[2023-06-28 00:28:24,010] [INFO] DFAST_QC pipeline started.
[2023-06-28 00:28:24,016] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 00:28:24,016] [INFO] DQC Reference Directory: /var/lib/cwl/stga61e8467-e352-420e-bca8-c2746ccc8fa7/dqc_reference
[2023-06-28 00:28:25,421] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 00:28:25,423] [INFO] Task started: Prodigal
[2023-06-28 00:28:25,423] [INFO] Running command: gunzip -c /var/lib/cwl/stg3fb9fc19-1c45-4f3d-a068-fabbd40bff8a/GCA_017520845.1_ASM1752084v1_genomic.fna.gz | prodigal -d GCA_017520845.1_ASM1752084v1_genomic.fna/cds.fna -a GCA_017520845.1_ASM1752084v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 00:28:31,699] [INFO] Task succeeded: Prodigal
[2023-06-28 00:28:31,699] [INFO] Task started: HMMsearch
[2023-06-28 00:28:31,699] [INFO] Running command: hmmsearch --tblout GCA_017520845.1_ASM1752084v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga61e8467-e352-420e-bca8-c2746ccc8fa7/dqc_reference/reference_markers.hmm GCA_017520845.1_ASM1752084v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 00:28:31,948] [INFO] Task succeeded: HMMsearch
[2023-06-28 00:28:31,950] [INFO] Found 6/6 markers.
[2023-06-28 00:28:31,976] [INFO] Query marker FASTA was written to GCA_017520845.1_ASM1752084v1_genomic.fna/markers.fasta
[2023-06-28 00:28:31,977] [INFO] Task started: Blastn
[2023-06-28 00:28:31,977] [INFO] Running command: blastn -query GCA_017520845.1_ASM1752084v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga61e8467-e352-420e-bca8-c2746ccc8fa7/dqc_reference/reference_markers.fasta -out GCA_017520845.1_ASM1752084v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 00:28:32,613] [INFO] Task succeeded: Blastn
[2023-06-28 00:28:32,617] [INFO] Selected 27 target genomes.
[2023-06-28 00:28:32,617] [INFO] Target genome list was writen to GCA_017520845.1_ASM1752084v1_genomic.fna/target_genomes.txt
[2023-06-28 00:28:32,641] [INFO] Task started: fastANI
[2023-06-28 00:28:32,641] [INFO] Running command: fastANI --query /var/lib/cwl/stg3fb9fc19-1c45-4f3d-a068-fabbd40bff8a/GCA_017520845.1_ASM1752084v1_genomic.fna.gz --refList GCA_017520845.1_ASM1752084v1_genomic.fna/target_genomes.txt --output GCA_017520845.1_ASM1752084v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 00:28:50,342] [INFO] Task succeeded: fastANI
[2023-06-28 00:28:50,343] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga61e8467-e352-420e-bca8-c2746ccc8fa7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 00:28:50,343] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga61e8467-e352-420e-bca8-c2746ccc8fa7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 00:28:50,346] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 00:28:50,346] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 00:28:50,346] [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 00:28:50,350] [INFO] DFAST Taxonomy check result was written to GCA_017520845.1_ASM1752084v1_genomic.fna/tc_result.tsv
[2023-06-28 00:28:50,351] [INFO] ===== Taxonomy check completed =====
[2023-06-28 00:28:50,351] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 00:28:50,351] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga61e8467-e352-420e-bca8-c2746ccc8fa7/dqc_reference/checkm_data
[2023-06-28 00:28:50,354] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 00:28:50,386] [INFO] Task started: CheckM
[2023-06-28 00:28:50,386] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017520845.1_ASM1752084v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017520845.1_ASM1752084v1_genomic.fna/checkm_input GCA_017520845.1_ASM1752084v1_genomic.fna/checkm_result
[2023-06-28 00:29:15,659] [INFO] Task succeeded: CheckM
[2023-06-28 00:29:15,661] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.45%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 00:29:15,688] [INFO] ===== Completeness check finished =====
[2023-06-28 00:29:15,688] [INFO] ===== Start GTDB Search =====
[2023-06-28 00:29:15,689] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017520845.1_ASM1752084v1_genomic.fna/markers.fasta)
[2023-06-28 00:29:15,689] [INFO] Task started: Blastn
[2023-06-28 00:29:15,689] [INFO] Running command: blastn -query GCA_017520845.1_ASM1752084v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga61e8467-e352-420e-bca8-c2746ccc8fa7/dqc_reference/reference_markers_gtdb.fasta -out GCA_017520845.1_ASM1752084v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 00:29:16,637] [INFO] Task succeeded: Blastn
[2023-06-28 00:29:16,642] [INFO] Selected 17 target genomes.
[2023-06-28 00:29:16,643] [INFO] Target genome list was writen to GCA_017520845.1_ASM1752084v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 00:29:16,649] [INFO] Task started: fastANI
[2023-06-28 00:29:16,649] [INFO] Running command: fastANI --query /var/lib/cwl/stg3fb9fc19-1c45-4f3d-a068-fabbd40bff8a/GCA_017520845.1_ASM1752084v1_genomic.fna.gz --refList GCA_017520845.1_ASM1752084v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017520845.1_ASM1752084v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 00:29:24,265] [INFO] Task succeeded: fastANI
[2023-06-28 00:29:24,285] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 00:29:24,285] [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_017520845.1	s__UBA1067 sp017520845	100.0	853	858	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1067	95.0	97.62	97.62	0.84	0.84	2	conclusive
GCA_017648225.1	s__UBA1067 sp017648225	92.3046	371	858	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1067	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017631385.1	s__UBA1067 sp017631385	80.5843	238	858	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1067	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017508315.1	s__UBA1067 sp017508315	79.8453	126	858	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1067	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017406465.1	s__UBA1067 sp017406465	78.9895	144	858	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1067	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017463935.1	s__UBA1067 sp017463935	78.6254	124	858	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1067	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902780865.1	s__UBA1067 sp902780865	78.3297	136	858	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1067	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017628165.1	s__UBA1067 sp017628165	78.2679	116	858	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1067	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902761275.1	s__UBA1067 sp902761275	77.9731	129	858	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1067	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017432385.1	s__UBA1067 sp017432385	77.9051	100	858	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1067	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900320855.1	s__UBA1067 sp900320855	77.8804	112	858	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1067	95.0	100.00	100.00	0.99	0.99	2	-
GCA_902799385.1	s__UBA1067 sp902799385	77.8439	136	858	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1067	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002395905.1	s__UBA1067 sp002395905	77.4695	98	858	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1067	95.0	97.54	97.54	0.77	0.77	2	-
GCA_017507065.1	s__UBA1067 sp017507065	77.3788	59	858	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1067	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017412325.1	s__UBA1067 sp017412325	77.2896	59	858	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1067	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017650345.1	s__UBA1067 sp017650345	77.256	84	858	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1067	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017418445.1	s__UBA1067 sp017418445	77.176	68	858	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1067	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 00:29:24,287] [INFO] GTDB search result was written to GCA_017520845.1_ASM1752084v1_genomic.fna/result_gtdb.tsv
[2023-06-28 00:29:24,288] [INFO] ===== GTDB Search completed =====
[2023-06-28 00:29:24,291] [INFO] DFAST_QC result json was written to GCA_017520845.1_ASM1752084v1_genomic.fna/dqc_result.json
[2023-06-28 00:29:24,292] [INFO] DFAST_QC completed!
[2023-06-28 00:29:24,292] [INFO] Total running time: 0h1m0s