[2023-06-29 03:21:15,914] [INFO] DFAST_QC pipeline started.
[2023-06-29 03:21:15,919] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 03:21:15,919] [INFO] DQC Reference Directory: /var/lib/cwl/stgf98cf7b8-56f8-4aba-813a-00f45bfb5ea1/dqc_reference
[2023-06-29 03:21:17,774] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 03:21:17,775] [INFO] Task started: Prodigal
[2023-06-29 03:21:17,775] [INFO] Running command: gunzip -c /var/lib/cwl/stg4613a977-9d68-4d11-8fc6-bdaa2daff6fd/GCA_020072645.1_ASM2007264v1_genomic.fna.gz | prodigal -d GCA_020072645.1_ASM2007264v1_genomic.fna/cds.fna -a GCA_020072645.1_ASM2007264v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 03:21:37,151] [INFO] Task succeeded: Prodigal
[2023-06-29 03:21:37,152] [INFO] Task started: HMMsearch
[2023-06-29 03:21:37,152] [INFO] Running command: hmmsearch --tblout GCA_020072645.1_ASM2007264v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf98cf7b8-56f8-4aba-813a-00f45bfb5ea1/dqc_reference/reference_markers.hmm GCA_020072645.1_ASM2007264v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 03:21:37,429] [INFO] Task succeeded: HMMsearch
[2023-06-29 03:21:37,430] [INFO] Found 6/6 markers.
[2023-06-29 03:21:37,476] [INFO] Query marker FASTA was written to GCA_020072645.1_ASM2007264v1_genomic.fna/markers.fasta
[2023-06-29 03:21:37,476] [INFO] Task started: Blastn
[2023-06-29 03:21:37,477] [INFO] Running command: blastn -query GCA_020072645.1_ASM2007264v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf98cf7b8-56f8-4aba-813a-00f45bfb5ea1/dqc_reference/reference_markers.fasta -out GCA_020072645.1_ASM2007264v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 03:21:38,046] [INFO] Task succeeded: Blastn
[2023-06-29 03:21:38,049] [INFO] Selected 25 target genomes.
[2023-06-29 03:21:38,049] [INFO] Target genome list was writen to GCA_020072645.1_ASM2007264v1_genomic.fna/target_genomes.txt
[2023-06-29 03:21:38,052] [INFO] Task started: fastANI
[2023-06-29 03:21:38,052] [INFO] Running command: fastANI --query /var/lib/cwl/stg4613a977-9d68-4d11-8fc6-bdaa2daff6fd/GCA_020072645.1_ASM2007264v1_genomic.fna.gz --refList GCA_020072645.1_ASM2007264v1_genomic.fna/target_genomes.txt --output GCA_020072645.1_ASM2007264v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 03:21:54,822] [INFO] Task succeeded: fastANI
[2023-06-29 03:21:54,823] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf98cf7b8-56f8-4aba-813a-00f45bfb5ea1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 03:21:54,823] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf98cf7b8-56f8-4aba-813a-00f45bfb5ea1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 03:21:54,830] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 03:21:54,830] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 03:21:54,830] [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
Silvibacterium bohemicum	strain=DSM 103733	GCA_014201455.1	1577686	1577686	type	True	76.4741	60	2123	95	below_threshold
Silvibacterium bohemicum	strain=S15	GCA_001006305.1	1577686	1577686	type	True	76.4545	59	2123	95	below_threshold
Occallatibacter riparius	strain=DSM 25168	GCA_025264625.1	1002689	1002689	type	True	76.1593	55	2123	95	below_threshold
Paracidobacterium acidisoli	strain=4G-K13	GCA_003428625.2	2303751	2303751	type	True	76.1095	55	2123	95	below_threshold
Acidobacterium capsulatum	strain=ATCC 51196	GCA_000022565.1	33075	33075	type	True	75.9841	63	2123	95	below_threshold
Acidipila rosea	strain=DSM 103428	GCA_004339725.1	768535	768535	type	True	75.8046	58	2123	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 03:21:54,831] [INFO] DFAST Taxonomy check result was written to GCA_020072645.1_ASM2007264v1_genomic.fna/tc_result.tsv
[2023-06-29 03:21:54,832] [INFO] ===== Taxonomy check completed =====
[2023-06-29 03:21:54,832] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 03:21:54,832] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf98cf7b8-56f8-4aba-813a-00f45bfb5ea1/dqc_reference/checkm_data
[2023-06-29 03:21:54,833] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 03:21:54,890] [INFO] Task started: CheckM
[2023-06-29 03:21:54,890] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020072645.1_ASM2007264v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020072645.1_ASM2007264v1_genomic.fna/checkm_input GCA_020072645.1_ASM2007264v1_genomic.fna/checkm_result
[2023-06-29 03:22:50,440] [INFO] Task succeeded: CheckM
[2023-06-29 03:22:50,441] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 03:22:50,458] [INFO] ===== Completeness check finished =====
[2023-06-29 03:22:50,459] [INFO] ===== Start GTDB Search =====
[2023-06-29 03:22:50,459] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020072645.1_ASM2007264v1_genomic.fna/markers.fasta)
[2023-06-29 03:22:50,459] [INFO] Task started: Blastn
[2023-06-29 03:22:50,459] [INFO] Running command: blastn -query GCA_020072645.1_ASM2007264v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf98cf7b8-56f8-4aba-813a-00f45bfb5ea1/dqc_reference/reference_markers_gtdb.fasta -out GCA_020072645.1_ASM2007264v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 03:22:51,268] [INFO] Task succeeded: Blastn
[2023-06-29 03:22:51,272] [INFO] Selected 31 target genomes.
