[2023-06-05 02:53:58,231] [INFO] DFAST_QC pipeline started.
[2023-06-05 02:53:58,234] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 02:53:58,234] [INFO] DQC Reference Directory: /var/lib/cwl/stg1d61033b-8e9d-49c3-87dd-90c6137b7f14/dqc_reference
[2023-06-05 02:54:00,522] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 02:54:00,523] [INFO] Task started: Prodigal
[2023-06-05 02:54:00,523] [INFO] Running command: gunzip -c /var/lib/cwl/stg7c26eb4e-05d3-4286-b325-62f5da882fdc/GCA_934630975.1_ERR7738631_bin.67_genomic.fna.gz | prodigal -d GCA_934630975.1_ERR7738631_bin.67_genomic.fna/cds.fna -a GCA_934630975.1_ERR7738631_bin.67_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 02:54:07,059] [INFO] Task succeeded: Prodigal
[2023-06-05 02:54:07,060] [INFO] Task started: HMMsearch
[2023-06-05 02:54:07,060] [INFO] Running command: hmmsearch --tblout GCA_934630975.1_ERR7738631_bin.67_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1d61033b-8e9d-49c3-87dd-90c6137b7f14/dqc_reference/reference_markers.hmm GCA_934630975.1_ERR7738631_bin.67_genomic.fna/protein.faa > /dev/null
[2023-06-05 02:54:07,291] [INFO] Task succeeded: HMMsearch
[2023-06-05 02:54:07,293] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg7c26eb4e-05d3-4286-b325-62f5da882fdc/GCA_934630975.1_ERR7738631_bin.67_genomic.fna.gz]
[2023-06-05 02:54:07,324] [INFO] Query marker FASTA was written to GCA_934630975.1_ERR7738631_bin.67_genomic.fna/markers.fasta
[2023-06-05 02:54:07,325] [INFO] Task started: Blastn
[2023-06-05 02:54:07,325] [INFO] Running command: blastn -query GCA_934630975.1_ERR7738631_bin.67_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d61033b-8e9d-49c3-87dd-90c6137b7f14/dqc_reference/reference_markers.fasta -out GCA_934630975.1_ERR7738631_bin.67_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:54:08,050] [INFO] Task succeeded: Blastn
[2023-06-05 02:54:08,055] [INFO] Selected 22 target genomes.
[2023-06-05 02:54:08,055] [INFO] Target genome list was writen to GCA_934630975.1_ERR7738631_bin.67_genomic.fna/target_genomes.txt
[2023-06-05 02:54:08,062] [INFO] Task started: fastANI
[2023-06-05 02:54:08,062] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c26eb4e-05d3-4286-b325-62f5da882fdc/GCA_934630975.1_ERR7738631_bin.67_genomic.fna.gz --refList GCA_934630975.1_ERR7738631_bin.67_genomic.fna/target_genomes.txt --output GCA_934630975.1_ERR7738631_bin.67_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 02:54:22,139] [INFO] Task succeeded: fastANI
[2023-06-05 02:54:22,140] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1d61033b-8e9d-49c3-87dd-90c6137b7f14/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 02:54:22,141] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1d61033b-8e9d-49c3-87dd-90c6137b7f14/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 02:54:22,150] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 02:54:22,151] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 02:54:22,151] [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
Catenulispora pinisilvae	strain=NH11	GCA_015356865.1	2705253	2705253	type	True	74.9009	52	768	95	below_threshold
Saccharothrix coeruleofusca	strain=JCM 3313	GCA_014648515.1	33919	33919	type	True	74.8144	54	768	95	below_threshold
Saccharothrix coeruleofusca	strain=DSM 43679	GCA_017876325.1	33919	33919	type	True	74.7635	54	768	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 02:54:22,153] [INFO] DFAST Taxonomy check result was written to GCA_934630975.1_ERR7738631_bin.67_genomic.fna/tc_result.tsv
[2023-06-05 02:54:22,154] [INFO] ===== Taxonomy check completed =====
[2023-06-05 02:54:22,154] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 02:54:22,155] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1d61033b-8e9d-49c3-87dd-90c6137b7f14/dqc_reference/checkm_data
[2023-06-05 02:54:22,157] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 02:54:22,185] [INFO] Task started: CheckM
