[2024-01-25 18:54:05,623] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:54:05,627] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:54:05,627] [INFO] DQC Reference Directory: /var/lib/cwl/stgc8729b80-f7e2-48f2-8301-7eab97c13c85/dqc_reference
[2024-01-25 18:54:06,781] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:54:06,782] [INFO] Task started: Prodigal
[2024-01-25 18:54:06,782] [INFO] Running command: gunzip -c /var/lib/cwl/stg63e8219e-a281-47ea-9d70-2a05525029e8/GCF_018128945.1_ASM1812894v1_genomic.fna.gz | prodigal -d GCF_018128945.1_ASM1812894v1_genomic.fna/cds.fna -a GCF_018128945.1_ASM1812894v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:54:15,314] [INFO] Task succeeded: Prodigal
[2024-01-25 18:54:15,315] [INFO] Task started: HMMsearch
[2024-01-25 18:54:15,315] [INFO] Running command: hmmsearch --tblout GCF_018128945.1_ASM1812894v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc8729b80-f7e2-48f2-8301-7eab97c13c85/dqc_reference/reference_markers.hmm GCF_018128945.1_ASM1812894v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:54:15,544] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:54:15,545] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg63e8219e-a281-47ea-9d70-2a05525029e8/GCF_018128945.1_ASM1812894v1_genomic.fna.gz]
[2024-01-25 18:54:15,575] [INFO] Query marker FASTA was written to GCF_018128945.1_ASM1812894v1_genomic.fna/markers.fasta
[2024-01-25 18:54:15,575] [INFO] Task started: Blastn
[2024-01-25 18:54:15,575] [INFO] Running command: blastn -query GCF_018128945.1_ASM1812894v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8729b80-f7e2-48f2-8301-7eab97c13c85/dqc_reference/reference_markers.fasta -out GCF_018128945.1_ASM1812894v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:54:16,179] [INFO] Task succeeded: Blastn
[2024-01-25 18:54:16,182] [INFO] Selected 20 target genomes.
[2024-01-25 18:54:16,182] [INFO] Target genome list was writen to GCF_018128945.1_ASM1812894v1_genomic.fna/target_genomes.txt
[2024-01-25 18:54:16,207] [INFO] Task started: fastANI
[2024-01-25 18:54:16,207] [INFO] Running command: fastANI --query /var/lib/cwl/stg63e8219e-a281-47ea-9d70-2a05525029e8/GCF_018128945.1_ASM1812894v1_genomic.fna.gz --refList GCF_018128945.1_ASM1812894v1_genomic.fna/target_genomes.txt --output GCF_018128945.1_ASM1812894v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:54:30,187] [INFO] Task succeeded: fastANI
[2024-01-25 18:54:30,187] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc8729b80-f7e2-48f2-8301-7eab97c13c85/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:54:30,187] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc8729b80-f7e2-48f2-8301-7eab97c13c85/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:54:30,189] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:54:30,189] [INFO] The taxonomy check result is classified as 'no_hit'.
[2024-01-25 18:54:30,189] [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
--------------------------------------------------------------------------------
[2024-01-25 18:54:30,190] [INFO] DFAST Taxonomy check result was written to GCF_018128945.1_ASM1812894v1_genomic.fna/tc_result.tsv
[2024-01-25 18:54:30,191] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:54:30,191] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:54:30,191] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc8729b80-f7e2-48f2-8301-7eab97c13c85/dqc_reference/checkm_data
[2024-01-25 18:54:30,194] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:54:30,232] [INFO] Task started: CheckM
[2024-01-25 18:54:30,232] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018128945.1_ASM1812894v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018128945.1_ASM1812894v1_genomic.fna/checkm_input GCF_018128945.1_ASM1812894v1_genomic.fna/checkm_result
[2024-01-25 18:55:00,287] [INFO] Task succeeded: CheckM
[2024-01-25 18:55:00,288] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:55:00,307] [INFO] ===== Completeness check finished =====
[2024-01-25 18:55:00,307] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:55:00,307] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018128945.1_ASM1812894v1_genomic.fna/markers.fasta)
[2024-01-25 18:55:00,308] [INFO] Task started: Blastn
[2024-01-25 18:55:00,308] [INFO] Running command: blastn -query GCF_018128945.1_ASM1812894v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8729b80-f7e2-48f2-8301-7eab97c13c85/dqc_reference/reference_markers_gtdb.fasta -out GCF_018128945.1_ASM1812894v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:55:01,340] [INFO] Task succeeded: Blastn
[2024-01-25 18:55:01,343] [INFO] Selected 7 target genomes.
[2024-01-25 18:55:01,343] [INFO] Target genome list was writen to GCF_018128945.1_ASM1812894v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:55:01,356] [INFO] Task started: fastANI
[2024-01-25 18:55:01,357] [INFO] Running command: fastANI --query /var/lib/cwl/stg63e8219e-a281-47ea-9d70-2a05525029e8/GCF_018128945.1_ASM1812894v1_genomic.fna.gz --refList GCF_018128945.1_ASM1812894v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018128945.1_ASM1812894v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:55:06,925] [INFO] Task succeeded: fastANI
[2024-01-25 18:55:06,930] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:55:06,930] [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_018128945.1	s__GCA-900199385 sp900199385	100.0	1130	1130	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__GCA-900199385	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_017569305.1	s__GCA-900199385 sp900322155	94.3936	972	1130	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__GCA-900199385	95.0	98.53	98.29	0.93	0.91	5	-
GCA_017428385.1	s__GCA-900199385 sp017428385	92.8649	899	1130	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__GCA-900199385	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900315675.1	s__GCA-900199385 sp900315675	85.1014	765	1130	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__GCA-900199385	95.0	98.62	97.73	0.95	0.88	5	-
GCA_018118585.1	s__GCA-900199385 sp900176495	83.5795	676	1130	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__GCA-900199385	95.0	100.00	100.00	1.00	1.00	2	-
GCA_017615475.1	s__GCA-900199385 sp017615475	83.2348	438	1130	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__GCA-900199385	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017569285.1	s__GCA-900199385 sp017569285	79.8801	339	1130	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__GCA-900199385	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:55:06,931] [INFO] GTDB search result was written to GCF_018128945.1_ASM1812894v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:55:06,932] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:55:06,934] [INFO] DFAST_QC result json was written to GCF_018128945.1_ASM1812894v1_genomic.fna/dqc_result.json
[2024-01-25 18:55:06,934] [INFO] DFAST_QC completed!
[2024-01-25 18:55:06,934] [INFO] Total running time: 0h1m1s