[2023-06-27 07:56:37,421] [INFO] DFAST_QC pipeline started.
[2023-06-27 07:56:37,428] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 07:56:37,429] [INFO] DQC Reference Directory: /var/lib/cwl/stg8ce52a62-7424-4ca6-b2a7-5d21be94b875/dqc_reference
[2023-06-27 07:56:38,853] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 07:56:38,854] [INFO] Task started: Prodigal
[2023-06-27 07:56:38,854] [INFO] Running command: gunzip -c /var/lib/cwl/stge4456914-6bd1-4c21-8d58-7d13a9fb9747/GCA_002310135.1_ASM231013v1_genomic.fna.gz | prodigal -d GCA_002310135.1_ASM231013v1_genomic.fna/cds.fna -a GCA_002310135.1_ASM231013v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 07:56:40,810] [INFO] Task succeeded: Prodigal
[2023-06-27 07:56:40,811] [INFO] Task started: HMMsearch
[2023-06-27 07:56:40,811] [INFO] Running command: hmmsearch --tblout GCA_002310135.1_ASM231013v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8ce52a62-7424-4ca6-b2a7-5d21be94b875/dqc_reference/reference_markers.hmm GCA_002310135.1_ASM231013v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 07:56:41,081] [INFO] Task succeeded: HMMsearch
[2023-06-27 07:56:41,083] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge4456914-6bd1-4c21-8d58-7d13a9fb9747/GCA_002310135.1_ASM231013v1_genomic.fna.gz]
[2023-06-27 07:56:41,101] [INFO] Query marker FASTA was written to GCA_002310135.1_ASM231013v1_genomic.fna/markers.fasta
[2023-06-27 07:56:41,101] [INFO] Task started: Blastn
[2023-06-27 07:56:41,101] [INFO] Running command: blastn -query GCA_002310135.1_ASM231013v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ce52a62-7424-4ca6-b2a7-5d21be94b875/dqc_reference/reference_markers.fasta -out GCA_002310135.1_ASM231013v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 07:56:41,687] [INFO] Task succeeded: Blastn
[2023-06-27 07:56:41,709] [INFO] Selected 23 target genomes.
[2023-06-27 07:56:41,710] [INFO] Target genome list was writen to GCA_002310135.1_ASM231013v1_genomic.fna/target_genomes.txt
[2023-06-27 07:56:41,716] [INFO] Task started: fastANI
[2023-06-27 07:56:41,716] [INFO] Running command: fastANI --query /var/lib/cwl/stge4456914-6bd1-4c21-8d58-7d13a9fb9747/GCA_002310135.1_ASM231013v1_genomic.fna.gz --refList GCA_002310135.1_ASM231013v1_genomic.fna/target_genomes.txt --output GCA_002310135.1_ASM231013v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 07:56:51,367] [INFO] Task succeeded: fastANI
[2023-06-27 07:56:51,368] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8ce52a62-7424-4ca6-b2a7-5d21be94b875/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 07:56:51,368] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8ce52a62-7424-4ca6-b2a7-5d21be94b875/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 07:56:51,384] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 07:56:51,384] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 07:56:51,384] [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
--------------------------------------------------------------------------------
[2023-06-27 07:56:51,386] [INFO] DFAST Taxonomy check result was written to GCA_002310135.1_ASM231013v1_genomic.fna/tc_result.tsv
[2023-06-27 07:56:51,387] [INFO] ===== Taxonomy check completed =====
[2023-06-27 07:56:51,387] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 07:56:51,387] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8ce52a62-7424-4ca6-b2a7-5d21be94b875/dqc_reference/checkm_data
[2023-06-27 07:56:51,390] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 07:56:51,404] [INFO] Task started: CheckM
[2023-06-27 07:56:51,405] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002310135.1_ASM231013v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002310135.1_ASM231013v1_genomic.fna/checkm_input GCA_002310135.1_ASM231013v1_genomic.fna/checkm_result
[2023-06-27 07:57:06,045] [INFO] Task succeeded: CheckM
[2023-06-27 07:57:06,047] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 07:57:06,068] [INFO] ===== Completeness check finished =====
[2023-06-27 07:57:06,069] [INFO] ===== Start GTDB Search =====
[2023-06-27 07:57:06,069] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002310135.1_ASM231013v1_genomic.fna/markers.fasta)
[2023-06-27 07:57:06,069] [INFO] Task started: Blastn
[2023-06-27 07:57:06,070] [INFO] Running command: blastn -query GCA_002310135.1_ASM231013v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ce52a62-7424-4ca6-b2a7-5d21be94b875/dqc_reference/reference_markers_gtdb.fasta -out GCA_002310135.1_ASM231013v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 07:57:06,846] [INFO] Task succeeded: Blastn
[2023-06-27 07:57:06,854] [INFO] Selected 22 target genomes.
[2023-06-27 07:57:06,854] [INFO] Target genome list was writen to GCA_002310135.1_ASM231013v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 07:57:06,867] [INFO] Task started: fastANI
[2023-06-27 07:57:06,868] [INFO] Running command: fastANI --query /var/lib/cwl/stge4456914-6bd1-4c21-8d58-7d13a9fb9747/GCA_002310135.1_ASM231013v1_genomic.fna.gz --refList GCA_002310135.1_ASM231013v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002310135.1_ASM231013v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 07:57:12,107] [INFO] Task succeeded: fastANI
[2023-06-27 07:57:12,113] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 07:57:12,113] [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_002310135.1	s__UBA1188 sp002310135	100.0	373	373	d__Bacteria;p__Firmicutes;c__Bacilli;o__Izemoplasmatales;f__UBA1188;g__UBA1188	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017541975.1	s__UBA1188 sp017541975	78.3021	69	373	d__Bacteria;p__Firmicutes;c__Bacilli;o__Izemoplasmatales;f__UBA1188;g__UBA1188	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017960565.1	s__UBA1188 sp017960565	77.9553	80	373	d__Bacteria;p__Firmicutes;c__Bacilli;o__Izemoplasmatales;f__UBA1188;g__UBA1188	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900318975.1	s__UBA1188 sp900318975	77.8513	61	373	d__Bacteria;p__Firmicutes;c__Bacilli;o__Izemoplasmatales;f__UBA1188;g__UBA1188	95.0	100.00	100.00	0.99	0.99	2	-
GCA_905235635.1	s__UBA1188 sp905235635	76.3463	50	373	d__Bacteria;p__Firmicutes;c__Bacilli;o__Izemoplasmatales;f__UBA1188;g__UBA1188	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 07:57:12,115] [INFO] GTDB search result was written to GCA_002310135.1_ASM231013v1_genomic.fna/result_gtdb.tsv
[2023-06-27 07:57:12,115] [INFO] ===== GTDB Search completed =====
[2023-06-27 07:57:12,125] [INFO] DFAST_QC result json was written to GCA_002310135.1_ASM231013v1_genomic.fna/dqc_result.json
[2023-06-27 07:57:12,126] [INFO] DFAST_QC completed!
[2023-06-27 07:57:12,126] [INFO] Total running time: 0h0m35s