[2023-06-29 09:55:27,289] [INFO] DFAST_QC pipeline started.
[2023-06-29 09:55:27,290] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 09:55:27,291] [INFO] DQC Reference Directory: /var/lib/cwl/stg8c7fa4f5-f892-4f9f-ae31-fbf77284b3d3/dqc_reference
[2023-06-29 09:55:29,300] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 09:55:29,301] [INFO] Task started: Prodigal
[2023-06-29 09:55:29,301] [INFO] Running command: gunzip -c /var/lib/cwl/stg00e9323c-c299-44ef-9abf-42d4167d2b91/GCA_012960105.1_ASM1296010v1_genomic.fna.gz | prodigal -d GCA_012960105.1_ASM1296010v1_genomic.fna/cds.fna -a GCA_012960105.1_ASM1296010v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 09:55:34,185] [INFO] Task succeeded: Prodigal
[2023-06-29 09:55:34,185] [INFO] Task started: HMMsearch
[2023-06-29 09:55:34,185] [INFO] Running command: hmmsearch --tblout GCA_012960105.1_ASM1296010v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8c7fa4f5-f892-4f9f-ae31-fbf77284b3d3/dqc_reference/reference_markers.hmm GCA_012960105.1_ASM1296010v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 09:55:34,401] [INFO] Task succeeded: HMMsearch
[2023-06-29 09:55:34,402] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg00e9323c-c299-44ef-9abf-42d4167d2b91/GCA_012960105.1_ASM1296010v1_genomic.fna.gz]
[2023-06-29 09:55:34,425] [INFO] Query marker FASTA was written to GCA_012960105.1_ASM1296010v1_genomic.fna/markers.fasta
[2023-06-29 09:55:34,425] [INFO] Task started: Blastn
[2023-06-29 09:55:34,425] [INFO] Running command: blastn -query GCA_012960105.1_ASM1296010v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c7fa4f5-f892-4f9f-ae31-fbf77284b3d3/dqc_reference/reference_markers.fasta -out GCA_012960105.1_ASM1296010v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 09:55:35,015] [INFO] Task succeeded: Blastn
[2023-06-29 09:55:35,018] [INFO] Selected 27 target genomes.
[2023-06-29 09:55:35,019] [INFO] Target genome list was writen to GCA_012960105.1_ASM1296010v1_genomic.fna/target_genomes.txt
[2023-06-29 09:55:35,045] [INFO] Task started: fastANI
[2023-06-29 09:55:35,045] [INFO] Running command: fastANI --query /var/lib/cwl/stg00e9323c-c299-44ef-9abf-42d4167d2b91/GCA_012960105.1_ASM1296010v1_genomic.fna.gz --refList GCA_012960105.1_ASM1296010v1_genomic.fna/target_genomes.txt --output GCA_012960105.1_ASM1296010v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 09:55:49,615] [INFO] Task succeeded: fastANI
[2023-06-29 09:55:49,616] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8c7fa4f5-f892-4f9f-ae31-fbf77284b3d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 09:55:49,616] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8c7fa4f5-f892-4f9f-ae31-fbf77284b3d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 09:55:49,618] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 09:55:49,618] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 09:55:49,618] [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
--------------------------------------------------------------------------------
[2023-06-29 09:55:49,620] [INFO] DFAST Taxonomy check result was written to GCA_012960105.1_ASM1296010v1_genomic.fna/tc_result.tsv
[2023-06-29 09:55:49,620] [INFO] ===== Taxonomy check completed =====
[2023-06-29 09:55:49,620] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 09:55:49,621] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8c7fa4f5-f892-4f9f-ae31-fbf77284b3d3/dqc_reference/checkm_data
[2023-06-29 09:55:49,623] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 09:55:49,649] [INFO] Task started: CheckM
[2023-06-29 09:55:49,650] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_012960105.1_ASM1296010v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_012960105.1_ASM1296010v1_genomic.fna/checkm_input GCA_012960105.1_ASM1296010v1_genomic.fna/checkm_result
[2023-06-29 09:56:10,594] [INFO] Task succeeded: CheckM
[2023-06-29 09:56:10,595] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 09:56:10,611] [INFO] ===== Completeness check finished =====
[2023-06-29 09:56:10,611] [INFO] ===== Start GTDB Search =====
[2023-06-29 09:56:10,612] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_012960105.1_ASM1296010v1_genomic.fna/markers.fasta)
[2023-06-29 09:56:10,612] [INFO] Task started: Blastn
[2023-06-29 09:56:10,612] [INFO] Running command: blastn -query GCA_012960105.1_ASM1296010v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c7fa4f5-f892-4f9f-ae31-fbf77284b3d3/dqc_reference/reference_markers_gtdb.fasta -out GCA_012960105.1_ASM1296010v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 09:56:11,449] [INFO] Task succeeded: Blastn
[2023-06-29 09:56:11,453] [INFO] Selected 17 target genomes.
[2023-06-29 09:56:11,453] [INFO] Target genome list was writen to GCA_012960105.1_ASM1296010v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 09:56:11,464] [INFO] Task started: fastANI
[2023-06-29 09:56:11,464] [INFO] Running command: fastANI --query /var/lib/cwl/stg00e9323c-c299-44ef-9abf-42d4167d2b91/GCA_012960105.1_ASM1296010v1_genomic.fna.gz --refList GCA_012960105.1_ASM1296010v1_genomic.fna/target_genomes_gtdb.txt --output GCA_012960105.1_ASM1296010v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 09:56:18,868] [INFO] Task succeeded: fastANI
[2023-06-29 09:56:18,873] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 09:56:18,873] [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_012960105.1	s__UBA7359 sp012960105	100.0	781	784	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA4486;f__UBA4486;g__UBA7359	95.0	99.96	99.96	0.93	0.93	2	conclusive
GCA_013112535.1	s__UBA7359 sp013112535	78.5062	319	784	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA4486;f__UBA4486;g__UBA7359	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002292815.1	s__UBA7359 sp002292815	77.3825	174	784	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA4486;f__UBA4486;g__UBA7359	95.0	99.97	99.97	0.97	0.97	2	-
GCA_002470825.1	s__UBA7359 sp002470825	76.8691	92	784	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA4486;f__UBA4486;g__UBA7359	95.0	99.91	99.91	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2023-06-29 09:56:18,875] [INFO] GTDB search result was written to GCA_012960105.1_ASM1296010v1_genomic.fna/result_gtdb.tsv
[2023-06-29 09:56:18,876] [INFO] ===== GTDB Search completed =====
[2023-06-29 09:56:18,878] [INFO] DFAST_QC result json was written to GCA_012960105.1_ASM1296010v1_genomic.fna/dqc_result.json
[2023-06-29 09:56:18,878] [INFO] DFAST_QC completed!
[2023-06-29 09:56:18,879] [INFO] Total running time: 0h0m52s