[2023-06-29 16:18:32,606] [INFO] DFAST_QC pipeline started.
[2023-06-29 16:18:32,610] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 16:18:32,610] [INFO] DQC Reference Directory: /var/lib/cwl/stgced54a9b-f403-4cc0-9db5-081518d007ae/dqc_reference
[2023-06-29 16:18:33,939] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 16:18:33,940] [INFO] Task started: Prodigal
[2023-06-29 16:18:33,940] [INFO] Running command: gunzip -c /var/lib/cwl/stgee71aeb9-dfdf-4d89-8f10-c5ce8d8bee25/GCA_021806005.1_ASM2180600v1_genomic.fna.gz | prodigal -d GCA_021806005.1_ASM2180600v1_genomic.fna/cds.fna -a GCA_021806005.1_ASM2180600v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 16:18:45,302] [INFO] Task succeeded: Prodigal
[2023-06-29 16:18:45,303] [INFO] Task started: HMMsearch
[2023-06-29 16:18:45,303] [INFO] Running command: hmmsearch --tblout GCA_021806005.1_ASM2180600v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgced54a9b-f403-4cc0-9db5-081518d007ae/dqc_reference/reference_markers.hmm GCA_021806005.1_ASM2180600v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 16:18:45,593] [INFO] Task succeeded: HMMsearch
[2023-06-29 16:18:45,594] [INFO] Found 6/6 markers.
[2023-06-29 16:18:45,638] [INFO] Query marker FASTA was written to GCA_021806005.1_ASM2180600v1_genomic.fna/markers.fasta
[2023-06-29 16:18:45,638] [INFO] Task started: Blastn
[2023-06-29 16:18:45,638] [INFO] Running command: blastn -query GCA_021806005.1_ASM2180600v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgced54a9b-f403-4cc0-9db5-081518d007ae/dqc_reference/reference_markers.fasta -out GCA_021806005.1_ASM2180600v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:18:46,275] [INFO] Task succeeded: Blastn
[2023-06-29 16:18:46,279] [INFO] Selected 17 target genomes.
[2023-06-29 16:18:46,280] [INFO] Target genome list was writen to GCA_021806005.1_ASM2180600v1_genomic.fna/target_genomes.txt
[2023-06-29 16:18:46,281] [INFO] Task started: fastANI
[2023-06-29 16:18:46,281] [INFO] Running command: fastANI --query /var/lib/cwl/stgee71aeb9-dfdf-4d89-8f10-c5ce8d8bee25/GCA_021806005.1_ASM2180600v1_genomic.fna.gz --refList GCA_021806005.1_ASM2180600v1_genomic.fna/target_genomes.txt --output GCA_021806005.1_ASM2180600v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 16:19:00,784] [INFO] Task succeeded: fastANI
[2023-06-29 16:19:00,785] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgced54a9b-f403-4cc0-9db5-081518d007ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 16:19:00,786] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgced54a9b-f403-4cc0-9db5-081518d007ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 16:19:00,803] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 16:19:00,803] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 16:19:00,803] [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 mallensis	strain=MP5ACTX8	GCA_000178955.2	940614	940614	type	True	77.5587	231	1273	95	below_threshold
Bryocella elongata	strain=DSM 22489	GCA_900108185.1	863522	863522	type	True	77.2403	224	1273	95	below_threshold
Edaphobacter aggregans	strain=DSM 19364	GCA_000745965.1	570835	570835	type	True	77.167	174	1273	95	below_threshold
Edaphobacter dinghuensis	strain=CGMCC 1.12997	GCA_014640335.1	1560005	1560005	type	True	77.0721	136	1273	95	below_threshold
Edaphobacter modestus	strain=DSM 18101	GCA_004217555.1	388466	388466	type	True	76.9655	133	1273	95	below_threshold
Granulicella rosea	strain=DSM 18704	GCA_900188085.1	474952	474952	type	True	76.921	164	1273	95	below_threshold
Edaphobacter flagellatus	strain=HZ411	GCA_025264665.1	1933044	1933044	type	True	76.8957	128	1273	95	below_threshold
Pseudacidobacterium ailaaui	strain=PMMR2	GCA_000688455.1	1382359	1382359	type	True	76.8873	66	1273	95	below_threshold
Terriglobus roseus	strain=DSM 18391	GCA_000265425.1	392734	392734	type	True	76.6785	112	1273	95	below_threshold
Granulicella pectinivorans	strain=DSM 21001	GCA_900114625.1	474950	474950	type	True	76.6598	161	1273	95	below_threshold
Paracidobacterium acidisoli	strain=4G-K13	GCA_003428625.2	2303751	2303751	type	True	76.4766	113	1273	95	below_threshold
Silvibacterium dinghuense	strain=DHOF10	GCA_004123295.1	1560006	1560006	type	True	76.4528	135	1273	95	below_threshold
Silvibacterium dinghuense	strain=CGMCC 1.13007	GCA_014640355.1	1560006	1560006	type	True	76.4341	136	1273	95	below_threshold
Acidobacterium capsulatum	strain=ATCC 51196	GCA_000022565.1	33075	33075	type	True	76.3487	113	1273	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 16:19:00,805] [INFO] DFAST Taxonomy check result was written to GCA_021806005.1_ASM2180600v1_genomic.fna/tc_result.tsv
[2023-06-29 16:19:00,805] [INFO] ===== Taxonomy check completed =====
