[2024-01-25 17:48:50,550] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:48:50,551] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:48:50,551] [INFO] DQC Reference Directory: /var/lib/cwl/stg744509ab-011d-4394-a2ca-763f21b9f4fc/dqc_reference
[2024-01-25 17:48:51,651] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:48:51,651] [INFO] Task started: Prodigal
[2024-01-25 17:48:51,652] [INFO] Running command: gunzip -c /var/lib/cwl/stg9b08df52-a0b6-46ce-88ce-ec10651baab5/GCF_025685655.1_ASM2568565v1_genomic.fna.gz | prodigal -d GCF_025685655.1_ASM2568565v1_genomic.fna/cds.fna -a GCF_025685655.1_ASM2568565v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:49:06,161] [INFO] Task succeeded: Prodigal
[2024-01-25 17:49:06,161] [INFO] Task started: HMMsearch
[2024-01-25 17:49:06,161] [INFO] Running command: hmmsearch --tblout GCF_025685655.1_ASM2568565v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg744509ab-011d-4394-a2ca-763f21b9f4fc/dqc_reference/reference_markers.hmm GCF_025685655.1_ASM2568565v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:49:06,510] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:49:06,511] [INFO] Found 6/6 markers.
[2024-01-25 17:49:06,556] [INFO] Query marker FASTA was written to GCF_025685655.1_ASM2568565v1_genomic.fna/markers.fasta
[2024-01-25 17:49:06,556] [INFO] Task started: Blastn
[2024-01-25 17:49:06,556] [INFO] Running command: blastn -query GCF_025685655.1_ASM2568565v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg744509ab-011d-4394-a2ca-763f21b9f4fc/dqc_reference/reference_markers.fasta -out GCF_025685655.1_ASM2568565v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:49:07,144] [INFO] Task succeeded: Blastn
[2024-01-25 17:49:07,147] [INFO] Selected 18 target genomes.
[2024-01-25 17:49:07,147] [INFO] Target genome list was writen to GCF_025685655.1_ASM2568565v1_genomic.fna/target_genomes.txt
[2024-01-25 17:49:07,197] [INFO] Task started: fastANI
[2024-01-25 17:49:07,197] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b08df52-a0b6-46ce-88ce-ec10651baab5/GCF_025685655.1_ASM2568565v1_genomic.fna.gz --refList GCF_025685655.1_ASM2568565v1_genomic.fna/target_genomes.txt --output GCF_025685655.1_ASM2568565v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:49:24,529] [INFO] Task succeeded: fastANI
[2024-01-25 17:49:24,529] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg744509ab-011d-4394-a2ca-763f21b9f4fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:49:24,530] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg744509ab-011d-4394-a2ca-763f21b9f4fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:49:24,541] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:49:24,541] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:49:24,541] [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
Acidisarcina polymorpha	strain=SBC82	GCA_003330725.1	2211140	2211140	type	True	77.6953	123	1885	95	below_threshold
Edaphobacter lichenicola	strain=DSM 104462	GCA_025264645.1	2051959	2051959	suspected-type	True	77.3613	112	1885	95	below_threshold
Terriglobus roseus	strain=DSM 18391	GCA_000265425.1	392734	392734	type	True	77.2415	83	1885	95	below_threshold
Silvibacterium bohemicum	strain=DSM 103733	GCA_014201455.1	1577686	1577686	type	True	77.1124	165	1885	95	below_threshold
Alloacidobacterium dinghuense	strain=4Y35	GCA_014274465.1	2763107	2763107	type	True	77.0851	90	1885	95	below_threshold
Acidipila rosea	strain=DSM 103428	GCA_004339725.1	768535	768535	type	True	77.0838	117	1885	95	below_threshold
Occallatibacter riparius	strain=DSM 25168	GCA_025264625.1	1002689	1002689	type	True	77.039	135	1885	95	below_threshold
Acidobacterium capsulatum	strain=ATCC 51196	GCA_000022565.1	33075	33075	type	True	77.013	110	1885	95	below_threshold
Silvibacterium dinghuense	strain=CGMCC 1.13007	GCA_014640355.1	1560006	1560006	type	True	77.007	144	1885	95	below_threshold
Silvibacterium dinghuense	strain=DHOF10	GCA_004123295.1	1560006	1560006	type	True	76.9326	143	1885	95	below_threshold
Terracidiphilus gabretensis	strain=S55	GCA_001449115.1	1577687	1577687	type	True	76.9285	148	1885	95	below_threshold
Edaphobacter dinghuensis	strain=CGMCC 1.12997	GCA_014640335.1	1560005	1560005	type	True	76.8771	112	1885	95	below_threshold
Edaphobacter aggregans	strain=DSM 19364	GCA_000745965.1	570835	570835	type	True	76.8542	119	1885	95	below_threshold
Edaphobacter modestus	strain=DSM 18101	GCA_004217555.1	388466	388466	type	True	76.6563	126	1885	95	below_threshold
Paracidobacterium acidisoli	strain=4G-K13	GCA_003428625.2	2303751	2303751	type	True	76.5028	138	1885	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:49:24,542] [INFO] DFAST Taxonomy check result was written to GCF_025685655.1_ASM2568565v1_genomic.fna/tc_result.tsv
