[2023-06-18 18:31:16,038] [INFO] DFAST_QC pipeline started.
[2023-06-18 18:31:16,040] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 18:31:16,041] [INFO] DQC Reference Directory: /var/lib/cwl/stg6b2b1f7f-1085-484a-a0ea-091665cb0982/dqc_reference
[2023-06-18 18:31:17,249] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 18:31:17,251] [INFO] Task started: Prodigal
[2023-06-18 18:31:17,252] [INFO] Running command: gunzip -c /var/lib/cwl/stg688d3146-d60a-4cc3-8f17-f91169e80509/GCA_018054485.1_ASM1805448v1_genomic.fna.gz | prodigal -d GCA_018054485.1_ASM1805448v1_genomic.fna/cds.fna -a GCA_018054485.1_ASM1805448v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 18:31:19,694] [INFO] Task succeeded: Prodigal
[2023-06-18 18:31:19,694] [INFO] Task started: HMMsearch
[2023-06-18 18:31:19,695] [INFO] Running command: hmmsearch --tblout GCA_018054485.1_ASM1805448v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6b2b1f7f-1085-484a-a0ea-091665cb0982/dqc_reference/reference_markers.hmm GCA_018054485.1_ASM1805448v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 18:31:19,927] [INFO] Task succeeded: HMMsearch
[2023-06-18 18:31:19,928] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg688d3146-d60a-4cc3-8f17-f91169e80509/GCA_018054485.1_ASM1805448v1_genomic.fna.gz]
[2023-06-18 18:31:19,943] [INFO] Query marker FASTA was written to GCA_018054485.1_ASM1805448v1_genomic.fna/markers.fasta
[2023-06-18 18:31:19,943] [INFO] Task started: Blastn
[2023-06-18 18:31:19,943] [INFO] Running command: blastn -query GCA_018054485.1_ASM1805448v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b2b1f7f-1085-484a-a0ea-091665cb0982/dqc_reference/reference_markers.fasta -out GCA_018054485.1_ASM1805448v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 18:31:20,708] [INFO] Task succeeded: Blastn
[2023-06-18 18:31:20,712] [INFO] Selected 31 target genomes.
[2023-06-18 18:31:20,712] [INFO] Target genome list was writen to GCA_018054485.1_ASM1805448v1_genomic.fna/target_genomes.txt
[2023-06-18 18:31:20,733] [INFO] Task started: fastANI
[2023-06-18 18:31:20,734] [INFO] Running command: fastANI --query /var/lib/cwl/stg688d3146-d60a-4cc3-8f17-f91169e80509/GCA_018054485.1_ASM1805448v1_genomic.fna.gz --refList GCA_018054485.1_ASM1805448v1_genomic.fna/target_genomes.txt --output GCA_018054485.1_ASM1805448v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 18:31:38,233] [INFO] Task succeeded: fastANI
[2023-06-18 18:31:38,233] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6b2b1f7f-1085-484a-a0ea-091665cb0982/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 18:31:38,234] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6b2b1f7f-1085-484a-a0ea-091665cb0982/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 18:31:38,235] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 18:31:38,235] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 18:31:38,236] [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 18:31:38,245] [INFO] DFAST Taxonomy check result was written to GCA_018054485.1_ASM1805448v1_genomic.fna/tc_result.tsv
[2023-06-18 18:31:38,245] [INFO] ===== Taxonomy check completed =====
[2023-06-18 18:31:38,246] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 18:31:38,246] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6b2b1f7f-1085-484a-a0ea-091665cb0982/dqc_reference/checkm_data
[2023-06-18 18:31:38,251] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 18:31:38,266] [INFO] Task started: CheckM
[2023-06-18 18:31:38,266] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018054485.1_ASM1805448v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018054485.1_ASM1805448v1_genomic.fna/checkm_input GCA_018054485.1_ASM1805448v1_genomic.fna/checkm_result
[2023-06-18 18:31:54,095] [INFO] Task succeeded: CheckM
[2023-06-18 18:31:54,097] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 43.98%
Contamintation: 6.02%
Strain heterogeneity: 40.00%
--------------------------------------------------------------------------------
[2023-06-18 18:31:54,113] [INFO] ===== Completeness check finished =====
[2023-06-18 18:31:54,114] [INFO] ===== Start GTDB Search =====
[2023-06-18 18:31:54,114] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018054485.1_ASM1805448v1_genomic.fna/markers.fasta)
[2023-06-18 18:31:54,114] [INFO] Task started: Blastn
[2023-06-18 18:31:54,115] [INFO] Running command: blastn -query GCA_018054485.1_ASM1805448v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b2b1f7f-1085-484a-a0ea-091665cb0982/dqc_reference/reference_markers_gtdb.fasta -out GCA_018054485.1_ASM1805448v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 18:31:55,136] [INFO] Task succeeded: Blastn
[2023-06-18 18:31:55,149] [INFO] Selected 6 target genomes.
[2023-06-18 18:31:55,149] [INFO] Target genome list was writen to GCA_018054485.1_ASM1805448v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 18:31:55,153] [INFO] Task started: fastANI
[2023-06-18 18:31:55,153] [INFO] Running command: fastANI --query /var/lib/cwl/stg688d3146-d60a-4cc3-8f17-f91169e80509/GCA_018054485.1_ASM1805448v1_genomic.fna.gz --refList GCA_018054485.1_ASM1805448v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018054485.1_ASM1805448v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 18:31:57,329] [INFO] Task succeeded: fastANI
[2023-06-18 18:31:57,336] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 18:31:57,336] [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_000432375.1	s__CAG-103 sp000432375	98.2989	215	231	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-103	95.0	98.15	97.87	0.87	0.82	10	conclusive
GCA_900317855.1	s__CAG-103 sp900317855	94.1677	210	231	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-103	95.0	97.11	95.56	0.88	0.84	11	-
GCA_900757655.1	s__CAG-103 sp900757655	93.2597	200	231	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-103	95.0	96.74	95.66	0.88	0.82	7	-
GCA_900543625.1	s__CAG-103 sp900543625	91.1943	217	231	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-103	95.0	96.93	95.23	0.89	0.87	12	-
GCA_004556965.1	s__CAG-103 sp004556965	80.7493	157	231	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-103	95.0	98.49	98.32	0.91	0.88	6	-
GCA_018265835.1	s__CAG-103 sp018265835	80.6998	157	231	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-103	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 18:31:57,338] [INFO] GTDB search result was written to GCA_018054485.1_ASM1805448v1_genomic.fna/result_gtdb.tsv
[2023-06-18 18:31:57,338] [INFO] ===== GTDB Search completed =====
[2023-06-18 18:31:57,341] [INFO] DFAST_QC result json was written to GCA_018054485.1_ASM1805448v1_genomic.fna/dqc_result.json
[2023-06-18 18:31:57,341] [INFO] DFAST_QC completed!
[2023-06-18 18:31:57,341] [INFO] Total running time: 0h0m41s