[2023-06-30 07:30:41,589] [INFO] DFAST_QC pipeline started.
[2023-06-30 07:30:41,596] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 07:30:41,596] [INFO] DQC Reference Directory: /var/lib/cwl/stg07224b65-fdfb-4fb8-ac5a-3bfc9243bacf/dqc_reference
[2023-06-30 07:30:42,952] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 07:30:42,953] [INFO] Task started: Prodigal
[2023-06-30 07:30:42,953] [INFO] Running command: gunzip -c /var/lib/cwl/stg646a8dc5-d9d8-4452-be18-0b913443b89e/GCA_007124635.1_ASM712463v1_genomic.fna.gz | prodigal -d GCA_007124635.1_ASM712463v1_genomic.fna/cds.fna -a GCA_007124635.1_ASM712463v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 07:31:01,144] [INFO] Task succeeded: Prodigal
[2023-06-30 07:31:01,145] [INFO] Task started: HMMsearch
[2023-06-30 07:31:01,145] [INFO] Running command: hmmsearch --tblout GCA_007124635.1_ASM712463v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg07224b65-fdfb-4fb8-ac5a-3bfc9243bacf/dqc_reference/reference_markers.hmm GCA_007124635.1_ASM712463v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 07:31:01,413] [INFO] Task succeeded: HMMsearch
[2023-06-30 07:31:01,414] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg646a8dc5-d9d8-4452-be18-0b913443b89e/GCA_007124635.1_ASM712463v1_genomic.fna.gz]
[2023-06-30 07:31:01,448] [INFO] Query marker FASTA was written to GCA_007124635.1_ASM712463v1_genomic.fna/markers.fasta
[2023-06-30 07:31:01,449] [INFO] Task started: Blastn
[2023-06-30 07:31:01,449] [INFO] Running command: blastn -query GCA_007124635.1_ASM712463v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg07224b65-fdfb-4fb8-ac5a-3bfc9243bacf/dqc_reference/reference_markers.fasta -out GCA_007124635.1_ASM712463v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 07:31:02,051] [INFO] Task succeeded: Blastn
[2023-06-30 07:31:02,056] [INFO] Selected 18 target genomes.
[2023-06-30 07:31:02,057] [INFO] Target genome list was writen to GCA_007124635.1_ASM712463v1_genomic.fna/target_genomes.txt
[2023-06-30 07:31:02,061] [INFO] Task started: fastANI
[2023-06-30 07:31:02,062] [INFO] Running command: fastANI --query /var/lib/cwl/stg646a8dc5-d9d8-4452-be18-0b913443b89e/GCA_007124635.1_ASM712463v1_genomic.fna.gz --refList GCA_007124635.1_ASM712463v1_genomic.fna/target_genomes.txt --output GCA_007124635.1_ASM712463v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 07:31:14,841] [INFO] Task succeeded: fastANI
[2023-06-30 07:31:14,841] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg07224b65-fdfb-4fb8-ac5a-3bfc9243bacf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 07:31:14,842] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg07224b65-fdfb-4fb8-ac5a-3bfc9243bacf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 07:31:14,844] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 07:31:14,844] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 07:31:14,844] [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 07:31:14,846] [INFO] DFAST Taxonomy check result was written to GCA_007124635.1_ASM712463v1_genomic.fna/tc_result.tsv
[2023-06-30 07:31:14,846] [INFO] ===== Taxonomy check completed =====
[2023-06-30 07:31:14,846] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 07:31:14,847] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg07224b65-fdfb-4fb8-ac5a-3bfc9243bacf/dqc_reference/checkm_data
[2023-06-30 07:31:14,849] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 07:31:14,895] [INFO] Task started: CheckM
[2023-06-30 07:31:14,895] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_007124635.1_ASM712463v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_007124635.1_ASM712463v1_genomic.fna/checkm_input GCA_007124635.1_ASM712463v1_genomic.fna/checkm_result
[2023-06-30 07:32:10,449] [INFO] Task succeeded: CheckM
[2023-06-30 07:32:10,451] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 07:32:10,473] [INFO] ===== Completeness check finished =====
[2023-06-30 07:32:10,474] [INFO] ===== Start GTDB Search =====
[2023-06-30 07:32:10,474] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_007124635.1_ASM712463v1_genomic.fna/markers.fasta)
[2023-06-30 07:32:10,474] [INFO] Task started: Blastn
[2023-06-30 07:32:10,474] [INFO] Running command: blastn -query GCA_007124635.1_ASM712463v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg07224b65-fdfb-4fb8-ac5a-3bfc9243bacf/dqc_reference/reference_markers_gtdb.fasta -out GCA_007124635.1_ASM712463v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 07:32:11,292] [INFO] Task succeeded: Blastn
[2023-06-30 07:32:11,297] [INFO] Selected 16 target genomes.
[2023-06-30 07:32:11,297] [INFO] Target genome list was writen to GCA_007124635.1_ASM712463v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 07:32:11,307] [INFO] Task started: fastANI
[2023-06-30 07:32:11,308] [INFO] Running command: fastANI --query /var/lib/cwl/stg646a8dc5-d9d8-4452-be18-0b913443b89e/GCA_007124635.1_ASM712463v1_genomic.fna.gz --refList GCA_007124635.1_ASM712463v1_genomic.fna/target_genomes_gtdb.txt --output GCA_007124635.1_ASM712463v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 07:32:21,277] [INFO] Task succeeded: fastANI
[2023-06-30 07:32:21,285] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 07:32:21,286] [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_007118695.1	s__SKRC01 sp007118695	99.5407	983	1112	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__SKRC01	95.0	99.52	99.50	0.88	0.87	3	conclusive
GCA_007132385.1	s__SLOU01 sp007132385	76.9245	78	1112	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__SLOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007123785.1	s__UBA2664 sp007123785	76.8718	59	1112	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__UBA2664	95.0	98.99	98.99	0.79	0.79	2	-
--------------------------------------------------------------------------------
[2023-06-30 07:32:21,288] [INFO] GTDB search result was written to GCA_007124635.1_ASM712463v1_genomic.fna/result_gtdb.tsv
[2023-06-30 07:32:21,289] [INFO] ===== GTDB Search completed =====
[2023-06-30 07:32:21,291] [INFO] DFAST_QC result json was written to GCA_007124635.1_ASM712463v1_genomic.fna/dqc_result.json
[2023-06-30 07:32:21,292] [INFO] DFAST_QC completed!
[2023-06-30 07:32:21,292] [INFO] Total running time: 0h1m40s