[2023-06-27 02:40:56,145] [INFO] DFAST_QC pipeline started.
[2023-06-27 02:40:56,178] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 02:40:56,178] [INFO] DQC Reference Directory: /var/lib/cwl/stgc43bbea4-856a-4bc5-a844-64e58fe88d8c/dqc_reference
[2023-06-27 02:40:57,351] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 02:40:57,351] [INFO] Task started: Prodigal
[2023-06-27 02:40:57,352] [INFO] Running command: gunzip -c /var/lib/cwl/stg225d9424-1e6a-4182-8882-69e339eb8440/GCA_002314435.1_ASM231443v1_genomic.fna.gz | prodigal -d GCA_002314435.1_ASM231443v1_genomic.fna/cds.fna -a GCA_002314435.1_ASM231443v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 02:41:08,223] [INFO] Task succeeded: Prodigal
[2023-06-27 02:41:08,224] [INFO] Task started: HMMsearch
[2023-06-27 02:41:08,224] [INFO] Running command: hmmsearch --tblout GCA_002314435.1_ASM231443v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc43bbea4-856a-4bc5-a844-64e58fe88d8c/dqc_reference/reference_markers.hmm GCA_002314435.1_ASM231443v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 02:41:08,440] [INFO] Task succeeded: HMMsearch
[2023-06-27 02:41:08,441] [INFO] Found 6/6 markers.
[2023-06-27 02:41:08,489] [INFO] Query marker FASTA was written to GCA_002314435.1_ASM231443v1_genomic.fna/markers.fasta
[2023-06-27 02:41:08,490] [INFO] Task started: Blastn
[2023-06-27 02:41:08,490] [INFO] Running command: blastn -query GCA_002314435.1_ASM231443v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc43bbea4-856a-4bc5-a844-64e58fe88d8c/dqc_reference/reference_markers.fasta -out GCA_002314435.1_ASM231443v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 02:41:09,093] [INFO] Task succeeded: Blastn
[2023-06-27 02:41:09,096] [INFO] Selected 22 target genomes.
[2023-06-27 02:41:09,097] [INFO] Target genome list was writen to GCA_002314435.1_ASM231443v1_genomic.fna/target_genomes.txt
[2023-06-27 02:41:09,121] [INFO] Task started: fastANI
[2023-06-27 02:41:09,122] [INFO] Running command: fastANI --query /var/lib/cwl/stg225d9424-1e6a-4182-8882-69e339eb8440/GCA_002314435.1_ASM231443v1_genomic.fna.gz --refList GCA_002314435.1_ASM231443v1_genomic.fna/target_genomes.txt --output GCA_002314435.1_ASM231443v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 02:41:27,087] [INFO] Task succeeded: fastANI
[2023-06-27 02:41:27,088] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc43bbea4-856a-4bc5-a844-64e58fe88d8c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 02:41:27,088] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc43bbea4-856a-4bc5-a844-64e58fe88d8c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 02:41:27,101] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 02:41:27,101] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 02:41:27,101] [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	77.6379	328	1198	95	below_threshold
Terracidiphilus gabretensis	strain=S55	GCA_001449115.1	1577687	1577687	type	True	77.3852	228	1198	95	below_threshold
Acidobacterium capsulatum	strain=ATCC 51196	GCA_000022565.1	33075	33075	type	True	76.8982	154	1198	95	below_threshold
Silvibacterium bohemicum	strain=S15	GCA_001006305.1	1577686	1577686	type	True	76.7241	147	1198	95	below_threshold
Silvibacterium bohemicum	strain=DSM 103733	GCA_014201455.1	1577686	1577686	type	True	76.6827	147	1198	95	below_threshold
Silvibacterium dinghuense	strain=DHOF10	GCA_004123295.1	1560006	1560006	type	True	76.6585	174	1198	95	below_threshold
Paracidobacterium acidisoli	strain=4G-K13	GCA_003428625.2	2303751	2303751	type	True	76.6052	174	1198	95	below_threshold
Silvibacterium dinghuense	strain=CGMCC 1.13007	GCA_014640355.1	1560006	1560006	type	True	76.6042	178	1198	95	below_threshold
Alloacidobacterium dinghuense	strain=4Y35	GCA_014274465.1	2763107	2763107	type	True	76.5458	112	1198	95	below_threshold
Terriglobus roseus	strain=DSM 18391	GCA_000265425.1	392734	392734	type	True	76.4074	83	1198	95	below_threshold
Edaphobacter aggregans	strain=DSM 19364	GCA_000745965.1	570835	570835	type	True	76.389	145	1198	95	below_threshold
Edaphobacter lichenicola	strain=DSM 104462	GCA_025264645.1	2051959	2051959	suspected-type	True	76.3658	64	1198	95	below_threshold
Edaphobacter modestus	strain=DSM 18101	GCA_004217555.1	388466	388466	type	True	76.3614	81	1198	95	below_threshold
Edaphobacter dinghuensis	strain=CGMCC 1.12997	GCA_014640335.1	1560005	1560005	type	True	76.2833	109	1198	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 02:41:27,103] [INFO] DFAST Taxonomy check result was written to GCA_002314435.1_ASM231443v1_genomic.fna/tc_result.tsv
[2023-06-27 02:41:27,104] [INFO] ===== Taxonomy check completed =====
[2023-06-27 02:41:27,104] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 02:41:27,104] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc43bbea4-856a-4bc5-a844-64e58fe88d8c/dqc_reference/checkm_data
