[2023-06-27 22:54:08,243] [INFO] DFAST_QC pipeline started.
[2023-06-27 22:54:08,245] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 22:54:08,245] [INFO] DQC Reference Directory: /var/lib/cwl/stgc9cb9fca-6ec8-47b8-bf3a-95c07ddead33/dqc_reference
[2023-06-27 22:54:09,482] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 22:54:09,483] [INFO] Task started: Prodigal
[2023-06-27 22:54:09,483] [INFO] Running command: gunzip -c /var/lib/cwl/stg631834ac-b768-4352-a29b-ef2dd3901ea2/GCA_002310055.1_ASM231005v1_genomic.fna.gz | prodigal -d GCA_002310055.1_ASM231005v1_genomic.fna/cds.fna -a GCA_002310055.1_ASM231005v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 22:54:14,308] [INFO] Task succeeded: Prodigal
[2023-06-27 22:54:14,308] [INFO] Task started: HMMsearch
[2023-06-27 22:54:14,308] [INFO] Running command: hmmsearch --tblout GCA_002310055.1_ASM231005v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc9cb9fca-6ec8-47b8-bf3a-95c07ddead33/dqc_reference/reference_markers.hmm GCA_002310055.1_ASM231005v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 22:54:14,557] [INFO] Task succeeded: HMMsearch
[2023-06-27 22:54:14,559] [INFO] Found 6/6 markers.
[2023-06-27 22:54:14,578] [INFO] Query marker FASTA was written to GCA_002310055.1_ASM231005v1_genomic.fna/markers.fasta
[2023-06-27 22:54:14,579] [INFO] Task started: Blastn
[2023-06-27 22:54:14,579] [INFO] Running command: blastn -query GCA_002310055.1_ASM231005v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9cb9fca-6ec8-47b8-bf3a-95c07ddead33/dqc_reference/reference_markers.fasta -out GCA_002310055.1_ASM231005v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 22:54:15,246] [INFO] Task succeeded: Blastn
[2023-06-27 22:54:15,252] [INFO] Selected 16 target genomes.
[2023-06-27 22:54:15,252] [INFO] Target genome list was writen to GCA_002310055.1_ASM231005v1_genomic.fna/target_genomes.txt
[2023-06-27 22:54:15,268] [INFO] Task started: fastANI
[2023-06-27 22:54:15,269] [INFO] Running command: fastANI --query /var/lib/cwl/stg631834ac-b768-4352-a29b-ef2dd3901ea2/GCA_002310055.1_ASM231005v1_genomic.fna.gz --refList GCA_002310055.1_ASM231005v1_genomic.fna/target_genomes.txt --output GCA_002310055.1_ASM231005v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 22:54:24,175] [INFO] Task succeeded: fastANI
[2023-06-27 22:54:24,176] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc9cb9fca-6ec8-47b8-bf3a-95c07ddead33/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 22:54:24,176] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc9cb9fca-6ec8-47b8-bf3a-95c07ddead33/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 22:54:24,178] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 22:54:24,178] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 22:54:24,178] [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 22:54:24,180] [INFO] DFAST Taxonomy check result was written to GCA_002310055.1_ASM231005v1_genomic.fna/tc_result.tsv
[2023-06-27 22:54:24,181] [INFO] ===== Taxonomy check completed =====
[2023-06-27 22:54:24,181] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 22:54:24,181] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc9cb9fca-6ec8-47b8-bf3a-95c07ddead33/dqc_reference/checkm_data
[2023-06-27 22:54:24,184] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 22:54:24,210] [INFO] Task started: CheckM
[2023-06-27 22:54:24,210] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002310055.1_ASM231005v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002310055.1_ASM231005v1_genomic.fna/checkm_input GCA_002310055.1_ASM231005v1_genomic.fna/checkm_result
[2023-06-27 22:54:44,731] [INFO] Task succeeded: CheckM
[2023-06-27 22:54:44,733] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 22:54:44,755] [INFO] ===== Completeness check finished =====
[2023-06-27 22:54:44,756] [INFO] ===== Start GTDB Search =====
[2023-06-27 22:54:44,756] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002310055.1_ASM231005v1_genomic.fna/markers.fasta)
[2023-06-27 22:54:44,757] [INFO] Task started: Blastn
[2023-06-27 22:54:44,757] [INFO] Running command: blastn -query GCA_002310055.1_ASM231005v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9cb9fca-6ec8-47b8-bf3a-95c07ddead33/dqc_reference/reference_markers_gtdb.fasta -out GCA_002310055.1_ASM231005v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 22:54:45,857] [INFO] Task succeeded: Blastn
[2023-06-27 22:54:45,862] [INFO] Selected 15 target genomes.
[2023-06-27 22:54:45,862] [INFO] Target genome list was writen to GCA_002310055.1_ASM231005v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 22:54:45,882] [INFO] Task started: fastANI
[2023-06-27 22:54:45,882] [INFO] Running command: fastANI --query /var/lib/cwl/stg631834ac-b768-4352-a29b-ef2dd3901ea2/GCA_002310055.1_ASM231005v1_genomic.fna.gz --refList GCA_002310055.1_ASM231005v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002310055.1_ASM231005v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 22:54:52,186] [INFO] Task succeeded: fastANI
[2023-06-27 22:54:52,193] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 22:54:52,194] [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_002310055.1	s__UBA1206 sp002310055	100.0	624	626	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-382;g__UBA1206	95.0	97.41	97.28	0.95	0.91	6	conclusive
GCA_017429165.1	s__UBA1206 sp017429165	94.3761	560	626	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-382;g__UBA1206	95.0	98.02	98.02	0.92	0.92	2	-
GCA_902772845.1	s__UBA1206 sp902772845	82.1453	381	626	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-382;g__UBA1206	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 22:54:52,196] [INFO] GTDB search result was written to GCA_002310055.1_ASM231005v1_genomic.fna/result_gtdb.tsv
[2023-06-27 22:54:52,196] [INFO] ===== GTDB Search completed =====
[2023-06-27 22:54:52,198] [INFO] DFAST_QC result json was written to GCA_002310055.1_ASM231005v1_genomic.fna/dqc_result.json
[2023-06-27 22:54:52,198] [INFO] DFAST_QC completed!
[2023-06-27 22:54:52,199] [INFO] Total running time: 0h0m44s