[2024-01-25 20:12:05,989] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:12:05,991] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:12:05,992] [INFO] DQC Reference Directory: /var/lib/cwl/stg1d4030d2-2ebd-42e0-938d-b28bd8039b52/dqc_reference
[2024-01-25 20:12:07,180] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:12:07,181] [INFO] Task started: Prodigal
[2024-01-25 20:12:07,181] [INFO] Running command: gunzip -c /var/lib/cwl/stg8fbae6c2-2aa9-4e11-8eda-bee336a5e5a0/GCF_025685575.1_ASM2568557v1_genomic.fna.gz | prodigal -d GCF_025685575.1_ASM2568557v1_genomic.fna/cds.fna -a GCF_025685575.1_ASM2568557v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:12:18,221] [INFO] Task succeeded: Prodigal
[2024-01-25 20:12:18,221] [INFO] Task started: HMMsearch
[2024-01-25 20:12:18,221] [INFO] Running command: hmmsearch --tblout GCF_025685575.1_ASM2568557v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1d4030d2-2ebd-42e0-938d-b28bd8039b52/dqc_reference/reference_markers.hmm GCF_025685575.1_ASM2568557v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:12:18,458] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:12:18,460] [INFO] Found 6/6 markers.
[2024-01-25 20:12:18,499] [INFO] Query marker FASTA was written to GCF_025685575.1_ASM2568557v1_genomic.fna/markers.fasta
[2024-01-25 20:12:18,499] [INFO] Task started: Blastn
[2024-01-25 20:12:18,499] [INFO] Running command: blastn -query GCF_025685575.1_ASM2568557v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d4030d2-2ebd-42e0-938d-b28bd8039b52/dqc_reference/reference_markers.fasta -out GCF_025685575.1_ASM2568557v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:12:19,113] [INFO] Task succeeded: Blastn
[2024-01-25 20:12:19,115] [INFO] Selected 16 target genomes.
[2024-01-25 20:12:19,115] [INFO] Target genome list was writen to GCF_025685575.1_ASM2568557v1_genomic.fna/target_genomes.txt
[2024-01-25 20:12:19,156] [INFO] Task started: fastANI
[2024-01-25 20:12:19,156] [INFO] Running command: fastANI --query /var/lib/cwl/stg8fbae6c2-2aa9-4e11-8eda-bee336a5e5a0/GCF_025685575.1_ASM2568557v1_genomic.fna.gz --refList GCF_025685575.1_ASM2568557v1_genomic.fna/target_genomes.txt --output GCF_025685575.1_ASM2568557v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:12:33,457] [INFO] Task succeeded: fastANI
[2024-01-25 20:12:33,457] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1d4030d2-2ebd-42e0-938d-b28bd8039b52/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:12:33,458] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1d4030d2-2ebd-42e0-938d-b28bd8039b52/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:12:33,467] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:12:33,468] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:12:33,468] [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
Bryocella elongata	strain=DSM 22489	GCA_900108185.1	863522	863522	type	True	78.218	378	1358	95	below_threshold
Granulicella mallensis	strain=MP5ACTX8	GCA_000178955.2	940614	940614	type	True	78.1623	325	1358	95	below_threshold
Granulicella rosea	strain=DSM 18704	GCA_900188085.1	474952	474952	type	True	77.876	321	1358	95	below_threshold
Granulicella pectinivorans	strain=DSM 21001	GCA_900114625.1	474950	474950	type	True	77.5938	232	1358	95	below_threshold
Edaphobacter dinghuensis	strain=CGMCC 1.12997	GCA_014640335.1	1560005	1560005	type	True	77.5931	196	1358	95	below_threshold
Edaphobacter aggregans	strain=DSM 19364	GCA_000745965.1	570835	570835	type	True	77.5338	238	1358	95	below_threshold
Acidipila rosea	strain=DSM 103428	GCA_004339725.1	768535	768535	type	True	77.5183	118	1358	95	below_threshold
Terriglobus saanensis	strain=SP1PR4	GCA_000179915.2	870903	870903	type	True	77.4714	176	1358	95	below_threshold
Granulicella sibirica	strain=AF10	GCA_004115155.1	2479048	2479048	type	True	77.4582	195	1358	95	below_threshold
Edaphobacter acidisoli	strain=CGMCC 1.15447	GCA_014642855.1	2040573	2040573	type	True	77.3809	202	1358	95	below_threshold
Terriglobus roseus	strain=DSM 18391	GCA_000265425.1	392734	392734	type	True	77.2438	206	1358	95	below_threshold
Granulicella tundricola	strain=MP5ACTX9	GCA_000178975.2	940615	940615	type	True	77.1721	193	1358	95	below_threshold
Silvibacterium dinghuense	strain=DHOF10	GCA_004123295.1	1560006	1560006	type	True	77.1573	190	1358	95	below_threshold
Acidobacterium capsulatum	strain=ATCC 51196	GCA_000022565.1	33075	33075	type	True	77.1446	117	1358	95	below_threshold
Silvibacterium dinghuense	strain=CGMCC 1.13007	GCA_014640355.1	1560006	1560006	type	True	77.0939	189	1358	95	below_threshold
Edaphobacter modestus	strain=DSM 18101	GCA_004217555.1	388466	388466	type	True	77.0793	175	1358	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:12:33,471] [INFO] DFAST Taxonomy check result was written to GCF_025685575.1_ASM2568557v1_genomic.fna/tc_result.tsv