[2023-06-05 02:54:22,185] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934630975.1_ERR7738631_bin.67_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934630975.1_ERR7738631_bin.67_genomic.fna/checkm_input GCA_934630975.1_ERR7738631_bin.67_genomic.fna/checkm_result
[2023-06-05 02:54:47,043] [INFO] Task succeeded: CheckM
[2023-06-05 02:54:47,044] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.74%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 02:54:47,065] [INFO] ===== Completeness check finished =====
[2023-06-05 02:54:47,066] [INFO] ===== Start GTDB Search =====
[2023-06-05 02:54:47,066] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934630975.1_ERR7738631_bin.67_genomic.fna/markers.fasta)
[2023-06-05 02:54:47,066] [INFO] Task started: Blastn
[2023-06-05 02:54:47,067] [INFO] Running command: blastn -query GCA_934630975.1_ERR7738631_bin.67_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d61033b-8e9d-49c3-87dd-90c6137b7f14/dqc_reference/reference_markers_gtdb.fasta -out GCA_934630975.1_ERR7738631_bin.67_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:54:48,258] [INFO] Task succeeded: Blastn
[2023-06-05 02:54:48,264] [INFO] Selected 12 target genomes.
[2023-06-05 02:54:48,264] [INFO] Target genome list was writen to GCA_934630975.1_ERR7738631_bin.67_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 02:54:48,270] [INFO] Task started: fastANI
[2023-06-05 02:54:48,271] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c26eb4e-05d3-4286-b325-62f5da882fdc/GCA_934630975.1_ERR7738631_bin.67_genomic.fna.gz --refList GCA_934630975.1_ERR7738631_bin.67_genomic.fna/target_genomes_gtdb.txt --output GCA_934630975.1_ERR7738631_bin.67_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 02:54:54,178] [INFO] Task succeeded: fastANI
[2023-06-05 02:54:54,193] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 02:54:54,193] [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_900542395.1	s__Ventricola sp900542395	90.0161	522	768	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Ventricola	95.0	97.33	97.06	0.84	0.79	5	-
GCA_900542445.1	s__Ventricola sp900542445	87.3638	586	768	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Ventricola	95.0	98.97	98.40	0.91	0.87	4	-
GCA_900548125.1	s__Ventricola sp900548125	81.8923	329	768	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Ventricola	95.0	97.02	96.93	0.87	0.87	4	-
GCA_004555535.1	s__Ventricola sp004555535	80.7329	369	768	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Ventricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004556985.1	s__Ventricola sp004556985	80.5283	348	768	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Ventricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004557905.1	s__Ventricola sp004557905	80.2725	360	768	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Ventricola	95.0	98.75	98.68	0.87	0.86	3	-
GCA_017937505.1	s__Ventricola sp017937505	80.1946	337	768	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Ventricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018716525.1	s__Ventricola gallistercoris	79.8271	280	768	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Ventricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017936375.1	s__Ventricola sp017936375	79.3458	295	768	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Ventricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017545905.1	s__Ventricola sp017545905	79.0473	236	768	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Ventricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015056305.1	s__Ventricola sp015056305	78.9729	280	768	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Ventricola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 02:54:54,195] [INFO] GTDB search result was written to GCA_934630975.1_ERR7738631_bin.67_genomic.fna/result_gtdb.tsv
[2023-06-05 02:54:54,196] [INFO] ===== GTDB Search completed =====
[2023-06-05 02:54:54,198] [INFO] DFAST_QC result json was written to GCA_934630975.1_ERR7738631_bin.67_genomic.fna/dqc_result.json
[2023-06-05 02:54:54,199] [INFO] DFAST_QC completed!
[2023-06-05 02:54:54,199] [INFO] Total running time: 0h0m56s