[2023-06-29 16:35:32,409] [INFO] DFAST_QC pipeline started.
[2023-06-29 16:35:32,411] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 16:35:32,412] [INFO] DQC Reference Directory: /var/lib/cwl/stg9b496288-ab68-4e68-913a-e500a9071b26/dqc_reference
[2023-06-29 16:35:33,725] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 16:35:33,726] [INFO] Task started: Prodigal
[2023-06-29 16:35:33,726] [INFO] Running command: gunzip -c /var/lib/cwl/stg4baaa3a6-030e-4ea3-9b60-2505b2021544/GCA_021793405.1_ASM2179340v1_genomic.fna.gz | prodigal -d GCA_021793405.1_ASM2179340v1_genomic.fna/cds.fna -a GCA_021793405.1_ASM2179340v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 16:35:47,474] [INFO] Task succeeded: Prodigal
[2023-06-29 16:35:47,474] [INFO] Task started: HMMsearch
[2023-06-29 16:35:47,475] [INFO] Running command: hmmsearch --tblout GCA_021793405.1_ASM2179340v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9b496288-ab68-4e68-913a-e500a9071b26/dqc_reference/reference_markers.hmm GCA_021793405.1_ASM2179340v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 16:35:47,770] [INFO] Task succeeded: HMMsearch
[2023-06-29 16:35:47,772] [INFO] Found 6/6 markers.
[2023-06-29 16:35:47,815] [INFO] Query marker FASTA was written to GCA_021793405.1_ASM2179340v1_genomic.fna/markers.fasta
[2023-06-29 16:35:47,815] [INFO] Task started: Blastn
[2023-06-29 16:35:47,815] [INFO] Running command: blastn -query GCA_021793405.1_ASM2179340v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b496288-ab68-4e68-913a-e500a9071b26/dqc_reference/reference_markers.fasta -out GCA_021793405.1_ASM2179340v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:35:48,424] [INFO] Task succeeded: Blastn
[2023-06-29 16:35:48,428] [INFO] Selected 18 target genomes.
[2023-06-29 16:35:48,429] [INFO] Target genome list was writen to GCA_021793405.1_ASM2179340v1_genomic.fna/target_genomes.txt
[2023-06-29 16:35:48,433] [INFO] Task started: fastANI
[2023-06-29 16:35:48,433] [INFO] Running command: fastANI --query /var/lib/cwl/stg4baaa3a6-030e-4ea3-9b60-2505b2021544/GCA_021793405.1_ASM2179340v1_genomic.fna.gz --refList GCA_021793405.1_ASM2179340v1_genomic.fna/target_genomes.txt --output GCA_021793405.1_ASM2179340v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 16:36:02,503] [INFO] Task succeeded: fastANI
[2023-06-29 16:36:02,504] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9b496288-ab68-4e68-913a-e500a9071b26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 16:36:02,504] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9b496288-ab68-4e68-913a-e500a9071b26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 16:36:02,515] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 16:36:02,515] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 16:36:02,516] [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
Acidipila rosea	strain=DSM 103428	GCA_004339725.1	768535	768535	type	True	77.5489	98	1467	95	below_threshold
Acidobacterium capsulatum	strain=ATCC 51196	GCA_000022565.1	33075	33075	type	True	76.4428	84	1467	95	below_threshold
Silvibacterium bohemicum	strain=S15	GCA_001006305.1	1577686	1577686	type	True	76.2386	99	1467	95	below_threshold
Silvibacterium bohemicum	strain=DSM 103733	GCA_014201455.1	1577686	1577686	type	True	76.2066	97	1467	95	below_threshold
Paracidobacterium acidisoli	strain=4G-K13	GCA_003428625.2	2303751	2303751	type	True	76.1345	108	1467	95	below_threshold
Acidisarcina polymorpha	strain=SBC82	GCA_003330725.1	2211140	2211140	type	True	76.0672	56	1467	95	below_threshold
Terriglobus saanensis	strain=SP1PR4	GCA_000179915.2	870903	870903	type	True	76.0121	50	1467	95	below_threshold
Silvibacterium dinghuense	strain=DHOF10	GCA_004123295.1	1560006	1560006	type	True	75.9874	86	1467	95	below_threshold
Silvibacterium dinghuense	strain=CGMCC 1.13007	GCA_014640355.1	1560006	1560006	type	True	75.8996	86	1467	95	below_threshold
Alloacidobacterium dinghuense	strain=4Y35	GCA_014274465.1	2763107	2763107	type	True	75.7918	78	1467	95	below_threshold
Granulicella rosea	strain=DSM 18704	GCA_900188085.1	474952	474952	type	True	75.7318	66	1467	95	below_threshold
Granulicella mallensis	strain=MP5ACTX8	GCA_000178955.2	940614	940614	type	True	75.6326	56	1467	95	below_threshold
Granulicella tundricola	strain=MP5ACTX9	GCA_000178975.2	940615	940615	type	True	75.3186	53	1467	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 16:36:02,518] [INFO] DFAST Taxonomy check result was written to GCA_021793405.1_ASM2179340v1_genomic.fna/tc_result.tsv
[2023-06-29 16:36:02,519] [INFO] ===== Taxonomy check completed =====
[2023-06-29 16:36:02,519] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 16:36:02,519] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9b496288-ab68-4e68-913a-e500a9071b26/dqc_reference/checkm_data
[2023-06-29 16:36:02,521] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 16:36:02,574] [INFO] Task started: CheckM
[2023-06-29 16:36:02,574] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021793405.1_ASM2179340v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021793405.1_ASM2179340v1_genomic.fna/checkm_input GCA_021793405.1_ASM2179340v1_genomic.fna/checkm_result
[2023-06-29 16:36:44,708] [INFO] Task succeeded: CheckM
