[2023-06-18 17:22:54,406] [INFO] DFAST_QC pipeline started.
[2023-06-18 17:22:54,408] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 17:22:54,408] [INFO] DQC Reference Directory: /var/lib/cwl/stg531bc12b-6a21-42fc-8f65-813475b97eca/dqc_reference
[2023-06-18 17:22:55,500] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 17:22:55,501] [INFO] Task started: Prodigal
[2023-06-18 17:22:55,501] [INFO] Running command: gunzip -c /var/lib/cwl/stg281710a3-5224-4e20-a2ce-02e940c41168/GCA_014858445.1_ASM1485844v1_genomic.fna.gz | prodigal -d GCA_014858445.1_ASM1485844v1_genomic.fna/cds.fna -a GCA_014858445.1_ASM1485844v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 17:23:00,735] [INFO] Task succeeded: Prodigal
[2023-06-18 17:23:00,735] [INFO] Task started: HMMsearch
[2023-06-18 17:23:00,735] [INFO] Running command: hmmsearch --tblout GCA_014858445.1_ASM1485844v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg531bc12b-6a21-42fc-8f65-813475b97eca/dqc_reference/reference_markers.hmm GCA_014858445.1_ASM1485844v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 17:23:00,940] [INFO] Task succeeded: HMMsearch
[2023-06-18 17:23:00,944] [INFO] Found 6/6 markers.
[2023-06-18 17:23:00,972] [INFO] Query marker FASTA was written to GCA_014858445.1_ASM1485844v1_genomic.fna/markers.fasta
[2023-06-18 17:23:00,972] [INFO] Task started: Blastn
[2023-06-18 17:23:00,972] [INFO] Running command: blastn -query GCA_014858445.1_ASM1485844v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg531bc12b-6a21-42fc-8f65-813475b97eca/dqc_reference/reference_markers.fasta -out GCA_014858445.1_ASM1485844v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 17:23:01,494] [INFO] Task succeeded: Blastn
[2023-06-18 17:23:01,501] [INFO] Selected 22 target genomes.
[2023-06-18 17:23:01,502] [INFO] Target genome list was writen to GCA_014858445.1_ASM1485844v1_genomic.fna/target_genomes.txt
[2023-06-18 17:23:01,505] [INFO] Task started: fastANI
[2023-06-18 17:23:01,505] [INFO] Running command: fastANI --query /var/lib/cwl/stg281710a3-5224-4e20-a2ce-02e940c41168/GCA_014858445.1_ASM1485844v1_genomic.fna.gz --refList GCA_014858445.1_ASM1485844v1_genomic.fna/target_genomes.txt --output GCA_014858445.1_ASM1485844v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 17:23:14,943] [INFO] Task succeeded: fastANI
[2023-06-18 17:23:14,944] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg531bc12b-6a21-42fc-8f65-813475b97eca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 17:23:14,944] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg531bc12b-6a21-42fc-8f65-813475b97eca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 17:23:14,945] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 17:23:14,946] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 17:23:14,946] [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
--------------------------------------------------------------------------------
[2023-06-18 17:23:14,949] [INFO] DFAST Taxonomy check result was written to GCA_014858445.1_ASM1485844v1_genomic.fna/tc_result.tsv
[2023-06-18 17:23:14,949] [INFO] ===== Taxonomy check completed =====
[2023-06-18 17:23:14,949] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 17:23:14,950] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg531bc12b-6a21-42fc-8f65-813475b97eca/dqc_reference/checkm_data
[2023-06-18 17:23:14,952] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 17:23:14,979] [INFO] Task started: CheckM
[2023-06-18 17:23:14,979] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_014858445.1_ASM1485844v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_014858445.1_ASM1485844v1_genomic.fna/checkm_input GCA_014858445.1_ASM1485844v1_genomic.fna/checkm_result
[2023-06-18 17:23:36,478] [INFO] Task succeeded: CheckM
[2023-06-18 17:23:36,479] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 13.89%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-18 17:23:36,512] [INFO] ===== Completeness check finished =====
[2023-06-18 17:23:36,512] [INFO] ===== Start GTDB Search =====
[2023-06-18 17:23:36,513] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_014858445.1_ASM1485844v1_genomic.fna/markers.fasta)
[2023-06-18 17:23:36,514] [INFO] Task started: Blastn
[2023-06-18 17:23:36,514] [INFO] Running command: blastn -query GCA_014858445.1_ASM1485844v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg531bc12b-6a21-42fc-8f65-813475b97eca/dqc_reference/reference_markers_gtdb.fasta -out GCA_014858445.1_ASM1485844v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 17:23:37,267] [INFO] Task succeeded: Blastn
[2023-06-18 17:23:37,272] [INFO] Selected 9 target genomes.
[2023-06-18 17:23:37,272] [INFO] Target genome list was writen to GCA_014858445.1_ASM1485844v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 17:23:37,277] [INFO] Task started: fastANI
[2023-06-18 17:23:37,277] [INFO] Running command: fastANI --query /var/lib/cwl/stg281710a3-5224-4e20-a2ce-02e940c41168/GCA_014858445.1_ASM1485844v1_genomic.fna.gz --refList GCA_014858445.1_ASM1485844v1_genomic.fna/target_genomes_gtdb.txt --output GCA_014858445.1_ASM1485844v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 17:23:42,156] [INFO] Task succeeded: fastANI
[2023-06-18 17:23:42,167] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 17:23:42,167] [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_000434055.1	s__CAG-488 sp000434055	98.6308	661	818	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-488	95.0	98.16	97.80	0.89	0.77	5	conclusive
GCA_000434915.1	s__CAG-488 sp000434915	88.7397	628	818	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-488	95.0	98.43	98.24	0.92	0.89	3	-
GCA_900554995.1	s__CAG-488 sp900554995	86.6728	297	818	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-488	95.0	99.17	98.33	0.93	0.89	3	-
GCA_003486665.1	s__CAG-488 sp003486665	84.2251	375	818	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-488	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002449395.1	s__CAG-488 sp002449395	83.3431	511	818	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-488	95.0	98.19	97.50	0.90	0.86	5	-
GCA_016292785.1	s__CAG-488 sp016292785	81.4767	410	818	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-488	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017379935.1	s__CAG-488 sp017379935	78.3767	157	818	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-488	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017481575.1	s__CAG-488 sp017481575	78.3369	167	818	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-488	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017415025.1	s__CAG-488 sp017415025	78.332	171	818	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-488	95.0	97.47	97.27	0.84	0.82	3	-
--------------------------------------------------------------------------------
[2023-06-18 17:23:42,168] [INFO] GTDB search result was written to GCA_014858445.1_ASM1485844v1_genomic.fna/result_gtdb.tsv
[2023-06-18 17:23:42,168] [INFO] ===== GTDB Search completed =====
[2023-06-18 17:23:42,171] [INFO] DFAST_QC result json was written to GCA_014858445.1_ASM1485844v1_genomic.fna/dqc_result.json
[2023-06-18 17:23:42,171] [INFO] DFAST_QC completed!
[2023-06-18 17:23:42,171] [INFO] Total running time: 0h0m48s