[2023-06-28 21:14:40,572] [INFO] DFAST_QC pipeline started.
[2023-06-28 21:14:40,576] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 21:14:40,577] [INFO] DQC Reference Directory: /var/lib/cwl/stg4a2f6769-0bc4-480d-abbf-2218c4c4916a/dqc_reference
[2023-06-28 21:14:42,595] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 21:14:42,596] [INFO] Task started: Prodigal
[2023-06-28 21:14:42,596] [INFO] Running command: gunzip -c /var/lib/cwl/stg51150e95-eb34-4c16-91cc-1037418b19f6/GCA_017517525.1_ASM1751752v1_genomic.fna.gz | prodigal -d GCA_017517525.1_ASM1751752v1_genomic.fna/cds.fna -a GCA_017517525.1_ASM1751752v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 21:14:45,424] [INFO] Task succeeded: Prodigal
[2023-06-28 21:14:45,424] [INFO] Task started: HMMsearch
[2023-06-28 21:14:45,425] [INFO] Running command: hmmsearch --tblout GCA_017517525.1_ASM1751752v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4a2f6769-0bc4-480d-abbf-2218c4c4916a/dqc_reference/reference_markers.hmm GCA_017517525.1_ASM1751752v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 21:14:45,609] [INFO] Task succeeded: HMMsearch
[2023-06-28 21:14:45,610] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg51150e95-eb34-4c16-91cc-1037418b19f6/GCA_017517525.1_ASM1751752v1_genomic.fna.gz]
[2023-06-28 21:14:45,627] [INFO] Query marker FASTA was written to GCA_017517525.1_ASM1751752v1_genomic.fna/markers.fasta
[2023-06-28 21:14:45,627] [INFO] Task started: Blastn
[2023-06-28 21:14:45,627] [INFO] Running command: blastn -query GCA_017517525.1_ASM1751752v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a2f6769-0bc4-480d-abbf-2218c4c4916a/dqc_reference/reference_markers.fasta -out GCA_017517525.1_ASM1751752v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 21:14:46,228] [INFO] Task succeeded: Blastn
[2023-06-28 21:14:46,232] [INFO] Selected 21 target genomes.
[2023-06-28 21:14:46,232] [INFO] Target genome list was writen to GCA_017517525.1_ASM1751752v1_genomic.fna/target_genomes.txt
[2023-06-28 21:14:46,249] [INFO] Task started: fastANI
[2023-06-28 21:14:46,249] [INFO] Running command: fastANI --query /var/lib/cwl/stg51150e95-eb34-4c16-91cc-1037418b19f6/GCA_017517525.1_ASM1751752v1_genomic.fna.gz --refList GCA_017517525.1_ASM1751752v1_genomic.fna/target_genomes.txt --output GCA_017517525.1_ASM1751752v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 21:14:54,672] [INFO] Task succeeded: fastANI
[2023-06-28 21:14:54,673] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4a2f6769-0bc4-480d-abbf-2218c4c4916a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 21:14:54,673] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4a2f6769-0bc4-480d-abbf-2218c4c4916a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 21:14:54,675] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 21:14:54,675] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 21:14:54,675] [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 21:14:54,685] [INFO] DFAST Taxonomy check result was written to GCA_017517525.1_ASM1751752v1_genomic.fna/tc_result.tsv
[2023-06-28 21:14:54,688] [INFO] ===== Taxonomy check completed =====
[2023-06-28 21:14:54,688] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 21:14:54,688] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4a2f6769-0bc4-480d-abbf-2218c4c4916a/dqc_reference/checkm_data
[2023-06-28 21:14:54,692] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 21:14:54,712] [INFO] Task started: CheckM
[2023-06-28 21:14:54,713] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017517525.1_ASM1751752v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017517525.1_ASM1751752v1_genomic.fna/checkm_input GCA_017517525.1_ASM1751752v1_genomic.fna/checkm_result
[2023-06-28 21:15:10,503] [INFO] Task succeeded: CheckM
[2023-06-28 21:15:10,505] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.45%
Contamintation: 0.98%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-28 21:15:10,523] [INFO] ===== Completeness check finished =====
[2023-06-28 21:15:10,524] [INFO] ===== Start GTDB Search =====
[2023-06-28 21:15:10,524] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017517525.1_ASM1751752v1_genomic.fna/markers.fasta)
[2023-06-28 21:15:10,524] [INFO] Task started: Blastn
[2023-06-28 21:15:10,525] [INFO] Running command: blastn -query GCA_017517525.1_ASM1751752v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a2f6769-0bc4-480d-abbf-2218c4c4916a/dqc_reference/reference_markers_gtdb.fasta -out GCA_017517525.1_ASM1751752v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 21:15:11,477] [INFO] Task succeeded: Blastn
[2023-06-28 21:15:11,481] [INFO] Selected 17 target genomes.
[2023-06-28 21:15:11,481] [INFO] Target genome list was writen to GCA_017517525.1_ASM1751752v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 21:15:11,534] [INFO] Task started: fastANI
[2023-06-28 21:15:11,535] [INFO] Running command: fastANI --query /var/lib/cwl/stg51150e95-eb34-4c16-91cc-1037418b19f6/GCA_017517525.1_ASM1751752v1_genomic.fna.gz --refList GCA_017517525.1_ASM1751752v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017517525.1_ASM1751752v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 21:15:16,355] [INFO] Task succeeded: fastANI
[2023-06-28 21:15:16,368] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 21:15:16,369] [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_017503305.1	s__UBA737 sp017503305	96.2174	204	352	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA737	95.0	98.15	98.15	0.76	0.76	2	conclusive
GCA_017516445.1	s__UBA737 sp017516445	80.1681	119	352	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA737	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017403265.1	s__UBA737 sp017403265	80.0097	132	352	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA737	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015066095.1	s__UBA737 sp015066095	79.669	139	352	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA737	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017537195.1	s__UBA737 sp017537195	79.4333	115	352	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA737	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015066165.1	s__UBA737 sp015066165	79.22	116	352	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA737	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900768035.1	s__UBA737 sp900768035	78.888	78	352	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA737	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017622555.1	s__UBA737 sp017622555	78.8682	121	352	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA737	95.0	98.02	98.02	0.83	0.83	2	-
GCA_017549565.1	s__UBA737 sp017549565	78.8129	124	352	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA737	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017623315.1	s__UBA737 sp017623315	78.638	104	352	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA737	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015066445.1	s__UBA737 sp015066445	78.1232	79	352	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA737	95.0	98.29	98.29	0.89	0.89	2	-
GCA_017537365.1	s__UBA737 sp017537365	77.449	70	352	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA737	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017403065.1	s__UBA737 sp017403065	77.2482	64	352	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA737	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017507805.1	s__UBA737 sp017507805	76.5205	58	352	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA737	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 21:15:16,371] [INFO] GTDB search result was written to GCA_017517525.1_ASM1751752v1_genomic.fna/result_gtdb.tsv
[2023-06-28 21:15:16,371] [INFO] ===== GTDB Search completed =====
[2023-06-28 21:15:16,375] [INFO] DFAST_QC result json was written to GCA_017517525.1_ASM1751752v1_genomic.fna/dqc_result.json
[2023-06-28 21:15:16,375] [INFO] DFAST_QC completed!
[2023-06-28 21:15:16,376] [INFO] Total running time: 0h0m36s