[2023-06-30 13:54:53,823] [INFO] DFAST_QC pipeline started.
[2023-06-30 13:54:53,830] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 13:54:53,830] [INFO] DQC Reference Directory: /var/lib/cwl/stg60fe8152-be22-4ada-8912-35e4b186b72e/dqc_reference
[2023-06-30 13:54:56,175] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 13:54:56,176] [INFO] Task started: Prodigal
[2023-06-30 13:54:56,176] [INFO] Running command: gunzip -c /var/lib/cwl/stge2972ac7-44b7-4ce1-a135-699de5ff4cf2/GCA_024960695.1_ASM2496069v1_genomic.fna.gz | prodigal -d GCA_024960695.1_ASM2496069v1_genomic.fna/cds.fna -a GCA_024960695.1_ASM2496069v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 13:55:03,476] [INFO] Task succeeded: Prodigal
[2023-06-30 13:55:03,477] [INFO] Task started: HMMsearch
[2023-06-30 13:55:03,477] [INFO] Running command: hmmsearch --tblout GCA_024960695.1_ASM2496069v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg60fe8152-be22-4ada-8912-35e4b186b72e/dqc_reference/reference_markers.hmm GCA_024960695.1_ASM2496069v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 13:55:03,661] [INFO] Task succeeded: HMMsearch
[2023-06-30 13:55:03,662] [WARNING] Found 2/6 markers. [/var/lib/cwl/stge2972ac7-44b7-4ce1-a135-699de5ff4cf2/GCA_024960695.1_ASM2496069v1_genomic.fna.gz]
[2023-06-30 13:55:03,684] [INFO] Query marker FASTA was written to GCA_024960695.1_ASM2496069v1_genomic.fna/markers.fasta
[2023-06-30 13:55:03,684] [INFO] Task started: Blastn
[2023-06-30 13:55:03,684] [INFO] Running command: blastn -query GCA_024960695.1_ASM2496069v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg60fe8152-be22-4ada-8912-35e4b186b72e/dqc_reference/reference_markers.fasta -out GCA_024960695.1_ASM2496069v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 13:55:04,169] [INFO] Task succeeded: Blastn
[2023-06-30 13:55:04,174] [INFO] Selected 15 target genomes.
[2023-06-30 13:55:04,175] [INFO] Target genome list was writen to GCA_024960695.1_ASM2496069v1_genomic.fna/target_genomes.txt
[2023-06-30 13:55:04,178] [INFO] Task started: fastANI
[2023-06-30 13:55:04,178] [INFO] Running command: fastANI --query /var/lib/cwl/stge2972ac7-44b7-4ce1-a135-699de5ff4cf2/GCA_024960695.1_ASM2496069v1_genomic.fna.gz --refList GCA_024960695.1_ASM2496069v1_genomic.fna/target_genomes.txt --output GCA_024960695.1_ASM2496069v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 13:55:16,226] [INFO] Task succeeded: fastANI
[2023-06-30 13:55:16,226] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg60fe8152-be22-4ada-8912-35e4b186b72e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 13:55:16,227] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg60fe8152-be22-4ada-8912-35e4b186b72e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 13:55:16,229] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 13:55:16,229] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 13:55:16,229] [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
--------------------------------------------------------------------------------
[2023-06-30 13:55:16,232] [INFO] DFAST Taxonomy check result was written to GCA_024960695.1_ASM2496069v1_genomic.fna/tc_result.tsv
[2023-06-30 13:55:16,233] [INFO] ===== Taxonomy check completed =====
[2023-06-30 13:55:16,233] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 13:55:16,233] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg60fe8152-be22-4ada-8912-35e4b186b72e/dqc_reference/checkm_data
[2023-06-30 13:55:16,237] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 13:55:16,256] [INFO] Task started: CheckM
[2023-06-30 13:55:16,256] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024960695.1_ASM2496069v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024960695.1_ASM2496069v1_genomic.fna/checkm_input GCA_024960695.1_ASM2496069v1_genomic.fna/checkm_result
[2023-06-30 13:55:41,490] [INFO] Task succeeded: CheckM
[2023-06-30 13:55:41,491] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 59.43%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 13:55:41,512] [INFO] ===== Completeness check finished =====
[2023-06-30 13:55:41,512] [INFO] ===== Start GTDB Search =====
[2023-06-30 13:55:41,512] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024960695.1_ASM2496069v1_genomic.fna/markers.fasta)
[2023-06-30 13:55:41,513] [INFO] Task started: Blastn
[2023-06-30 13:55:41,513] [INFO] Running command: blastn -query GCA_024960695.1_ASM2496069v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg60fe8152-be22-4ada-8912-35e4b186b72e/dqc_reference/reference_markers_gtdb.fasta -out GCA_024960695.1_ASM2496069v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 13:55:42,045] [INFO] Task succeeded: Blastn
[2023-06-30 13:55:42,049] [INFO] Selected 8 target genomes.
[2023-06-30 13:55:42,049] [INFO] Target genome list was writen to GCA_024960695.1_ASM2496069v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 13:55:42,054] [INFO] Task started: fastANI
[2023-06-30 13:55:42,055] [INFO] Running command: fastANI --query /var/lib/cwl/stge2972ac7-44b7-4ce1-a135-699de5ff4cf2/GCA_024960695.1_ASM2496069v1_genomic.fna.gz --refList GCA_024960695.1_ASM2496069v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024960695.1_ASM2496069v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 13:55:44,810] [INFO] Task succeeded: fastANI
[2023-06-30 13:55:44,826] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 13:55:44,827] [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_002717365.1	s__UBA9410 sp002717365	90.6403	112	153	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016845305.1	s__UBA9410 sp016845305	80.9048	114	153	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014237715.1	s__UBA9410 sp014237715	80.3466	99	153	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	98.52	98.52	0.97	0.97	2	-
GCA_014239855.1	s__UBA9410 sp014239855	80.2913	99	153	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012961035.1	s__UBA9410 sp012961035	80.1961	100	153	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	99.67	99.67	0.93	0.93	2	-
GCA_003541675.1	s__UBA9410 sp003541675	79.7519	79	153	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014240365.1	s__UBA9410 sp014240365	79.4838	91	153	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	98.11	98.07	0.86	0.84	5	-
GCA_002346745.1	s__S20-B6 sp002346745	78.7922	67	153	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__S20-B6	95.0	97.72	96.97	0.85	0.81	8	-
--------------------------------------------------------------------------------
[2023-06-30 13:55:44,829] [INFO] GTDB search result was written to GCA_024960695.1_ASM2496069v1_genomic.fna/result_gtdb.tsv
[2023-06-30 13:55:44,830] [INFO] ===== GTDB Search completed =====
[2023-06-30 13:55:44,834] [INFO] DFAST_QC result json was written to GCA_024960695.1_ASM2496069v1_genomic.fna/dqc_result.json
[2023-06-30 13:55:44,834] [INFO] DFAST_QC completed!
[2023-06-30 13:55:44,835] [INFO] Total running time: 0h0m51s