[2023-06-29 14:58:29,216] [INFO] DFAST_QC pipeline started.
[2023-06-29 14:58:29,219] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 14:58:29,219] [INFO] DQC Reference Directory: /var/lib/cwl/stgde4662f1-9b07-4da3-974a-e517c28e2df1/dqc_reference
[2023-06-29 14:58:30,430] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 14:58:30,431] [INFO] Task started: Prodigal
[2023-06-29 14:58:30,432] [INFO] Running command: gunzip -c /var/lib/cwl/stg82b3cdae-95d7-47e2-a2f6-fef6447f13f4/GCA_021805705.1_ASM2180570v1_genomic.fna.gz | prodigal -d GCA_021805705.1_ASM2180570v1_genomic.fna/cds.fna -a GCA_021805705.1_ASM2180570v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 14:58:40,797] [INFO] Task succeeded: Prodigal
[2023-06-29 14:58:40,798] [INFO] Task started: HMMsearch
[2023-06-29 14:58:40,798] [INFO] Running command: hmmsearch --tblout GCA_021805705.1_ASM2180570v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgde4662f1-9b07-4da3-974a-e517c28e2df1/dqc_reference/reference_markers.hmm GCA_021805705.1_ASM2180570v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 14:58:41,049] [INFO] Task succeeded: HMMsearch
[2023-06-29 14:58:41,050] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg82b3cdae-95d7-47e2-a2f6-fef6447f13f4/GCA_021805705.1_ASM2180570v1_genomic.fna.gz]
[2023-06-29 14:58:41,088] [INFO] Query marker FASTA was written to GCA_021805705.1_ASM2180570v1_genomic.fna/markers.fasta
[2023-06-29 14:58:41,088] [INFO] Task started: Blastn
[2023-06-29 14:58:41,089] [INFO] Running command: blastn -query GCA_021805705.1_ASM2180570v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde4662f1-9b07-4da3-974a-e517c28e2df1/dqc_reference/reference_markers.fasta -out GCA_021805705.1_ASM2180570v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:58:41,668] [INFO] Task succeeded: Blastn
[2023-06-29 14:58:41,673] [INFO] Selected 25 target genomes.
[2023-06-29 14:58:41,673] [INFO] Target genome list was writen to GCA_021805705.1_ASM2180570v1_genomic.fna/target_genomes.txt
[2023-06-29 14:58:41,676] [INFO] Task started: fastANI
[2023-06-29 14:58:41,677] [INFO] Running command: fastANI --query /var/lib/cwl/stg82b3cdae-95d7-47e2-a2f6-fef6447f13f4/GCA_021805705.1_ASM2180570v1_genomic.fna.gz --refList GCA_021805705.1_ASM2180570v1_genomic.fna/target_genomes.txt --output GCA_021805705.1_ASM2180570v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 14:59:02,762] [INFO] Task succeeded: fastANI
[2023-06-29 14:59:02,762] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgde4662f1-9b07-4da3-974a-e517c28e2df1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 14:59:02,763] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgde4662f1-9b07-4da3-974a-e517c28e2df1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 14:59:02,774] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 14:59:02,774] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 14:59:02,774] [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
Acidobacterium capsulatum	strain=ATCC 51196	GCA_000022565.1	33075	33075	type	True	77.2435	70	877	95	below_threshold
Occallatibacter riparius	strain=DSM 25168	GCA_025264625.1	1002689	1002689	type	True	76.7504	89	877	95	below_threshold
Granulicella rosea	strain=DSM 18704	GCA_900188085.1	474952	474952	type	True	76.5253	80	877	95	below_threshold
Edaphobacter flagellatus	strain=HZ411	GCA_025264665.1	1933044	1933044	type	True	76.4478	57	877	95	below_threshold
Terracidiphilus gabretensis	strain=S55	GCA_001449115.1	1577687	1577687	type	True	76.4374	90	877	95	below_threshold
Granulicella mallensis	strain=MP5ACTX8	GCA_000178955.2	940614	940614	type	True	76.4029	51	877	95	below_threshold
Edaphobacter acidisoli	strain=CGMCC 1.15447	GCA_014642855.1	2040573	2040573	type	True	76.3824	73	877	95	below_threshold
Silvibacterium bohemicum	strain=DSM 103733	GCA_014201455.1	1577686	1577686	type	True	76.2403	71	877	95	below_threshold
Paracidobacterium acidisoli	strain=4G-K13	GCA_003428625.2	2303751	2303751	type	True	76.2202	86	877	95	below_threshold
Alloacidobacterium dinghuense	strain=4Y35	GCA_014274465.1	2763107	2763107	type	True	76.1937	50	877	95	below_threshold
Edaphobacter dinghuensis	strain=CGMCC 1.12997	GCA_014640335.1	1560005	1560005	type	True	76.1833	62	877	95	below_threshold
Granulicella sibirica	strain=AF10	GCA_004115155.1	2479048	2479048	type	True	76.1072	59	877	95	below_threshold
Granulicella tundricola	strain=MP5ACTX9	GCA_000178975.2	940615	940615	type	True	75.8346	68	877	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 14:59:02,777] [INFO] DFAST Taxonomy check result was written to GCA_021805705.1_ASM2180570v1_genomic.fna/tc_result.tsv
[2023-06-29 14:59:02,777] [INFO] ===== Taxonomy check completed =====
[2023-06-29 14:59:02,777] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 14:59:02,777] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgde4662f1-9b07-4da3-974a-e517c28e2df1/dqc_reference/checkm_data
[2023-06-29 14:59:02,778] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 14:59:02,819] [INFO] Task started: CheckM
[2023-06-29 14:59:02,820] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021805705.1_ASM2180570v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021805705.1_ASM2180570v1_genomic.fna/checkm_input GCA_021805705.1_ASM2180570v1_genomic.fna/checkm_result
[2023-06-29 14:59:37,389] [INFO] Task succeeded: CheckM
[2023-06-29 14:59:37,390] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 44.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 14:59:37,412] [INFO] ===== Completeness check finished =====
[2023-06-29 14:59:37,412] [INFO] ===== Start GTDB Search =====
[2023-06-29 14:59:37,413] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021805705.1_ASM2180570v1_genomic.fna/markers.fasta)
[2023-06-29 14:59:37,413] [INFO] Task started: Blastn
[2023-06-29 14:59:37,413] [INFO] Running command: blastn -query GCA_021805705.1_ASM2180570v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde4662f1-9b07-4da3-974a-e517c28e2df1/dqc_reference/reference_markers_gtdb.fasta -out GCA_021805705.1_ASM2180570v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:59:38,214] [INFO] Task succeeded: Blastn
[2023-06-29 14:59:38,219] [INFO] Selected 22 target genomes.
