output GCA_017447775.1_ASM1744777v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 18:41:51,673] [INFO] Task succeeded: fastANI
[2023-06-28 18:41:51,674] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga6ba63a5-4810-447d-abe8-9b047dac6a38/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 18:41:51,674] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga6ba63a5-4810-447d-abe8-9b047dac6a38/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 18:41:51,676] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 18:41:51,676] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 18:41:51,677] [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
--------------------------------------------------------------------------------
[2023-06-28 18:41:51,680] [INFO] DFAST Taxonomy check result was written to GCA_017447775.1_ASM1744777v1_genomic.fna/tc_result.tsv
[2023-06-28 18:41:51,681] [INFO] ===== Taxonomy check completed =====
[2023-06-28 18:41:51,681] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 18:41:51,681] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga6ba63a5-4810-447d-abe8-9b047dac6a38/dqc_reference/checkm_data
[2023-06-28 18:41:51,686] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 18:41:51,710] [INFO] Task started: CheckM
[2023-06-28 18:41:51,710] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017447775.1_ASM1744777v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017447775.1_ASM1744777v1_genomic.fna/checkm_input GCA_017447775.1_ASM1744777v1_genomic.fna/checkm_result
[2023-06-28 18:42:11,909] [INFO] Task succeeded: CheckM
[2023-06-28 18:42:11,911] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 18:42:11,936] [INFO] ===== Completeness check finished =====
[2023-06-28 18:42:11,936] [INFO] ===== Start GTDB Search =====
[2023-06-28 18:42:11,937] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017447775.1_ASM1744777v1_genomic.fna/markers.fasta)
[2023-06-28 18:42:11,937] [INFO] Task started: Blastn
[2023-06-28 18:42:11,937] [INFO] Running command: blastn -query GCA_017447775.1_ASM1744777v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga6ba63a5-4810-447d-abe8-9b047dac6a38/dqc_reference/reference_markers_gtdb.fasta -out GCA_017447775.1_ASM1744777v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:42:13,010] [INFO] Task succeeded: Blastn
[2023-06-28 18:42:13,015] [INFO] Selected 18 target genomes.
[2023-06-28 18:42:13,015] [INFO] Target genome list was writen to GCA_017447775.1_ASM1744777v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 18:42:13,023] [INFO] Task started: fastANI
[2023-06-28 18:42:13,023] [INFO] Running command: fastANI --query /var/lib/cwl/stga74b96bc-e1ff-4523-ba68-2675d05cf238/GCA_017447775.1_ASM1744777v1_genomic.fna.gz --refList GCA_017447775.1_ASM1744777v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017447775.1_ASM1744777v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 18:42:19,194] [INFO] Task succeeded: fastANI
[2023-06-28 18:42:19,201] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 18:42:19,201] [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_017447775.1	s__RGIG6816 sp017447775	100.0	576	580	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__RGIG6816	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017542695.1	s__RGIG6816 sp017542695	79.4787	232	580	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__RGIG6816	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905235755.1	s__RGIG6816 sp905235755	78.878	162	580	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__RGIG6816	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 18:42:19,203] [INFO] GTDB search result was written to GCA_017447775.1_ASM1744777v1_genomic.fna/result_gtdb.tsv
[2023-06-28 18:42:19,204] [INFO] ===== GTDB Search completed =====
[2023-06-28 18:42:19,207] [INFO] DFAST_QC result json was written to GCA_017447775.1_ASM1744777v1_genomic.fna/dqc_result.json
[2023-06-28 18:42:19,207] [INFO] DFAST_QC completed!
[2023-06-28 18:42:19,208] [INFO] Total running time: 0h0m46s