[2023-06-17 01:34:00,220] [INFO] DFAST_QC pipeline started.
[2023-06-17 01:34:00,223] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 01:34:00,223] [INFO] DQC Reference Directory: /var/lib/cwl/stg60227d17-af9e-4eca-be45-47da9d3b6924/dqc_reference
[2023-06-17 01:34:01,435] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 01:34:01,436] [INFO] Task started: Prodigal
[2023-06-17 01:34:01,436] [INFO] Running command: gunzip -c /var/lib/cwl/stga2d44e28-fb5a-487a-8bc1-dc46ab363885/GCA_905204175.1_SRR5519181-mag-bin.7_genomic.fna.gz | prodigal -d GCA_905204175.1_SRR5519181-mag-bin.7_genomic.fna/cds.fna -a GCA_905204175.1_SRR5519181-mag-bin.7_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 01:34:02,965] [INFO] Task succeeded: Prodigal
[2023-06-17 01:34:02,966] [INFO] Task started: HMMsearch
[2023-06-17 01:34:02,966] [INFO] Running command: hmmsearch --tblout GCA_905204175.1_SRR5519181-mag-bin.7_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg60227d17-af9e-4eca-be45-47da9d3b6924/dqc_reference/reference_markers.hmm GCA_905204175.1_SRR5519181-mag-bin.7_genomic.fna/protein.faa > /dev/null
[2023-06-17 01:34:03,191] [INFO] Task succeeded: HMMsearch
[2023-06-17 01:34:03,192] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga2d44e28-fb5a-487a-8bc1-dc46ab363885/GCA_905204175.1_SRR5519181-mag-bin.7_genomic.fna.gz]
[2023-06-17 01:34:03,213] [INFO] Query marker FASTA was written to GCA_905204175.1_SRR5519181-mag-bin.7_genomic.fna/markers.fasta
[2023-06-17 01:34:03,213] [INFO] Task started: Blastn
[2023-06-17 01:34:03,214] [INFO] Running command: blastn -query GCA_905204175.1_SRR5519181-mag-bin.7_genomic.fna/markers.fasta -db /var/lib/cwl/stg60227d17-af9e-4eca-be45-47da9d3b6924/dqc_reference/reference_markers.fasta -out GCA_905204175.1_SRR5519181-mag-bin.7_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 01:34:03,817] [INFO] Task succeeded: Blastn
[2023-06-17 01:34:03,822] [INFO] Selected 25 target genomes.
[2023-06-17 01:34:03,822] [INFO] Target genome list was writen to GCA_905204175.1_SRR5519181-mag-bin.7_genomic.fna/target_genomes.txt
[2023-06-17 01:34:03,832] [INFO] Task started: fastANI
[2023-06-17 01:34:03,832] [INFO] Running command: fastANI --query /var/lib/cwl/stga2d44e28-fb5a-487a-8bc1-dc46ab363885/GCA_905204175.1_SRR5519181-mag-bin.7_genomic.fna.gz --refList GCA_905204175.1_SRR5519181-mag-bin.7_genomic.fna/target_genomes.txt --output GCA_905204175.1_SRR5519181-mag-bin.7_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 01:34:14,213] [INFO] Task succeeded: fastANI
[2023-06-17 01:34:14,214] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg60227d17-af9e-4eca-be45-47da9d3b6924/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 01:34:14,214] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg60227d17-af9e-4eca-be45-47da9d3b6924/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 01:34:14,216] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 01:34:14,217] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 01:34:14,217] [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
--------------------------------------------------------------------------------
[2023-06-17 01:34:14,219] [INFO] DFAST Taxonomy check result was written to GCA_905204175.1_SRR5519181-mag-bin.7_genomic.fna/tc_result.tsv
[2023-06-17 01:34:14,220] [INFO] ===== Taxonomy check completed =====
[2023-06-17 01:34:14,220] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 01:34:14,221] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg60227d17-af9e-4eca-be45-47da9d3b6924/dqc_reference/checkm_data
[2023-06-17 01:34:14,225] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 01:34:14,242] [INFO] Task started: CheckM
[2023-06-17 01:34:14,242] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905204175.1_SRR5519181-mag-bin.7_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905204175.1_SRR5519181-mag-bin.7_genomic.fna/checkm_input GCA_905204175.1_SRR5519181-mag-bin.7_genomic.fna/checkm_result
[2023-06-17 01:34:27,623] [INFO] Task succeeded: CheckM
[2023-06-17 01:34:27,625] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 01:34:27,645] [INFO] ===== Completeness check finished =====
[2023-06-17 01:34:27,645] [INFO] ===== Start GTDB Search =====
[2023-06-17 01:34:27,646] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905204175.1_SRR5519181-mag-bin.7_genomic.fna/markers.fasta)
[2023-06-17 01:34:27,646] [INFO] Task started: Blastn
[2023-06-17 01:34:27,646] [INFO] Running command: blastn -query GCA_905204175.1_SRR5519181-mag-bin.7_genomic.fna/markers.fasta -db /var/lib/cwl/stg60227d17-af9e-4eca-be45-47da9d3b6924/dqc_reference/reference_markers_gtdb.fasta -out GCA_905204175.1_SRR5519181-mag-bin.7_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 01:34:28,499] [INFO] Task succeeded: Blastn
[2023-06-17 01:34:28,503] [INFO] Selected 12 target genomes.
[2023-06-17 01:34:28,503] [INFO] Target genome list was writen to GCA_905204175.1_SRR5519181-mag-bin.7_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 01:34:28,530] [INFO] Task started: fastANI
[2023-06-17 01:34:28,530] [INFO] Running command: fastANI --query /var/lib/cwl/stga2d44e28-fb5a-487a-8bc1-dc46ab363885/GCA_905204175.1_SRR5519181-mag-bin.7_genomic.fna.gz --refList GCA_905204175.1_SRR5519181-mag-bin.7_genomic.fna/target_genomes_gtdb.txt --output GCA_905204175.1_SRR5519181-mag-bin.7_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 01:34:31,358] [INFO] Task succeeded: fastANI
[2023-06-17 01:34:31,370] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 01:34:31,371] [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_000438295.1	s__Onthousia sp000438295	96.7332	315	357	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Onthousia	95.0	96.69	96.41	0.79	0.73	4	conclusive
GCA_014846175.1	s__Onthousia sp014846175	88.3419	253	357	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Onthousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900758495.1	s__Onthousia sp900758495	83.8424	268	357	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Onthousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018715925.1	s__Onthousia faecipullorum	77.6614	106	357	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Onthousia	95.0	99.48	99.48	0.89	0.89	2	-
GCA_900760545.1	s__Onthousia sp900760545	77.594	82	357	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Onthousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904420615.1	s__Onthousia sp904420615	77.5798	83	357	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Onthousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018711135.1	s__Onthousia faecavium	77.543	82	357	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Onthousia	95.0	99.89	99.89	0.91	0.91	2	-
GCA_018716225.1	s__Onthousia faecigallinarum	77.3171	84	357	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Onthousia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 01:34:31,380] [INFO] GTDB search result was written to GCA_905204175.1_SRR5519181-mag-bin.7_genomic.fna/result_gtdb.tsv
[2023-06-17 01:34:31,381] [INFO] ===== GTDB Search completed =====
[2023-06-17 01:34:31,385] [INFO] DFAST_QC result json was written to GCA_905204175.1_SRR5519181-mag-bin.7_genomic.fna/dqc_result.json
[2023-06-17 01:34:31,385] [INFO] DFAST_QC completed!
[2023-06-17 01:34:31,385] [INFO] Total running time: 0h0m31s