[2024-01-24 14:28:15,694] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:15,699] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:15,699] [INFO] DQC Reference Directory: /var/lib/cwl/stg29a183fc-cfc1-4658-9f93-384566481053/dqc_reference
[2024-01-24 14:28:17,937] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:17,938] [INFO] Task started: Prodigal
[2024-01-24 14:28:17,938] [INFO] Running command: gunzip -c /var/lib/cwl/stg0d692175-77f7-4b60-a6f5-7d15c2b15b2e/GCF_025685545.1_ASM2568554v1_genomic.fna.gz | prodigal -d GCF_025685545.1_ASM2568554v1_genomic.fna/cds.fna -a GCF_025685545.1_ASM2568554v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:32,483] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:32,484] [INFO] Task started: HMMsearch
[2024-01-24 14:28:32,484] [INFO] Running command: hmmsearch --tblout GCF_025685545.1_ASM2568554v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg29a183fc-cfc1-4658-9f93-384566481053/dqc_reference/reference_markers.hmm GCF_025685545.1_ASM2568554v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:32,771] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:32,773] [INFO] Found 6/6 markers.
[2024-01-24 14:28:32,813] [INFO] Query marker FASTA was written to GCF_025685545.1_ASM2568554v1_genomic.fna/markers.fasta
[2024-01-24 14:28:32,813] [INFO] Task started: Blastn
[2024-01-24 14:28:32,813] [INFO] Running command: blastn -query GCF_025685545.1_ASM2568554v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg29a183fc-cfc1-4658-9f93-384566481053/dqc_reference/reference_markers.fasta -out GCF_025685545.1_ASM2568554v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:33,479] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:33,483] [INFO] Selected 22 target genomes.
[2024-01-24 14:28:33,484] [INFO] Target genome list was writen to GCF_025685545.1_ASM2568554v1_genomic.fna/target_genomes.txt
[2024-01-24 14:28:33,515] [INFO] Task started: fastANI
[2024-01-24 14:28:33,515] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d692175-77f7-4b60-a6f5-7d15c2b15b2e/GCF_025685545.1_ASM2568554v1_genomic.fna.gz --refList GCF_025685545.1_ASM2568554v1_genomic.fna/target_genomes.txt --output GCF_025685545.1_ASM2568554v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:28:53,709] [INFO] Task succeeded: fastANI
[2024-01-24 14:28:53,710] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg29a183fc-cfc1-4658-9f93-384566481053/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:28:53,710] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg29a183fc-cfc1-4658-9f93-384566481053/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:28:53,723] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:28:53,724] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:28:53,724] [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
Granulicella pectinivorans	strain=DSM 21001	GCA_900114625.1	474950	474950	type	True	78.2721	270	1641	95	below_threshold
Granulicella mallensis	strain=MP5ACTX8	GCA_000178955.2	940614	940614	type	True	78.2496	394	1641	95	below_threshold
Edaphobacter aggregans	strain=DSM 19364	GCA_000745965.1	570835	570835	type	True	78.0616	257	1641	95	below_threshold
Bryocella elongata	strain=DSM 22489	GCA_900108185.1	863522	863522	type	True	78.059	408	1641	95	below_threshold
Edaphobacter modestus	strain=DSM 18101	GCA_004217555.1	388466	388466	type	True	77.8389	183	1641	95	below_threshold
Granulicella tundricola	strain=MP5ACTX9	GCA_000178975.2	940615	940615	type	True	77.7767	272	1641	95	below_threshold
Granulicella sibirica	strain=AF10	GCA_004115155.1	2479048	2479048	type	True	77.7376	217	1641	95	below_threshold
Edaphobacter dinghuensis	strain=CGMCC 1.12997	GCA_014640335.1	1560005	1560005	type	True	77.7186	203	1641	95	below_threshold
Edaphobacter flagellatus	strain=HZ411	GCA_025264665.1	1933044	1933044	type	True	77.6049	184	1641	95	below_threshold
Granulicella rosea	strain=DSM 18704	GCA_900188085.1	474952	474952	type	True	77.3778	322	1641	95	below_threshold
Terriglobus roseus	strain=DSM 18391	GCA_000265425.1	392734	392734	type	True	77.3615	173	1641	95	below_threshold
Silvibacterium dinghuense	strain=DHOF10	GCA_004123295.1	1560006	1560006	type	True	77.2085	163	1641	95	below_threshold
Silvibacterium dinghuense	strain=CGMCC 1.13007	GCA_014640355.1	1560006	1560006	type	True	77.1315	165	1641	95	below_threshold
Acidobacterium capsulatum	strain=ATCC 51196	GCA_000022565.1	33075	33075	type	True	76.9009	107	1641	95	below_threshold
Alloacidobacterium dinghuense	strain=4Y35	GCA_014274465.1	2763107	2763107	type	True	76.6937	101	1641	95	below_threshold
Silvibacterium bohemicum	strain=DSM 103733	GCA_014201455.1	1577686	1577686	type	True	76.6168	137	1641	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:28:53,725] [INFO] DFAST Taxonomy check result was written to GCF_025685545.1_ASM2568554v1_genomic.fna/tc_result.tsv
[2024-01-24 14:28:53,726] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:28:53,726] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:28:53,726] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg29a183fc-cfc1-4658-9f93-384566481053/dqc_reference/checkm_data