[2023-06-29 16:36:44,710] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 16:36:44,732] [INFO] ===== Completeness check finished =====
[2023-06-29 16:36:44,733] [INFO] ===== Start GTDB Search =====
[2023-06-29 16:36:44,733] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021793405.1_ASM2179340v1_genomic.fna/markers.fasta)
[2023-06-29 16:36:44,734] [INFO] Task started: Blastn
[2023-06-29 16:36:44,734] [INFO] Running command: blastn -query GCA_021793405.1_ASM2179340v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b496288-ab68-4e68-913a-e500a9071b26/dqc_reference/reference_markers_gtdb.fasta -out GCA_021793405.1_ASM2179340v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:36:45,544] [INFO] Task succeeded: Blastn
[2023-06-29 16:36:45,549] [INFO] Selected 33 target genomes.
[2023-06-29 16:36:45,549] [INFO] Target genome list was writen to GCA_021793405.1_ASM2179340v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 16:36:45,584] [INFO] Task started: fastANI
[2023-06-29 16:36:45,584] [INFO] Running command: fastANI --query /var/lib/cwl/stg4baaa3a6-030e-4ea3-9b60-2505b2021544/GCA_021793405.1_ASM2179340v1_genomic.fna.gz --refList GCA_021793405.1_ASM2179340v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021793405.1_ASM2179340v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 16:37:09,230] [INFO] Task succeeded: fastANI
[2023-06-29 16:37:09,251] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 16:37:09,252] [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
GCF_004339725.1	s__Acidipila rosea	77.5489	98	1467	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Acidipila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003138365.1	s__Terracidiphilus sp003138365	76.8607	61	1467	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	99.60	99.22	0.93	0.83	18	-
GCA_000421065.1	s__Edaphobacter sp000421065	76.5516	68	1467	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000022565.1	s__Acidobacterium capsulatum	76.4428	84	1467	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Acidobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009765985.1	s__Acidobacterium_A sp009765985	76.3747	86	1467	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Acidobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001006305.1	s__Silvibacterium bohemicum	76.2504	97	1467	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Silvibacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003428625.2	s__Palsa-343 sp003428625	76.1345	108	1467	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_003167305.1	s__Terracidiphilus sp003167305	76.1023	52	1467	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003330725.1	s__Acidisarcina polymorpha	76.0672	56	1467	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Acidisarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011333575.1	s__Acidobacterium capsulatum_A	76.0299	75	1467	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Acidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013285705.1	s__Acidobacterium_A sp013285705	76.0282	51	1467	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Acidobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745965.1	s__Edaphobacter aggregans	76.0023	93	1467	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004123295.1	s__Silvibacterium dinghuense	75.9874	86	1467	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Silvibacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000179915.2	s__Terriglobus saanensis	75.9833	51	1467	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terriglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003151435.1	s__Terracidiphilus sp003151435	75.9316	72	1467	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	99.67	99.67	0.90	0.90	2	-
GCA_001897435.1	s__Edaphobacter sp001897435	75.8598	76	1467	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	99.98	99.98	0.99	0.99	2	-
GCA_903842065.1	s__Terracidiphilus sp903842065	75.7786	50	1467	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015655315.1	s__Acidobacterium_A sp015655315	75.7515	53	1467	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Acidobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188085.1	s__Granulicella_C rosea	75.7318	66	1467	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Granulicella_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000178955.2	s__Granulicella_A mallensis	75.6544	55	1467	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Granulicella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410065.1	s__Granulicella_B arctica	75.6463	61	1467	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Granulicella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203225.1	s__Granulicella_A mallensis_A	75.4495	65	1467	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Granulicella_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 16:37:09,254] [INFO] GTDB search result was written to GCA_021793405.1_ASM2179340v1_genomic.fna/result_gtdb.tsv
[2023-06-29 16:37:09,254] [INFO] ===== GTDB Search completed =====
[2023-06-29 16:37:09,259] [INFO] DFAST_QC result json was written to GCA_021793405.1_ASM2179340v1_genomic.fna/dqc_result.json
[2023-06-29 16:37:09,259] [INFO] DFAST_QC completed!
[2023-06-29 16:37:09,259] [INFO] Total running time: 0h1m37s