[2023-06-17 09:32:58,473] [INFO] DFAST_QC pipeline started.
[2023-06-17 09:32:58,476] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 09:32:58,477] [INFO] DQC Reference Directory: /var/lib/cwl/stgb7e3992e-cf47-475d-bcde-cc02d4b724f1/dqc_reference
[2023-06-17 09:33:01,149] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 09:33:01,150] [INFO] Task started: Prodigal
[2023-06-17 09:33:01,150] [INFO] Running command: gunzip -c /var/lib/cwl/stg1b6ee944-1fa2-4fb3-8a6a-462fec2a028e/GCA_905187945.1_SRR5519182-mag-bin.6_genomic.fna.gz | prodigal -d GCA_905187945.1_SRR5519182-mag-bin.6_genomic.fna/cds.fna -a GCA_905187945.1_SRR5519182-mag-bin.6_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 09:33:09,087] [INFO] Task succeeded: Prodigal
[2023-06-17 09:33:09,087] [INFO] Task started: HMMsearch
[2023-06-17 09:33:09,087] [INFO] Running command: hmmsearch --tblout GCA_905187945.1_SRR5519182-mag-bin.6_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb7e3992e-cf47-475d-bcde-cc02d4b724f1/dqc_reference/reference_markers.hmm GCA_905187945.1_SRR5519182-mag-bin.6_genomic.fna/protein.faa > /dev/null
[2023-06-17 09:33:09,367] [INFO] Task succeeded: HMMsearch
[2023-06-17 09:33:09,371] [INFO] Found 6/6 markers.
[2023-06-17 09:33:09,404] [INFO] Query marker FASTA was written to GCA_905187945.1_SRR5519182-mag-bin.6_genomic.fna/markers.fasta
[2023-06-17 09:33:09,405] [INFO] Task started: Blastn
[2023-06-17 09:33:09,405] [INFO] Running command: blastn -query GCA_905187945.1_SRR5519182-mag-bin.6_genomic.fna/markers.fasta -db /var/lib/cwl/stgb7e3992e-cf47-475d-bcde-cc02d4b724f1/dqc_reference/reference_markers.fasta -out GCA_905187945.1_SRR5519182-mag-bin.6_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 09:33:10,117] [INFO] Task succeeded: Blastn
[2023-06-17 09:33:10,122] [INFO] Selected 29 target genomes.
[2023-06-17 09:33:10,122] [INFO] Target genome list was writen to GCA_905187945.1_SRR5519182-mag-bin.6_genomic.fna/target_genomes.txt
[2023-06-17 09:33:10,135] [INFO] Task started: fastANI
[2023-06-17 09:33:10,135] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b6ee944-1fa2-4fb3-8a6a-462fec2a028e/GCA_905187945.1_SRR5519182-mag-bin.6_genomic.fna.gz --refList GCA_905187945.1_SRR5519182-mag-bin.6_genomic.fna/target_genomes.txt --output GCA_905187945.1_SRR5519182-mag-bin.6_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 09:33:31,436] [INFO] Task succeeded: fastANI
[2023-06-17 09:33:31,437] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb7e3992e-cf47-475d-bcde-cc02d4b724f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 09:33:31,437] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb7e3992e-cf47-475d-bcde-cc02d4b724f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 09:33:31,439] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 09:33:31,439] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 09:33:31,439] [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 09:33:31,442] [INFO] DFAST Taxonomy check result was written to GCA_905187945.1_SRR5519182-mag-bin.6_genomic.fna/tc_result.tsv
[2023-06-17 09:33:31,442] [INFO] ===== Taxonomy check completed =====
[2023-06-17 09:33:31,443] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 09:33:31,443] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb7e3992e-cf47-475d-bcde-cc02d4b724f1/dqc_reference/checkm_data
[2023-06-17 09:33:31,448] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 09:33:31,479] [INFO] Task started: CheckM
[2023-06-17 09:33:31,479] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905187945.1_SRR5519182-mag-bin.6_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905187945.1_SRR5519182-mag-bin.6_genomic.fna/checkm_input GCA_905187945.1_SRR5519182-mag-bin.6_genomic.fna/checkm_result
[2023-06-17 09:34:01,572] [INFO] Task succeeded: CheckM
[2023-06-17 09:34:01,583] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 09:34:01,608] [INFO] ===== Completeness check finished =====
[2023-06-17 09:34:01,608] [INFO] ===== Start GTDB Search =====
[2023-06-17 09:34:01,608] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905187945.1_SRR5519182-mag-bin.6_genomic.fna/markers.fasta)
[2023-06-17 09:34:01,609] [INFO] Task started: Blastn
[2023-06-17 09:34:01,609] [INFO] Running command: blastn -query GCA_905187945.1_SRR5519182-mag-bin.6_genomic.fna/markers.fasta -db /var/lib/cwl/stgb7e3992e-cf47-475d-bcde-cc02d4b724f1/dqc_reference/reference_markers_gtdb.fasta -out GCA_905187945.1_SRR5519182-mag-bin.6_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 09:34:02,816] [INFO] Task succeeded: Blastn
[2023-06-17 09:34:02,821] [INFO] Selected 15 target genomes.
[2023-06-17 09:34:02,822] [INFO] Target genome list was writen to GCA_905187945.1_SRR5519182-mag-bin.6_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 09:34:02,841] [INFO] Task started: fastANI
[2023-06-17 09:34:02,841] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b6ee944-1fa2-4fb3-8a6a-462fec2a028e/GCA_905187945.1_SRR5519182-mag-bin.6_genomic.fna.gz --refList GCA_905187945.1_SRR5519182-mag-bin.6_genomic.fna/target_genomes_gtdb.txt --output GCA_905187945.1_SRR5519182-mag-bin.6_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 09:34:10,899] [INFO] Task succeeded: fastANI
[2023-06-17 09:34:10,913] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 09:34:10,914] [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_900548125.1	s__Ventricola sp900548125	96.6402	509	925	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	conclusive
GCA_900542445.1	s__Ventricola sp900542445	82.6241	515	925	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_900542395.1	s__Ventricola sp900542395	82.4082	465	925	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_004555535.1	s__Ventricola sp004555535	79.2836	308	925	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	79.1792	280	925	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_017937505.1	s__Ventricola sp017937505	79.0812	267	925	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	79.0771	290	925	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_017521565.1	s__Ventricola sp017521565	78.696	238	925	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	78.655	209	925	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	77.8626	248	925	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_017397695.1	s__Ventricola sp017397695	77.7032	215	925	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	-
--------------------------------------------------------------------------------
[2023-06-17 09:34:10,916] [INFO] GTDB search result was written to GCA_905187945.1_SRR5519182-mag-bin.6_genomic.fna/result_gtdb.tsv
[2023-06-17 09:34:10,916] [INFO] ===== GTDB Search completed =====
[2023-06-17 09:34:10,921] [INFO] DFAST_QC result json was written to GCA_905187945.1_SRR5519182-mag-bin.6_genomic.fna/dqc_result.json
[2023-06-17 09:34:10,922] [INFO] DFAST_QC completed!
[2023-06-17 09:34:10,922] [INFO] Total running time: 0h1m12s