[2023-06-29 03:22:51,272] [INFO] Target genome list was writen to GCA_020072645.1_ASM2007264v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 03:22:51,291] [INFO] Task started: fastANI
[2023-06-29 03:22:51,291] [INFO] Running command: fastANI --query /var/lib/cwl/stg4613a977-9d68-4d11-8fc6-bdaa2daff6fd/GCA_020072645.1_ASM2007264v1_genomic.fna.gz --refList GCA_020072645.1_ASM2007264v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020072645.1_ASM2007264v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 03:23:15,722] [INFO] Task succeeded: fastANI
[2023-06-29 03:23:15,736] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 03:23:15,737] [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_003223515.1	s__Gp1-AA17 sp003223515	77.328	289	2123	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Gp1-AA117;g__Gp1-AA17	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003140235.1	s__Gp1-AA17 sp003140235	76.7522	224	2123	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Gp1-AA117;g__Gp1-AA17	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003152695.1	s__Bog-257 sp003152695	76.2694	85	2123	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Koribacteraceae;g__Bog-257	95.0	99.78	99.24	0.95	0.92	6	-
GCA_903832295.1	s__TOLSYN sp903832295	76.2138	59	2123	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Koribacteraceae;g__TOLSYN	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013289685.1	s__Sulfotelmatobacter sp013289685	76.1989	97	2123	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__SbA1;g__Sulfotelmatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003140075.1	s__Sulfotelmatobacter sp003140075	76.1613	85	2123	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__SbA1;g__Sulfotelmatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003131315.1	s__Bog-209 sp003131315	76.1065	88	2123	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__SbA1;g__Bog-209	95.0	99.89	99.89	0.97	0.97	2	-
GCA_003138975.1	s__Sulfotelmatobacter sp003138975	76.067	62	2123	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__SbA1;g__Sulfotelmatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003160215.1	s__Bog-257 sp003160215	76.0338	72	2123	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Koribacteraceae;g__Bog-257	95.0	96.50	96.50	0.80	0.80	2	-
GCA_903851035.1	s__TOLSYN sp903851035	75.9938	84	2123	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Koribacteraceae;g__TOLSYN	95.0	99.85	99.84	0.94	0.92	5	-
GCA_018268755.1	s__KAN-5 sp018268755	75.993	93	2123	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__SbA1;g__KAN-5	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003151875.1	s__Bog-257 sp003151875	75.9733	65	2123	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Koribacteraceae;g__Bog-257	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019243475.1	s__Gp1-AA112 sp019243475	75.8813	63	2123	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Gp1-AA112;g__Gp1-AA112	95.0	98.96	98.93	0.84	0.83	3	-
GCA_003225215.1	s__Gp1-AA112 sp003225215	75.7811	56	2123	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Gp1-AA112;g__Gp1-AA112	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008682415.1	s__Terracidiphilus sp008682415	75.7256	54	2123	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003139795.1	s__Terracidiphilus sp003139795	75.5126	61	2123	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	99.74	99.71	0.89	0.87	5	-
GCF_000014905.1	s__Solibacter usitatus_A	75.2294	58	2123	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__Solibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 03:23:15,739] [INFO] GTDB search result was written to GCA_020072645.1_ASM2007264v1_genomic.fna/result_gtdb.tsv
[2023-06-29 03:23:15,739] [INFO] ===== GTDB Search completed =====
[2023-06-29 03:23:15,743] [INFO] DFAST_QC result json was written to GCA_020072645.1_ASM2007264v1_genomic.fna/dqc_result.json
[2023-06-29 03:23:15,743] [INFO] DFAST_QC completed!
[2023-06-29 03:23:15,743] [INFO] Total running time: 0h1m60s