[2023-06-27 02:41:27,106] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 02:41:27,147] [INFO] Task started: CheckM
[2023-06-27 02:41:27,148] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002314435.1_ASM231443v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002314435.1_ASM231443v1_genomic.fna/checkm_input GCA_002314435.1_ASM231443v1_genomic.fna/checkm_result
[2023-06-27 02:42:00,294] [INFO] Task succeeded: CheckM
[2023-06-27 02:42:00,295] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 02:42:00,317] [INFO] ===== Completeness check finished =====
[2023-06-27 02:42:00,317] [INFO] ===== Start GTDB Search =====
[2023-06-27 02:42:00,317] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002314435.1_ASM231443v1_genomic.fna/markers.fasta)
[2023-06-27 02:42:00,318] [INFO] Task started: Blastn
[2023-06-27 02:42:00,318] [INFO] Running command: blastn -query GCA_002314435.1_ASM231443v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc43bbea4-856a-4bc5-a844-64e58fe88d8c/dqc_reference/reference_markers_gtdb.fasta -out GCA_002314435.1_ASM231443v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 02:42:01,109] [INFO] Task succeeded: Blastn
[2023-06-27 02:42:01,112] [INFO] Selected 25 target genomes.
[2023-06-27 02:42:01,112] [INFO] Target genome list was writen to GCA_002314435.1_ASM231443v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 02:42:01,147] [INFO] Task started: fastANI
[2023-06-27 02:42:01,148] [INFO] Running command: fastANI --query /var/lib/cwl/stg225d9424-1e6a-4182-8882-69e339eb8440/GCA_002314435.1_ASM231443v1_genomic.fna.gz --refList GCA_002314435.1_ASM231443v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002314435.1_ASM231443v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 02:42:20,356] [INFO] Task succeeded: fastANI
[2023-06-27 02:42:20,372] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 02:42:20,372] [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_002314435.1	s__Terracidiphilus sp002314435	99.9999	1168	1198	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003170825.1	s__Terracidiphilus sp003170825	78.183	358	1198	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	99.88	99.70	0.95	0.95	8	-
GCA_903849645.1	s__Terracidiphilus sp903849645	77.9696	420	1198	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	99.99	99.99	0.99	0.99	2	-
GCA_015655365.1	s__Terracidiphilus sp015655365	77.8524	173	1198	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003165075.1	s__Terracidiphilus sp003165075	77.7698	378	1198	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003151435.1	s__Terracidiphilus sp003151435	77.7624	349	1198	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	99.67	99.67	0.90	0.90	2	-
GCA_008682415.1	s__Terracidiphilus sp008682415	77.7266	325	1198	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003131205.1	s__Terracidiphilus savannae	77.6522	282	1198	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903911925.1	s__Terracidiphilus sp903911925	77.6248	296	1198	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003161045.1	s__Terracidiphilus sp003161045	77.5946	267	1198	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	99.61	99.39	0.87	0.83	8	-
GCA_003138365.1	s__Terracidiphilus sp003138365	77.5868	329	1198	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	99.60	99.22	0.93	0.83	18	-
GCA_015654835.1	s__Terracidiphilus sp015654835	77.5661	291	1198	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	77.5448	321	1198	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	99.87	99.75	0.95	0.93	4	-
GCA_015655195.1	s__Terracidiphilus sp015655195	77.5193	280	1198	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903842065.1	s__Terracidiphilus sp903842065	77.4214	245	1198	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	77.3852	228	1198	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003138515.1	s__Terracidiphilus sp003138515	77.316	270	1198	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	99.80	99.73	0.97	0.96	5	-
GCA_003140785.1	s__Terracidiphilus sp003140785	77.2993	327	1198	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	98.14	96.92	0.80	0.78	3	-
GCA_018268915.1	s__Terracidiphilus sp018268915	77.1797	241	1198	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003134815.1	s__Terracidiphilus sp003134815	77.1786	207	1198	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 02:42:20,406] [INFO] GTDB search result was written to GCA_002314435.1_ASM231443v1_genomic.fna/result_gtdb.tsv
[2023-06-27 02:42:20,407] [INFO] ===== GTDB Search completed =====
[2023-06-27 02:42:20,411] [INFO] DFAST_QC result json was written to GCA_002314435.1_ASM231443v1_genomic.fna/dqc_result.json
[2023-06-27 02:42:20,411] [INFO] DFAST_QC completed!
[2023-06-27 02:42:20,411] [INFO] Total running time: 0h1m24s