[2023-06-29 14:59:38,219] [INFO] Target genome list was writen to GCA_021805705.1_ASM2180570v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 14:59:38,222] [INFO] Task started: fastANI
[2023-06-29 14:59:38,222] [INFO] Running command: fastANI --query /var/lib/cwl/stg82b3cdae-95d7-47e2-a2f6-fef6447f13f4/GCA_021805705.1_ASM2180570v1_genomic.fna.gz --refList GCA_021805705.1_ASM2180570v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021805705.1_ASM2180570v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 14:59:53,556] [INFO] Task succeeded: fastANI
[2023-06-29 14:59:53,580] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 14:59:53,580] [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_903842065.1	s__Terracidiphilus sp903842065	76.974	69	877	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903849645.1	s__Terracidiphilus sp903849645	76.892	122	877	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	99.99	99.99	0.99	0.99	2	-
GCA_003142015.1	s__Terracidiphilus sp003142015	76.694	82	877	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	99.69	99.69	0.91	0.91	2	-
GCF_900290245.1	s__Terracidiphilus gaucii	76.6704	70	877	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003167305.1	s__Terracidiphilus sp003167305	76.66	65	877	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011333575.1	s__Acidobacterium capsulatum_A	76.6539	88	877	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Acidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015655365.1	s__Terracidiphilus sp015655365	76.6458	58	877	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003134855.1	s__Terracidiphilus sp003134855	76.6353	92	877	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003170825.1	s__Terracidiphilus sp003170825	76.6322	110	877	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	99.88	99.70	0.95	0.95	8	-
GCA_000381585.1	s__KBS-83 sp000381585	76.5528	55	877	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__KBS-83	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002307235.1	s__Terracidiphilus sp002307235	76.5081	80	877	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	76.4441	116	877	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	99.74	99.71	0.89	0.87	5	-
GCA_003159355.1	s__Terracidiphilus sp003159355	76.4163	88	877	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	99.48	99.30	0.83	0.80	7	-
GCA_903832475.1	s__CAIVDV01 sp903832475	76.3789	96	877	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__CAIVDV01	95.0	98.66	98.66	0.84	0.84	2	-
GCA_003161045.1	s__Terracidiphilus sp003161045	76.3612	90	877	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	99.61	99.39	0.87	0.83	8	-
GCA_903828675.1	s__Terracidiphilus sp903828675	76.238	76	877	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	99.87	99.75	0.95	0.93	4	-
GCF_003428625.2	s__Palsa-343 sp003428625	76.2202	86	877	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_003171315.1	s__Terracidiphilus sp003171315	76.1966	74	877	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003140785.1	s__Terracidiphilus sp003140785	76.106	65	877	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	98.14	96.92	0.80	0.78	3	-
GCA_000620725.1	s__Terracidiphilus sp000620725	76.1036	85	877	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903832055.1	s__CAIVDV01 sp903832055	76.0814	102	877	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__CAIVDV01	95.0	100.00	100.00	0.99	0.99	4	-
GCA_003133425.1	s__Terracidiphilus sp003133425	76.024	82	877	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	99.36	99.32	0.83	0.80	3	-
--------------------------------------------------------------------------------
[2023-06-29 14:59:53,582] [INFO] GTDB search result was written to GCA_021805705.1_ASM2180570v1_genomic.fna/result_gtdb.tsv
[2023-06-29 14:59:53,583] [INFO] ===== GTDB Search completed =====
[2023-06-29 14:59:53,587] [INFO] DFAST_QC result json was written to GCA_021805705.1_ASM2180570v1_genomic.fna/dqc_result.json
[2023-06-29 14:59:53,587] [INFO] DFAST_QC completed!
[2023-06-29 14:59:53,588] [INFO] Total running time: 0h1m24s