[2024-01-25 20:12:33,472] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:12:33,472] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:12:33,472] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1d4030d2-2ebd-42e0-938d-b28bd8039b52/dqc_reference/checkm_data
[2024-01-25 20:12:33,473] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:12:33,515] [INFO] Task started: CheckM
[2024-01-25 20:12:33,516] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025685575.1_ASM2568557v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025685575.1_ASM2568557v1_genomic.fna/checkm_input GCF_025685575.1_ASM2568557v1_genomic.fna/checkm_result
[2024-01-25 20:13:08,211] [INFO] Task succeeded: CheckM
[2024-01-25 20:13:08,212] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:13:08,231] [INFO] ===== Completeness check finished =====
[2024-01-25 20:13:08,232] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:13:08,232] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025685575.1_ASM2568557v1_genomic.fna/markers.fasta)
[2024-01-25 20:13:08,232] [INFO] Task started: Blastn
[2024-01-25 20:13:08,232] [INFO] Running command: blastn -query GCF_025685575.1_ASM2568557v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d4030d2-2ebd-42e0-938d-b28bd8039b52/dqc_reference/reference_markers_gtdb.fasta -out GCF_025685575.1_ASM2568557v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:13:09,198] [INFO] Task succeeded: Blastn
[2024-01-25 20:13:09,204] [INFO] Selected 17 target genomes.
[2024-01-25 20:13:09,204] [INFO] Target genome list was writen to GCF_025685575.1_ASM2568557v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:13:09,217] [INFO] Task started: fastANI
[2024-01-25 20:13:09,217] [INFO] Running command: fastANI --query /var/lib/cwl/stg8fbae6c2-2aa9-4e11-8eda-bee336a5e5a0/GCF_025685575.1_ASM2568557v1_genomic.fna.gz --refList GCF_025685575.1_ASM2568557v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025685575.1_ASM2568557v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:13:24,702] [INFO] Task succeeded: fastANI
[2024-01-25 20:13:24,712] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:13:24,712] [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	78.3898	307	1358	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__UBA5172	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203225.1	s__Granulicella_A mallensis_A	78.2181	347	1358	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	78.218	378	1358	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Bryocella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000178955.2	s__Granulicella_A mallensis	78.1633	325	1358	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_009766105.1	s__Granulicella_A sp009766105	77.9969	299	1358	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_900188085.1	s__Granulicella_C rosea	77.8794	320	1358	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_018449715.1	s__Edaphobacter sp018449715	77.8099	231	1358	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903970395.1	s__UBA5172 sp903970395	77.7216	247	1358	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	77.6383	263	1358	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__CAIQPK01	95.0	99.92	99.91	0.95	0.94	3	-
GCF_900114625.1	s__Granulicella_C pectinivorans	77.5938	232	1358	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_000745965.1	s__Edaphobacter aggregans	77.5081	240	1358	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203275.1	s__Granulicella_D aggregans	77.4052	216	1358	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Granulicella_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268775.1	s__Edaphobacter sp018268775	77.3642	236	1358	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000265425.1	s__Terriglobus roseus	77.324	207	1358	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terriglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765785.1	s__UBA5172 sp009765785	77.284	240	1358	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__UBA5172	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410065.1	s__Granulicella_B arctica	77.2166	206	1358	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_008000815.1	s__Terriglobus_A albidus	77.0161	201	1358	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terriglobus_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:13:24,714] [INFO] GTDB search result was written to GCF_025685575.1_ASM2568557v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:13:24,714] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:13:24,742] [INFO] DFAST_QC result json was written to GCF_025685575.1_ASM2568557v1_genomic.fna/dqc_result.json
[2024-01-25 20:13:24,742] [INFO] DFAST_QC completed!
[2024-01-25 20:13:24,742] [INFO] Total running time: 0h1m19s