[2024-01-25 19:40:50,689] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:40:50,691] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:40:50,691] [INFO] DQC Reference Directory: /var/lib/cwl/stg690f8e86-1d6f-4d11-8358-cf7476c6b5bd/dqc_reference
[2024-01-25 19:40:51,897] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:40:51,897] [INFO] Task started: Prodigal
[2024-01-25 19:40:51,898] [INFO] Running command: gunzip -c /var/lib/cwl/stg979bdd43-b7a9-476c-9db2-68cf32d1bf43/GCF_025264625.1_ASM2526462v1_genomic.fna.gz | prodigal -d GCF_025264625.1_ASM2526462v1_genomic.fna/cds.fna -a GCF_025264625.1_ASM2526462v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:41:10,246] [INFO] Task succeeded: Prodigal
[2024-01-25 19:41:10,247] [INFO] Task started: HMMsearch
[2024-01-25 19:41:10,247] [INFO] Running command: hmmsearch --tblout GCF_025264625.1_ASM2526462v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg690f8e86-1d6f-4d11-8358-cf7476c6b5bd/dqc_reference/reference_markers.hmm GCF_025264625.1_ASM2526462v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:41:10,528] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:41:10,532] [INFO] Found 6/6 markers.
[2024-01-25 19:41:10,585] [INFO] Query marker FASTA was written to GCF_025264625.1_ASM2526462v1_genomic.fna/markers.fasta
[2024-01-25 19:41:10,585] [INFO] Task started: Blastn
[2024-01-25 19:41:10,586] [INFO] Running command: blastn -query GCF_025264625.1_ASM2526462v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg690f8e86-1d6f-4d11-8358-cf7476c6b5bd/dqc_reference/reference_markers.fasta -out GCF_025264625.1_ASM2526462v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:41:11,168] [INFO] Task succeeded: Blastn
[2024-01-25 19:41:11,170] [INFO] Selected 21 target genomes.
[2024-01-25 19:41:11,171] [INFO] Target genome list was writen to GCF_025264625.1_ASM2526462v1_genomic.fna/target_genomes.txt
[2024-01-25 19:41:11,186] [INFO] Task started: fastANI
[2024-01-25 19:41:11,186] [INFO] Running command: fastANI --query /var/lib/cwl/stg979bdd43-b7a9-476c-9db2-68cf32d1bf43/GCF_025264625.1_ASM2526462v1_genomic.fna.gz --refList GCF_025264625.1_ASM2526462v1_genomic.fna/target_genomes.txt --output GCF_025264625.1_ASM2526462v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:41:30,633] [INFO] Task succeeded: fastANI
[2024-01-25 19:41:30,633] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg690f8e86-1d6f-4d11-8358-cf7476c6b5bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:41:30,633] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg690f8e86-1d6f-4d11-8358-cf7476c6b5bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:41:30,643] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:41:30,643] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:41:30,643] [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
Occallatibacter riparius	strain=DSM 25168	GCA_025264625.1	1002689	1002689	type	True	100.0	2264	2264	95	conclusive
Terracidiphilus gabretensis	strain=S55	GCA_001449115.1	1577687	1577687	type	True	77.2158	325	2264	95	below_threshold
Silvibacterium dinghuense	strain=DHOF10	GCA_004123295.1	1560006	1560006	type	True	77.1773	184	2264	95	below_threshold
Silvibacterium dinghuense	strain=CGMCC 1.13007	GCA_014640355.1	1560006	1560006	type	True	77.1575	179	2264	95	below_threshold
Silvibacterium bohemicum	strain=DSM 103733	GCA_014201455.1	1577686	1577686	type	True	77.066	197	2264	95	below_threshold
Acidobacterium capsulatum	strain=ATCC 51196	GCA_000022565.1	33075	33075	type	True	76.8748	187	2264	95	below_threshold
Paracidobacterium acidisoli	strain=4G-K13	GCA_003428625.2	2303751	2303751	type	True	76.8015	233	2264	95	below_threshold
Edaphobacter modestus	strain=DSM 18101	GCA_004217555.1	388466	388466	type	True	76.7779	119	2264	95	below_threshold
Edaphobacter lichenicola	strain=DSM 104462	GCA_025264645.1	2051959	2051959	suspected-type	True	76.6417	111	2264	95	below_threshold
Acidipila rosea	strain=DSM 103428	GCA_004339725.1	768535	768535	type	True	76.5695	140	2264	95	below_threshold
Acidisarcina polymorpha	strain=SBC82	GCA_003330725.1	2211140	2211140	type	True	76.5063	115	2264	95	below_threshold
Granulicella mallensis	strain=MP5ACTX8	GCA_000178955.2	940614	940614	type	True	76.4431	137	2264	95	below_threshold
Granulicella rosea	strain=DSM 18704	GCA_900188085.1	474952	474952	type	True	76.4265	171	2264	95	below_threshold
Myxococcus fulvus	strain=NBRC 100333	GCA_007991095.1	33	33	type	True	75.0516	89	2264	95	below_threshold
Myxococcus fulvus	strain=DSM 16525	GCA_900111765.1	33	33	type	True	75.0439	90	2264	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:41:30,645] [INFO] DFAST Taxonomy check result was written to GCF_025264625.1_ASM2526462v1_genomic.fna/tc_result.tsv
[2024-01-25 19:41:30,645] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:41:30,645] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:41:30,645] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg690f8e86-1d6f-4d11-8358-cf7476c6b5bd/dqc_reference/checkm_data
