[2023-06-17 06:00:23,336] [INFO] DFAST_QC pipeline started.
[2023-06-17 06:00:23,341] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 06:00:23,341] [INFO] DQC Reference Directory: /var/lib/cwl/stg1d72a56d-7b94-42f8-89c5-4298dca640a8/dqc_reference
[2023-06-17 06:00:24,702] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 06:00:24,703] [INFO] Task started: Prodigal
[2023-06-17 06:00:24,704] [INFO] Running command: gunzip -c /var/lib/cwl/stg5ad92b11-80a1-4a1b-b218-7320c8b4fbf1/GCA_028705075.1_ASM2870507v1_genomic.fna.gz | prodigal -d GCA_028705075.1_ASM2870507v1_genomic.fna/cds.fna -a GCA_028705075.1_ASM2870507v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 06:00:36,713] [INFO] Task succeeded: Prodigal
[2023-06-17 06:00:36,714] [INFO] Task started: HMMsearch
[2023-06-17 06:00:36,714] [INFO] Running command: hmmsearch --tblout GCA_028705075.1_ASM2870507v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1d72a56d-7b94-42f8-89c5-4298dca640a8/dqc_reference/reference_markers.hmm GCA_028705075.1_ASM2870507v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 06:00:36,951] [INFO] Task succeeded: HMMsearch
[2023-06-17 06:00:36,953] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5ad92b11-80a1-4a1b-b218-7320c8b4fbf1/GCA_028705075.1_ASM2870507v1_genomic.fna.gz]
[2023-06-17 06:00:36,984] [INFO] Query marker FASTA was written to GCA_028705075.1_ASM2870507v1_genomic.fna/markers.fasta
[2023-06-17 06:00:36,984] [INFO] Task started: Blastn
[2023-06-17 06:00:36,984] [INFO] Running command: blastn -query GCA_028705075.1_ASM2870507v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d72a56d-7b94-42f8-89c5-4298dca640a8/dqc_reference/reference_markers.fasta -out GCA_028705075.1_ASM2870507v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 06:00:37,623] [INFO] Task succeeded: Blastn
[2023-06-17 06:00:37,628] [INFO] Selected 25 target genomes.
[2023-06-17 06:00:37,629] [INFO] Target genome list was writen to GCA_028705075.1_ASM2870507v1_genomic.fna/target_genomes.txt
[2023-06-17 06:00:37,640] [INFO] Task started: fastANI
[2023-06-17 06:00:37,640] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ad92b11-80a1-4a1b-b218-7320c8b4fbf1/GCA_028705075.1_ASM2870507v1_genomic.fna.gz --refList GCA_028705075.1_ASM2870507v1_genomic.fna/target_genomes.txt --output GCA_028705075.1_ASM2870507v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 06:00:55,202] [INFO] Task succeeded: fastANI
[2023-06-17 06:00:55,203] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1d72a56d-7b94-42f8-89c5-4298dca640a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 06:00:55,203] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1d72a56d-7b94-42f8-89c5-4298dca640a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 06:00:55,205] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 06:00:55,205] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 06:00:55,205] [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
--------------------------------------------------------------------------------
[2023-06-17 06:00:55,208] [INFO] DFAST Taxonomy check result was written to GCA_028705075.1_ASM2870507v1_genomic.fna/tc_result.tsv
[2023-06-17 06:00:55,209] [INFO] ===== Taxonomy check completed =====
[2023-06-17 06:00:55,209] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 06:00:55,210] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1d72a56d-7b94-42f8-89c5-4298dca640a8/dqc_reference/checkm_data
[2023-06-17 06:00:55,214] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 06:00:55,242] [INFO] Task started: CheckM
[2023-06-17 06:00:55,242] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028705075.1_ASM2870507v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028705075.1_ASM2870507v1_genomic.fna/checkm_input GCA_028705075.1_ASM2870507v1_genomic.fna/checkm_result
[2023-06-17 06:01:34,240] [INFO] Task succeeded: CheckM
[2023-06-17 06:01:34,242] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 6.02%
Strain heterogeneity: 80.00%
--------------------------------------------------------------------------------
[2023-06-17 06:01:34,267] [INFO] ===== Completeness check finished =====
[2023-06-17 06:01:34,268] [INFO] ===== Start GTDB Search =====
[2023-06-17 06:01:34,268] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028705075.1_ASM2870507v1_genomic.fna/markers.fasta)
[2023-06-17 06:01:34,268] [INFO] Task started: Blastn
[2023-06-17 06:01:34,268] [INFO] Running command: blastn -query GCA_028705075.1_ASM2870507v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d72a56d-7b94-42f8-89c5-4298dca640a8/dqc_reference/reference_markers_gtdb.fasta -out GCA_028705075.1_ASM2870507v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 06:01:35,213] [INFO] Task succeeded: Blastn
[2023-06-17 06:01:35,219] [INFO] Selected 22 target genomes.
[2023-06-17 06:01:35,219] [INFO] Target genome list was writen to GCA_028705075.1_ASM2870507v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 06:01:35,243] [INFO] Task started: fastANI
[2023-06-17 06:01:35,243] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ad92b11-80a1-4a1b-b218-7320c8b4fbf1/GCA_028705075.1_ASM2870507v1_genomic.fna.gz --refList GCA_028705075.1_ASM2870507v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028705075.1_ASM2870507v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 06:01:46,733] [INFO] Task succeeded: fastANI
[2023-06-17 06:01:46,739] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-17 06:01:46,739] [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_012511135.1	s__UBA1402 sp012511135	85.7439	310	637	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA1402;g__UBA1402	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002305085.1	s__UBA1402 sp002305085	83.3536	441	637	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA1402;g__UBA1402	95.0	97.52	97.31	0.93	0.88	11	-
--------------------------------------------------------------------------------
[2023-06-17 06:01:46,741] [INFO] GTDB search result was written to GCA_028705075.1_ASM2870507v1_genomic.fna/result_gtdb.tsv
[2023-06-17 06:01:46,741] [INFO] ===== GTDB Search completed =====
[2023-06-17 06:01:46,744] [INFO] DFAST_QC result json was written to GCA_028705075.1_ASM2870507v1_genomic.fna/dqc_result.json
[2023-06-17 06:01:46,744] [INFO] DFAST_QC completed!
[2023-06-17 06:01:46,744] [INFO] Total running time: 0h1m23s