[2024-01-25 17:49:24,543] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:49:24,543] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:49:24,543] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg744509ab-011d-4394-a2ca-763f21b9f4fc/dqc_reference/checkm_data
[2024-01-25 17:49:24,544] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:49:24,601] [INFO] Task started: CheckM
[2024-01-25 17:49:24,602] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025685655.1_ASM2568565v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025685655.1_ASM2568565v1_genomic.fna/checkm_input GCF_025685655.1_ASM2568565v1_genomic.fna/checkm_result
[2024-01-25 17:50:08,873] [INFO] Task succeeded: CheckM
[2024-01-25 17:50:08,874] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:50:08,891] [INFO] ===== Completeness check finished =====
[2024-01-25 17:50:08,891] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:50:08,892] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025685655.1_ASM2568565v1_genomic.fna/markers.fasta)
[2024-01-25 17:50:08,892] [INFO] Task started: Blastn
[2024-01-25 17:50:08,892] [INFO] Running command: blastn -query GCF_025685655.1_ASM2568565v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg744509ab-011d-4394-a2ca-763f21b9f4fc/dqc_reference/reference_markers_gtdb.fasta -out GCF_025685655.1_ASM2568565v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:50:09,815] [INFO] Task succeeded: Blastn
[2024-01-25 17:50:09,818] [INFO] Selected 20 target genomes.
[2024-01-25 17:50:09,818] [INFO] Target genome list was writen to GCF_025685655.1_ASM2568565v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:50:09,857] [INFO] Task started: fastANI
[2024-01-25 17:50:09,857] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b08df52-a0b6-46ce-88ce-ec10651baab5/GCF_025685655.1_ASM2568565v1_genomic.fna.gz --refList GCF_025685655.1_ASM2568565v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025685655.1_ASM2568565v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:50:27,046] [INFO] Task succeeded: fastANI
[2024-01-25 17:50:27,056] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 17:50:27,057] [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_903832055.1	s__CAIVDV01 sp903832055	78.1829	359	1885	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__CAIVDV01	95.0	100.00	100.00	0.99	0.99	4	-
GCA_903832475.1	s__CAIVDV01 sp903832475	77.8839	278	1885	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__CAIVDV01	95.0	98.66	98.66	0.84	0.84	2	-
GCA_903904755.1	s__CAIVDV01 sp903904755	77.8447	223	1885	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__CAIVDV01	95.0	99.92	99.89	0.96	0.95	6	-
GCA_903849645.1	s__Terracidiphilus sp903849645	77.3005	190	1885	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003131205.1	s__Terracidiphilus savannae	76.9852	149	1885	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001449115.1	s__Terracidiphilus gabretensis	76.9285	148	1885	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410875.1	s__Edaphobacter lichenicola_C	76.8911	117	1885	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015654835.1	s__Terracidiphilus sp015654835	76.7	150	1885	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201315.1	s__Edaphobacter lichenicola_B	76.65	107	1885	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003151435.1	s__Terracidiphilus sp003151435	76.5565	133	1885	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	99.67	99.67	0.90	0.90	2	-
GCF_003428625.2	s__Palsa-343 sp003428625	76.5028	138	1885	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Palsa-343	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903828675.1	s__Terracidiphilus sp903828675	76.49	132	1885	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	99.87	99.75	0.95	0.93	4	-
GCA_013289875.1	s__Silvibacterium sp013289875	76.4734	93	1885	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Silvibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903842845.1	s__CAIMNN01 sp903842845	76.4617	80	1885	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__CAIMNN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903873705.1	s__CAIQPK01 sp903873705	76.38	83	1885	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__CAIQPK01	95.0	99.92	99.91	0.95	0.94	3	-
GCA_003140785.1	s__Terracidiphilus sp003140785	76.2367	108	1885	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	98.14	96.92	0.80	0.78	3	-
GCA_003165935.1	s__Terracidiphilus sp003165935	76.1068	115	1885	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:50:27,058] [INFO] GTDB search result was written to GCF_025685655.1_ASM2568565v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:50:27,059] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:50:27,063] [INFO] DFAST_QC result json was written to GCF_025685655.1_ASM2568565v1_genomic.fna/dqc_result.json
[2024-01-25 17:50:27,063] [INFO] DFAST_QC completed!
[2024-01-25 17:50:27,063] [INFO] Total running time: 0h1m37s