[2023-06-28 05:15:00,767] [INFO] DFAST_QC pipeline started.
[2023-06-28 05:15:00,769] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 05:15:00,769] [INFO] DQC Reference Directory: /var/lib/cwl/stg0147e1c9-b488-44a0-a59b-f936b29f6ff7/dqc_reference
[2023-06-28 05:15:02,336] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 05:15:02,337] [INFO] Task started: Prodigal
[2023-06-28 05:15:02,337] [INFO] Running command: gunzip -c /var/lib/cwl/stgfc3cfe27-0d1d-4421-971f-82ddab35a745/GCA_017620175.1_ASM1762017v1_genomic.fna.gz | prodigal -d GCA_017620175.1_ASM1762017v1_genomic.fna/cds.fna -a GCA_017620175.1_ASM1762017v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 05:15:07,344] [INFO] Task succeeded: Prodigal
[2023-06-28 05:15:07,345] [INFO] Task started: HMMsearch
[2023-06-28 05:15:07,345] [INFO] Running command: hmmsearch --tblout GCA_017620175.1_ASM1762017v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0147e1c9-b488-44a0-a59b-f936b29f6ff7/dqc_reference/reference_markers.hmm GCA_017620175.1_ASM1762017v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 05:15:07,592] [INFO] Task succeeded: HMMsearch
[2023-06-28 05:15:07,594] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgfc3cfe27-0d1d-4421-971f-82ddab35a745/GCA_017620175.1_ASM1762017v1_genomic.fna.gz]
[2023-06-28 05:15:07,629] [INFO] Query marker FASTA was written to GCA_017620175.1_ASM1762017v1_genomic.fna/markers.fasta
[2023-06-28 05:15:07,630] [INFO] Task started: Blastn
[2023-06-28 05:15:07,630] [INFO] Running command: blastn -query GCA_017620175.1_ASM1762017v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0147e1c9-b488-44a0-a59b-f936b29f6ff7/dqc_reference/reference_markers.fasta -out GCA_017620175.1_ASM1762017v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 05:15:08,209] [INFO] Task succeeded: Blastn
[2023-06-28 05:15:08,216] [INFO] Selected 11 target genomes.
[2023-06-28 05:15:08,216] [INFO] Target genome list was writen to GCA_017620175.1_ASM1762017v1_genomic.fna/target_genomes.txt
[2023-06-28 05:15:08,221] [INFO] Task started: fastANI
[2023-06-28 05:15:08,221] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc3cfe27-0d1d-4421-971f-82ddab35a745/GCA_017620175.1_ASM1762017v1_genomic.fna.gz --refList GCA_017620175.1_ASM1762017v1_genomic.fna/target_genomes.txt --output GCA_017620175.1_ASM1762017v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 05:15:15,377] [INFO] Task succeeded: fastANI
[2023-06-28 05:15:15,378] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0147e1c9-b488-44a0-a59b-f936b29f6ff7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 05:15:15,378] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0147e1c9-b488-44a0-a59b-f936b29f6ff7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 05:15:15,380] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 05:15:15,380] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 05:15:15,381] [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 05:15:15,383] [INFO] DFAST Taxonomy check result was written to GCA_017620175.1_ASM1762017v1_genomic.fna/tc_result.tsv
[2023-06-28 05:15:15,383] [INFO] ===== Taxonomy check completed =====
[2023-06-28 05:15:15,384] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 05:15:15,384] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0147e1c9-b488-44a0-a59b-f936b29f6ff7/dqc_reference/checkm_data
[2023-06-28 05:15:15,388] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 05:15:15,417] [INFO] Task started: CheckM
[2023-06-28 05:15:15,417] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017620175.1_ASM1762017v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017620175.1_ASM1762017v1_genomic.fna/checkm_input GCA_017620175.1_ASM1762017v1_genomic.fna/checkm_result
[2023-06-28 05:15:36,958] [INFO] Task succeeded: CheckM
[2023-06-28 05:15:36,959] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 05:15:36,980] [INFO] ===== Completeness check finished =====
[2023-06-28 05:15:36,980] [INFO] ===== Start GTDB Search =====
[2023-06-28 05:15:36,980] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017620175.1_ASM1762017v1_genomic.fna/markers.fasta)
[2023-06-28 05:15:36,981] [INFO] Task started: Blastn
[2023-06-28 05:15:36,981] [INFO] Running command: blastn -query GCA_017620175.1_ASM1762017v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0147e1c9-b488-44a0-a59b-f936b29f6ff7/dqc_reference/reference_markers_gtdb.fasta -out GCA_017620175.1_ASM1762017v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 05:15:37,823] [INFO] Task succeeded: Blastn
[2023-06-28 05:15:37,828] [INFO] Selected 10 target genomes.
[2023-06-28 05:15:37,828] [INFO] Target genome list was writen to GCA_017620175.1_ASM1762017v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 05:15:37,849] [INFO] Task started: fastANI
[2023-06-28 05:15:37,849] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc3cfe27-0d1d-4421-971f-82ddab35a745/GCA_017620175.1_ASM1762017v1_genomic.fna.gz --refList GCA_017620175.1_ASM1762017v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017620175.1_ASM1762017v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 05:15:42,390] [INFO] Task succeeded: fastANI
[2023-06-28 05:15:42,399] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 05:15:42,399] [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_016285645.1	s__CAG-177 sp016285645	97.0145	633	706	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-177	95.0	97.57	97.01	0.93	0.90	3	conclusive
GCA_902787025.1	s__CAG-177 sp902787025	80.1807	333	706	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-177	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016288315.1	s__CAG-177 sp016288315	79.6435	324	706	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-177	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017428625.1	s__CAG-177 sp017428625	79.2477	335	706	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-177	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900319455.1	s__CAG-177 sp900319455	78.5523	241	706	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-177	95.0	98.34	97.29	0.87	0.72	5	-
GCA_900770255.1	s__CAG-177 sp900770255	76.867	57	706	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-177	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017428525.1	s__CAG-177 sp017428525	76.6535	97	706	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-177	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017623615.1	s__CAG-177 sp017623615	76.277	53	706	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-177	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 05:15:42,402] [INFO] GTDB search result was written to GCA_017620175.1_ASM1762017v1_genomic.fna/result_gtdb.tsv
[2023-06-28 05:15:42,402] [INFO] ===== GTDB Search completed =====
[2023-06-28 05:15:42,405] [INFO] DFAST_QC result json was written to GCA_017620175.1_ASM1762017v1_genomic.fna/dqc_result.json
[2023-06-28 05:15:42,405] [INFO] DFAST_QC completed!
[2023-06-28 05:15:42,405] [INFO] Total running time: 0h0m42s