[2023-06-18 20:10:19,867] [INFO] DFAST_QC pipeline started.
[2023-06-18 20:10:19,869] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 20:10:19,869] [INFO] DQC Reference Directory: /var/lib/cwl/stg0e6982d4-e877-4532-8690-0afc2a3f7f9d/dqc_reference
[2023-06-18 20:10:21,333] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 20:10:21,334] [INFO] Task started: Prodigal
[2023-06-18 20:10:21,334] [INFO] Running command: gunzip -c /var/lib/cwl/stgd9b0edf0-0dc7-4f96-ac24-4fd28409df30/GCA_018264875.1_ASM1826487v1_genomic.fna.gz | prodigal -d GCA_018264875.1_ASM1826487v1_genomic.fna/cds.fna -a GCA_018264875.1_ASM1826487v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 20:10:24,357] [INFO] Task succeeded: Prodigal
[2023-06-18 20:10:24,358] [INFO] Task started: HMMsearch
[2023-06-18 20:10:24,358] [INFO] Running command: hmmsearch --tblout GCA_018264875.1_ASM1826487v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0e6982d4-e877-4532-8690-0afc2a3f7f9d/dqc_reference/reference_markers.hmm GCA_018264875.1_ASM1826487v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 20:10:24,608] [INFO] Task succeeded: HMMsearch
[2023-06-18 20:10:24,610] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd9b0edf0-0dc7-4f96-ac24-4fd28409df30/GCA_018264875.1_ASM1826487v1_genomic.fna.gz]
[2023-06-18 20:10:24,632] [INFO] Query marker FASTA was written to GCA_018264875.1_ASM1826487v1_genomic.fna/markers.fasta
[2023-06-18 20:10:24,633] [INFO] Task started: Blastn
[2023-06-18 20:10:24,633] [INFO] Running command: blastn -query GCA_018264875.1_ASM1826487v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e6982d4-e877-4532-8690-0afc2a3f7f9d/dqc_reference/reference_markers.fasta -out GCA_018264875.1_ASM1826487v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 20:10:25,218] [INFO] Task succeeded: Blastn
[2023-06-18 20:10:25,221] [INFO] Selected 12 target genomes.
[2023-06-18 20:10:25,221] [INFO] Target genome list was writen to GCA_018264875.1_ASM1826487v1_genomic.fna/target_genomes.txt
[2023-06-18 20:10:25,224] [INFO] Task started: fastANI
[2023-06-18 20:10:25,225] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9b0edf0-0dc7-4f96-ac24-4fd28409df30/GCA_018264875.1_ASM1826487v1_genomic.fna.gz --refList GCA_018264875.1_ASM1826487v1_genomic.fna/target_genomes.txt --output GCA_018264875.1_ASM1826487v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 20:10:33,484] [INFO] Task succeeded: fastANI
[2023-06-18 20:10:33,485] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0e6982d4-e877-4532-8690-0afc2a3f7f9d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 20:10:33,485] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0e6982d4-e877-4532-8690-0afc2a3f7f9d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 20:10:33,487] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 20:10:33,487] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 20:10:33,487] [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 20:10:33,489] [INFO] DFAST Taxonomy check result was written to GCA_018264875.1_ASM1826487v1_genomic.fna/tc_result.tsv
[2023-06-18 20:10:33,489] [INFO] ===== Taxonomy check completed =====
[2023-06-18 20:10:33,489] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 20:10:33,490] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0e6982d4-e877-4532-8690-0afc2a3f7f9d/dqc_reference/checkm_data
[2023-06-18 20:10:33,492] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 20:10:33,513] [INFO] Task started: CheckM
[2023-06-18 20:10:33,514] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018264875.1_ASM1826487v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018264875.1_ASM1826487v1_genomic.fna/checkm_input GCA_018264875.1_ASM1826487v1_genomic.fna/checkm_result
[2023-06-18 20:10:50,872] [INFO] Task succeeded: CheckM
[2023-06-18 20:10:50,873] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 20:10:50,910] [INFO] ===== Completeness check finished =====
[2023-06-18 20:10:50,911] [INFO] ===== Start GTDB Search =====
[2023-06-18 20:10:50,911] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018264875.1_ASM1826487v1_genomic.fna/markers.fasta)
[2023-06-18 20:10:50,911] [INFO] Task started: Blastn
[2023-06-18 20:10:50,911] [INFO] Running command: blastn -query GCA_018264875.1_ASM1826487v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e6982d4-e877-4532-8690-0afc2a3f7f9d/dqc_reference/reference_markers_gtdb.fasta -out GCA_018264875.1_ASM1826487v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 20:10:51,747] [INFO] Task succeeded: Blastn
[2023-06-18 20:10:51,754] [INFO] Selected 17 target genomes.
[2023-06-18 20:10:51,755] [INFO] Target genome list was writen to GCA_018264875.1_ASM1826487v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 20:10:51,812] [INFO] Task started: fastANI
[2023-06-18 20:10:51,812] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9b0edf0-0dc7-4f96-ac24-4fd28409df30/GCA_018264875.1_ASM1826487v1_genomic.fna.gz --refList GCA_018264875.1_ASM1826487v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018264875.1_ASM1826487v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 20:10:57,862] [INFO] Task succeeded: fastANI
[2023-06-18 20:10:57,871] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 20:10:57,871] [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_000432435.1	s__Fimenecus sp000432435	98.4267	399	410	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Fimenecus	95.0	98.55	98.08	0.94	0.85	30	conclusive
GCA_002437245.1	s__Fimenecus sp002437245	89.7327	360	410	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Fimenecus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017438845.1	s__Fimenecus sp017438845	76.7884	75	410	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Fimenecus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015066565.1	s__SIG554 sp015066565	76.6406	54	410	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__SIG554	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900540295.1	s__Fimenecus sp900540295	76.5883	56	410	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Fimenecus	95.0	98.52	98.30	0.90	0.86	3	-
--------------------------------------------------------------------------------
[2023-06-18 20:10:57,873] [INFO] GTDB search result was written to GCA_018264875.1_ASM1826487v1_genomic.fna/result_gtdb.tsv
[2023-06-18 20:10:57,874] [INFO] ===== GTDB Search completed =====
[2023-06-18 20:10:57,876] [INFO] DFAST_QC result json was written to GCA_018264875.1_ASM1826487v1_genomic.fna/dqc_result.json
[2023-06-18 20:10:57,876] [INFO] DFAST_QC completed!
[2023-06-18 20:10:57,876] [INFO] Total running time: 0h0m38s