[2023-06-30 22:46:58,180] [INFO] DFAST_QC pipeline started.
[2023-06-30 22:46:58,182] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 22:46:58,183] [INFO] DQC Reference Directory: /var/lib/cwl/stgff87f373-f9ab-4cc3-9ea0-09eb1b9f2c43/dqc_reference
[2023-06-30 22:46:59,357] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 22:46:59,358] [INFO] Task started: Prodigal
[2023-06-30 22:46:59,359] [INFO] Running command: gunzip -c /var/lib/cwl/stgee856d92-2e55-4ca0-a7c3-f0bf7de4e0a7/GCA_025963735.1_ASM2596373v1_genomic.fna.gz | prodigal -d GCA_025963735.1_ASM2596373v1_genomic.fna/cds.fna -a GCA_025963735.1_ASM2596373v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 22:47:10,900] [INFO] Task succeeded: Prodigal
[2023-06-30 22:47:10,901] [INFO] Task started: HMMsearch
[2023-06-30 22:47:10,901] [INFO] Running command: hmmsearch --tblout GCA_025963735.1_ASM2596373v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgff87f373-f9ab-4cc3-9ea0-09eb1b9f2c43/dqc_reference/reference_markers.hmm GCA_025963735.1_ASM2596373v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 22:47:11,159] [INFO] Task succeeded: HMMsearch
[2023-06-30 22:47:11,161] [INFO] Found 6/6 markers.
[2023-06-30 22:47:11,193] [INFO] Query marker FASTA was written to GCA_025963735.1_ASM2596373v1_genomic.fna/markers.fasta
[2023-06-30 22:47:11,193] [INFO] Task started: Blastn
[2023-06-30 22:47:11,194] [INFO] Running command: blastn -query GCA_025963735.1_ASM2596373v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff87f373-f9ab-4cc3-9ea0-09eb1b9f2c43/dqc_reference/reference_markers.fasta -out GCA_025963735.1_ASM2596373v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 22:47:11,838] [INFO] Task succeeded: Blastn
[2023-06-30 22:47:11,843] [INFO] Selected 27 target genomes.
[2023-06-30 22:47:11,843] [INFO] Target genome list was writen to GCA_025963735.1_ASM2596373v1_genomic.fna/target_genomes.txt
[2023-06-30 22:47:11,854] [INFO] Task started: fastANI
[2023-06-30 22:47:11,855] [INFO] Running command: fastANI --query /var/lib/cwl/stgee856d92-2e55-4ca0-a7c3-f0bf7de4e0a7/GCA_025963735.1_ASM2596373v1_genomic.fna.gz --refList GCA_025963735.1_ASM2596373v1_genomic.fna/target_genomes.txt --output GCA_025963735.1_ASM2596373v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 22:47:29,717] [INFO] Task succeeded: fastANI
[2023-06-30 22:47:29,718] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgff87f373-f9ab-4cc3-9ea0-09eb1b9f2c43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 22:47:29,718] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgff87f373-f9ab-4cc3-9ea0-09eb1b9f2c43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 22:47:29,721] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 22:47:29,721] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 22:47:29,722] [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
--------------------------------------------------------------------------------
[2023-06-30 22:47:29,724] [INFO] DFAST Taxonomy check result was written to GCA_025963735.1_ASM2596373v1_genomic.fna/tc_result.tsv
[2023-06-30 22:47:29,725] [INFO] ===== Taxonomy check completed =====
[2023-06-30 22:47:29,725] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 22:47:29,726] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgff87f373-f9ab-4cc3-9ea0-09eb1b9f2c43/dqc_reference/checkm_data
[2023-06-30 22:47:29,730] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 22:47:29,787] [INFO] Task started: CheckM
[2023-06-30 22:47:29,788] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_025963735.1_ASM2596373v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_025963735.1_ASM2596373v1_genomic.fna/checkm_input GCA_025963735.1_ASM2596373v1_genomic.fna/checkm_result
[2023-06-30 22:48:07,108] [INFO] Task succeeded: CheckM
[2023-06-30 22:48:07,110] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 22:48:07,134] [INFO] ===== Completeness check finished =====
[2023-06-30 22:48:07,134] [INFO] ===== Start GTDB Search =====
[2023-06-30 22:48:07,134] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_025963735.1_ASM2596373v1_genomic.fna/markers.fasta)
[2023-06-30 22:48:07,135] [INFO] Task started: Blastn
[2023-06-30 22:48:07,135] [INFO] Running command: blastn -query GCA_025963735.1_ASM2596373v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff87f373-f9ab-4cc3-9ea0-09eb1b9f2c43/dqc_reference/reference_markers_gtdb.fasta -out GCA_025963735.1_ASM2596373v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 22:48:08,169] [INFO] Task succeeded: Blastn
[2023-06-30 22:48:08,174] [INFO] Selected 22 target genomes.
[2023-06-30 22:48:08,175] [INFO] Target genome list was writen to GCA_025963735.1_ASM2596373v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 22:48:08,188] [INFO] Task started: fastANI
[2023-06-30 22:48:08,188] [INFO] Running command: fastANI --query /var/lib/cwl/stgee856d92-2e55-4ca0-a7c3-f0bf7de4e0a7/GCA_025963735.1_ASM2596373v1_genomic.fna.gz --refList GCA_025963735.1_ASM2596373v1_genomic.fna/target_genomes_gtdb.txt --output GCA_025963735.1_ASM2596373v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 22:48:21,926] [INFO] Task succeeded: fastANI
[2023-06-30 22:48:21,944] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 22:48:21,944] [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_016185125.1	s__UBA2475 sp016185125	78.2907	367	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__UBA2475	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013816895.1	s__UBA2475 sp013816895	78.2098	353	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__UBA2475	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013288385.1	s__UBA2475 sp013288385	77.1123	66	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__UBA2475	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013816615.1	s__UBA2475 sp013816615	77.0546	187	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__UBA2475	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002342065.1	s__UBA2475 sp002342065	76.9109	189	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__UBA2475	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016705695.1	s__UBA2475 sp016705695	76.8978	92	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__UBA2475	95.0	96.82	95.10	0.91	0.90	4	-
GCA_002319075.1	s__UBA2475 sp002319075	76.8678	144	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__UBA2475	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016787785.1	s__UBA2475 sp016787785	76.7088	159	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__UBA2475	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013697245.1	s__UBA2475 sp013697245	76.681	188	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__UBA2475	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016787705.1	s__UBA2475 sp016787705	76.6804	188	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__UBA2475	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016715905.1	s__UBA2475 sp016715905	76.6354	117	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__UBA2475	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017303905.1	s__JAFLBH01 sp017303905	76.2943	92	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__JAFLBH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016788025.1	s__UBA2475 sp016788025	76.1899	71	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__UBA2475	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018267825.1	s__JAFDXR01 sp018267825	75.8478	52	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__JAFDXR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014378485.1	s__UBA4416 sp014378485	75.692	66	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__UBA4416	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003153315.1	s__PALSA-968 sp003153315	75.6641	50	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__PALSA-968	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 22:48:21,946] [INFO] GTDB search result was written to GCA_025963735.1_ASM2596373v1_genomic.fna/result_gtdb.tsv
[2023-06-30 22:48:21,947] [INFO] ===== GTDB Search completed =====
[2023-06-30 22:48:21,950] [INFO] DFAST_QC result json was written to GCA_025963735.1_ASM2596373v1_genomic.fna/dqc_result.json
[2023-06-30 22:48:21,950] [INFO] DFAST_QC completed!
[2023-06-30 22:48:21,950] [INFO] Total running time: 0h1m24s