[2024-01-24 14:28:53,727] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:28:53,775] [INFO] Task started: CheckM
[2024-01-24 14:28:53,776] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025685545.1_ASM2568554v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025685545.1_ASM2568554v1_genomic.fna/checkm_input GCF_025685545.1_ASM2568554v1_genomic.fna/checkm_result
[2024-01-24 14:29:38,677] [INFO] Task succeeded: CheckM
[2024-01-24 14:29:38,678] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:29:38,718] [INFO] ===== Completeness check finished =====
[2024-01-24 14:29:38,718] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:29:38,719] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025685545.1_ASM2568554v1_genomic.fna/markers.fasta)
[2024-01-24 14:29:38,719] [INFO] Task started: Blastn
[2024-01-24 14:29:38,719] [INFO] Running command: blastn -query GCF_025685545.1_ASM2568554v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg29a183fc-cfc1-4658-9f93-384566481053/dqc_reference/reference_markers_gtdb.fasta -out GCF_025685545.1_ASM2568554v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:29:39,712] [INFO] Task succeeded: Blastn
[2024-01-24 14:29:39,716] [INFO] Selected 23 target genomes.
[2024-01-24 14:29:39,716] [INFO] Target genome list was writen to GCF_025685545.1_ASM2568554v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:29:39,735] [INFO] Task started: fastANI
[2024-01-24 14:29:39,735] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d692175-77f7-4b60-a6f5-7d15c2b15b2e/GCF_025685545.1_ASM2568554v1_genomic.fna.gz --refList GCF_025685545.1_ASM2568554v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025685545.1_ASM2568554v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:29:59,120] [INFO] Task succeeded: fastANI
[2024-01-24 14:29:59,137] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:29:59,137] [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_014083945.1	s__UBA5172 sp014083945	79.7499	607	1641	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__UBA5172	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903970395.1	s__UBA5172 sp903970395	79.4873	517	1641	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__UBA5172	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765785.1	s__UBA5172 sp009765785	78.6428	319	1641	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__UBA5172	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903873705.1	s__CAIQPK01 sp903873705	78.539	311	1641	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__CAIQPK01	95.0	99.92	99.91	0.95	0.94	3	-
GCA_003138795.1	s__UBA5172 sp003138795	78.5233	298	1641	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__UBA5172	95.0	99.74	99.67	0.90	0.89	6	-
GCF_014203225.1	s__Granulicella_A mallensis_A	78.4468	397	1641	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_000178955.2	s__Granulicella_A mallensis	78.301	388	1641	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_900114625.1	s__Granulicella_C pectinivorans	78.2721	270	1641	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_900108185.1	s__Bryocella elongata	78.0841	405	1641	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Bryocella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009766105.1	s__Granulicella_A sp009766105	78.0438	355	1641	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Granulicella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000421065.1	s__Edaphobacter sp000421065	77.605	217	1641	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001897435.1	s__Edaphobacter sp001897435	77.5564	210	1641	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	99.98	99.98	0.99	0.99	2	-
GCA_002197545.1	s__Edaphobacter sp002197545	77.5494	180	1641	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188085.1	s__Granulicella_C rosea	77.3982	321	1641	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Granulicella_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903970445.1	s__Tous-C9LFEB sp903970445	77.3751	195	1641	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Tous-C9LFEB	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000265425.1	s__Terriglobus roseus	77.3585	174	1641	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terriglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903849645.1	s__Terracidiphilus sp903849645	76.9088	108	1641	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	99.99	99.99	0.99	0.99	2	-
GCA_003139795.1	s__Terracidiphilus sp003139795	76.1889	97	1641	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	99.74	99.71	0.89	0.87	5	-
GCA_003131315.1	s__Bog-209 sp003131315	75.5419	53	1641	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__SbA1;g__Bog-209	95.0	99.89	99.89	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:29:59,140] [INFO] GTDB search result was written to GCF_025685545.1_ASM2568554v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:29:59,141] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:29:59,145] [INFO] DFAST_QC result json was written to GCF_025685545.1_ASM2568554v1_genomic.fna/dqc_result.json
[2024-01-24 14:29:59,146] [INFO] DFAST_QC completed!
[2024-01-24 14:29:59,146] [INFO] Total running time: 0h1m43s