[2023-06-29 16:19:00,806] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 16:19:00,806] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgced54a9b-f403-4cc0-9db5-081518d007ae/dqc_reference/checkm_data
[2023-06-29 16:19:00,807] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 16:19:00,846] [INFO] Task started: CheckM
[2023-06-29 16:19:00,846] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021806005.1_ASM2180600v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021806005.1_ASM2180600v1_genomic.fna/checkm_input GCA_021806005.1_ASM2180600v1_genomic.fna/checkm_result
[2023-06-29 16:19:36,676] [INFO] Task succeeded: CheckM
[2023-06-29 16:19:36,678] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 16:19:36,700] [INFO] ===== Completeness check finished =====
[2023-06-29 16:19:36,701] [INFO] ===== Start GTDB Search =====
[2023-06-29 16:19:36,701] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021806005.1_ASM2180600v1_genomic.fna/markers.fasta)
[2023-06-29 16:19:36,701] [INFO] Task started: Blastn
[2023-06-29 16:19:36,702] [INFO] Running command: blastn -query GCA_021806005.1_ASM2180600v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgced54a9b-f403-4cc0-9db5-081518d007ae/dqc_reference/reference_markers_gtdb.fasta -out GCA_021806005.1_ASM2180600v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:19:37,582] [INFO] Task succeeded: Blastn
[2023-06-29 16:19:37,587] [INFO] Selected 19 target genomes.
[2023-06-29 16:19:37,588] [INFO] Target genome list was writen to GCA_021806005.1_ASM2180600v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 16:19:37,596] [INFO] Task started: fastANI
[2023-06-29 16:19:37,596] [INFO] Running command: fastANI --query /var/lib/cwl/stgee71aeb9-dfdf-4d89-8f10-c5ce8d8bee25/GCA_021806005.1_ASM2180600v1_genomic.fna.gz --refList GCA_021806005.1_ASM2180600v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021806005.1_ASM2180600v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 16:19:51,086] [INFO] Task succeeded: fastANI
[2023-06-29 16:19:51,104] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 16:19:51,105] [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_009765785.1	s__UBA5172 sp009765785	77.8606	361	1273	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__UBA5172	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003138795.1	s__UBA5172 sp003138795	77.8323	330	1273	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__UBA5172	95.0	99.74	99.67	0.90	0.89	6	-
GCF_014083945.1	s__UBA5172 sp014083945	77.7829	257	1273	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__UBA5172	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000178955.2	s__Granulicella_A mallensis	77.5455	232	1273	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_014203225.1	s__Granulicella_A mallensis_A	77.371	255	1273	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_903970395.1	s__UBA5172 sp903970395	77.3516	189	1273	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__UBA5172	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009766105.1	s__Granulicella_A sp009766105	77.2699	229	1273	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_900108185.1	s__Bryocella elongata	77.2403	224	1273	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Bryocella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003132145.1	s__Palsa-288 sp003132145	77.0678	167	1273	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Palsa-288	95.0	99.75	99.72	0.90	0.88	3	-
GCA_000421065.1	s__Edaphobacter sp000421065	77.0247	172	1273	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018449715.1	s__Edaphobacter sp018449715	76.9879	148	1273	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217555.1	s__Edaphobacter modestus	76.9655	133	1273	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903932155.1	s__Palsa-288 sp903932155	76.6968	125	1273	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Palsa-288	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009766095.1	s__Edaphobacter sp009766095	76.5904	126	1273	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011333575.1	s__Acidobacterium capsulatum_A	76.4027	92	1273	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Acidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000022565.1	s__Acidobacterium capsulatum	76.3487	113	1273	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Acidobacterium	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-06-29 16:19:51,107] [INFO] GTDB search result was written to GCA_021806005.1_ASM2180600v1_genomic.fna/result_gtdb.tsv
[2023-06-29 16:19:51,107] [INFO] ===== GTDB Search completed =====
[2023-06-29 16:19:51,111] [INFO] DFAST_QC result json was written to GCA_021806005.1_ASM2180600v1_genomic.fna/dqc_result.json
[2023-06-29 16:19:51,111] [INFO] DFAST_QC completed!
[2023-06-29 16:19:51,111] [INFO] Total running time: 0h1m19s