[2024-01-25 19:41:30,646] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:41:30,710] [INFO] Task started: CheckM
[2024-01-25 19:41:30,710] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025264625.1_ASM2526462v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025264625.1_ASM2526462v1_genomic.fna/checkm_input GCF_025264625.1_ASM2526462v1_genomic.fna/checkm_result
[2024-01-25 19:42:21,869] [INFO] Task succeeded: CheckM
[2024-01-25 19:42:21,870] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:42:21,892] [INFO] ===== Completeness check finished =====
[2024-01-25 19:42:21,892] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:42:21,893] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025264625.1_ASM2526462v1_genomic.fna/markers.fasta)
[2024-01-25 19:42:21,893] [INFO] Task started: Blastn
[2024-01-25 19:42:21,894] [INFO] Running command: blastn -query GCF_025264625.1_ASM2526462v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg690f8e86-1d6f-4d11-8358-cf7476c6b5bd/dqc_reference/reference_markers_gtdb.fasta -out GCF_025264625.1_ASM2526462v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:42:22,870] [INFO] Task succeeded: Blastn
[2024-01-25 19:42:22,872] [INFO] Selected 22 target genomes.
[2024-01-25 19:42:22,873] [INFO] Target genome list was writen to GCF_025264625.1_ASM2526462v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:42:22,905] [INFO] Task started: fastANI
[2024-01-25 19:42:22,905] [INFO] Running command: fastANI --query /var/lib/cwl/stg979bdd43-b7a9-476c-9db2-68cf32d1bf43/GCF_025264625.1_ASM2526462v1_genomic.fna.gz --refList GCF_025264625.1_ASM2526462v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025264625.1_ASM2526462v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:42:44,180] [INFO] Task succeeded: fastANI
[2024-01-25 19:42:44,192] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:42:44,192] [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_000620725.1	s__Terracidiphilus sp000620725	78.6554	762	2264	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008682415.1	s__Terracidiphilus sp008682415	77.8192	512	2264	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	77.5988	297	2264	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	99.88	99.70	0.95	0.95	8	-
GCF_003131205.1	s__Terracidiphilus savannae	77.5352	398	2264	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	77.4731	384	2264	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	99.99	99.99	0.99	0.99	2	-
GCA_002314435.1	s__Terracidiphilus sp002314435	77.4452	351	2264	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268915.1	s__Terracidiphilus sp018268915	77.3109	307	2264	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003142935.1	s__Terracidiphilus sp003142935	77.3069	279	2264	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	99.68	99.68	0.90	0.90	2	-
GCA_003151435.1	s__Terracidiphilus sp003151435	77.2762	374	2264	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	99.67	99.67	0.90	0.90	2	-
GCA_903842065.1	s__Terracidiphilus sp903842065	77.2373	241	2264	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	77.2075	326	2264	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	77.1916	360	2264	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	99.74	99.71	0.89	0.87	5	-
GCA_015654835.1	s__Terracidiphilus sp015654835	77.1372	266	2264	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903828675.1	s__Terracidiphilus sp903828675	77.1012	277	2264	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	99.87	99.75	0.95	0.93	4	-
GCA_002307235.1	s__Terracidiphilus sp002307235	77.0142	230	2264	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	76.9683	214	2264	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903904755.1	s__CAIVDV01 sp903904755	76.9561	226	2264	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__CAIVDV01	95.0	99.92	99.89	0.96	0.95	6	-
GCA_003133425.1	s__Terracidiphilus sp003133425	76.8334	282	2264	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	99.36	99.32	0.83	0.80	3	-
GCA_003162495.1	s__Terracidiphilus sp003162495	76.7795	201	2264	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	76.707	208	2264	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__CAIVDV01	95.0	100.00	100.00	0.99	0.99	4	-
--------------------------------------------------------------------------------
[2024-01-25 19:42:44,193] [INFO] GTDB search result was written to GCF_025264625.1_ASM2526462v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:42:44,194] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:42:44,197] [INFO] DFAST_QC result json was written to GCF_025264625.1_ASM2526462v1_genomic.fna/dqc_result.json
[2024-01-25 19:42:44,198] [INFO] DFAST_QC completed!
[2024-01-25 19:42:44,198] [INFO] Total running time: 0h1m54s