[2024-01-24 11:26:28,088] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:28,089] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:28,090] [INFO] DQC Reference Directory: /var/lib/cwl/stgd31b6ee4-e300-4fe2-9065-8589588254ad/dqc_reference
[2024-01-24 11:26:29,340] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:29,341] [INFO] Task started: Prodigal
[2024-01-24 11:26:29,341] [INFO] Running command: gunzip -c /var/lib/cwl/stgae7215f1-f82d-4ce1-83f5-3f789aa244c3/GCF_014642855.1_ASM1464285v1_genomic.fna.gz | prodigal -d GCF_014642855.1_ASM1464285v1_genomic.fna/cds.fna -a GCF_014642855.1_ASM1464285v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:41,812] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:41,813] [INFO] Task started: HMMsearch
[2024-01-24 11:26:41,813] [INFO] Running command: hmmsearch --tblout GCF_014642855.1_ASM1464285v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd31b6ee4-e300-4fe2-9065-8589588254ad/dqc_reference/reference_markers.hmm GCF_014642855.1_ASM1464285v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:42,122] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:42,123] [INFO] Found 6/6 markers.
[2024-01-24 11:26:42,167] [INFO] Query marker FASTA was written to GCF_014642855.1_ASM1464285v1_genomic.fna/markers.fasta
[2024-01-24 11:26:42,174] [INFO] Task started: Blastn
[2024-01-24 11:26:42,174] [INFO] Running command: blastn -query GCF_014642855.1_ASM1464285v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd31b6ee4-e300-4fe2-9065-8589588254ad/dqc_reference/reference_markers.fasta -out GCF_014642855.1_ASM1464285v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:42,821] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:42,824] [INFO] Selected 18 target genomes.
[2024-01-24 11:26:42,824] [INFO] Target genome list was writen to GCF_014642855.1_ASM1464285v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:42,831] [INFO] Task started: fastANI
[2024-01-24 11:26:42,832] [INFO] Running command: fastANI --query /var/lib/cwl/stgae7215f1-f82d-4ce1-83f5-3f789aa244c3/GCF_014642855.1_ASM1464285v1_genomic.fna.gz --refList GCF_014642855.1_ASM1464285v1_genomic.fna/target_genomes.txt --output GCF_014642855.1_ASM1464285v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:58,612] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:58,612] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd31b6ee4-e300-4fe2-9065-8589588254ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:58,613] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd31b6ee4-e300-4fe2-9065-8589588254ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:58,624] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:26:58,624] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:26:58,625] [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
Edaphobacter acidisoli	strain=CGMCC 1.15447	GCA_014642855.1	2040573	2040573	type	True	100.0	1394	1395	95	conclusive
Edaphobacter aggregans	strain=DSM 19364	GCA_000745965.1	570835	570835	type	True	79.0728	422	1395	95	below_threshold
Edaphobacter dinghuensis	strain=CGMCC 1.12997	GCA_014640335.1	1560005	1560005	type	True	78.4408	399	1395	95	below_threshold
Edaphobacter flagellatus	strain=HZ411	GCA_025264665.1	1933044	1933044	type	True	78.3008	320	1395	95	below_threshold
Edaphobacter modestus	strain=DSM 18101	GCA_004217555.1	388466	388466	type	True	78.271	312	1395	95	below_threshold
Granulicella sibirica	strain=AF10	GCA_004115155.1	2479048	2479048	type	True	77.9614	237	1395	95	below_threshold
Bryocella elongata	strain=DSM 22489	GCA_900108185.1	863522	863522	type	True	77.9267	209	1395	95	below_threshold
Granulicella pectinivorans	strain=DSM 21001	GCA_900114625.1	474950	474950	type	True	77.9062	268	1395	95	below_threshold
Granulicella rosea	strain=DSM 18704	GCA_900188085.1	474952	474952	type	True	77.8887	311	1395	95	below_threshold
Paracidobacterium acidisoli	strain=4G-K13	GCA_003428625.2	2303751	2303751	type	True	77.5479	184	1395	95	below_threshold
Silvibacterium bohemicum	strain=DSM 103733	GCA_014201455.1	1577686	1577686	type	True	77.258	140	1395	95	below_threshold
Silvibacterium bohemicum	strain=S15	GCA_001006305.1	1577686	1577686	type	True	77.2394	143	1395	95	below_threshold
Terriglobus saanensis	strain=SP1PR4	GCA_000179915.2	870903	870903	type	True	76.9193	163	1395	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:58,627] [INFO] DFAST Taxonomy check result was written to GCF_014642855.1_ASM1464285v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:58,627] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:58,627] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:58,628] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd31b6ee4-e300-4fe2-9065-8589588254ad/dqc_reference/checkm_data
[2024-01-24 11:26:58,629] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:58,682] [INFO] Task started: CheckM
[2024-01-24 11:26:58,683] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014642855.1_ASM1464285v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014642855.1_ASM1464285v1_genomic.fna/checkm_input GCF_014642855.1_ASM1464285v1_genomic.fna/checkm_result
[2024-01-24 11:27:39,002] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:39,003] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:39,025] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:39,025] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:39,026] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014642855.1_ASM1464285v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:39,026] [INFO] Task started: Blastn
[2024-01-24 11:27:39,027] [INFO] Running command: blastn -query GCF_014642855.1_ASM1464285v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd31b6ee4-e300-4fe2-9065-8589588254ad/dqc_reference/reference_markers_gtdb.fasta -out GCF_014642855.1_ASM1464285v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:39,894] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:39,898] [INFO] Selected 22 target genomes.
[2024-01-24 11:27:39,899] [INFO] Target genome list was writen to GCF_014642855.1_ASM1464285v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:39,934] [INFO] Task started: fastANI
[2024-01-24 11:27:39,934] [INFO] Running command: fastANI --query /var/lib/cwl/stgae7215f1-f82d-4ce1-83f5-3f789aa244c3/GCF_014642855.1_ASM1464285v1_genomic.fna.gz --refList GCF_014642855.1_ASM1464285v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014642855.1_ASM1464285v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:00,454] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:00,474] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:28:00,474] [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_014642855.1	s__Edaphobacter acidisoli	100.0	1394	1395	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009765825.1	s__Edaphobacter sp009765825	79.1193	369	1395	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745965.1	s__Edaphobacter aggregans	79.0664	421	1395	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201315.1	s__Edaphobacter lichenicola_B	79.0435	392	1395	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003751275.1	s__Edaphobacter sp003751275	78.9776	406	1395	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410875.1	s__Edaphobacter lichenicola_C	78.898	372	1395	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002197545.1	s__Edaphobacter sp002197545	78.7447	337	1395	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410115.1	s__Edaphobacter lichenicola_A	78.6927	369	1395	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	98.03	98.03	0.94	0.94	2	-
GCF_003633965.1	s__Edaphobacter dinghuensis_A	78.6465	332	1395	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765835.1	s__Edaphobacter sp009765835	78.6001	419	1395	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201335.1	s__Edaphobacter lichenicola_E	78.5958	344	1395	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	78.4579	392	1395	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	99.98	99.98	0.99	0.99	2	-
GCA_015655585.1	s__Edaphobacter sp015655585	78.4554	283	1395	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014640335.1	s__Edaphobacter dinghuensis	78.4306	400	1395	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009766095.1	s__Edaphobacter sp009766095	78.4062	350	1395	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268895.1	s__Edaphobacter sp018268895	78.3304	356	1395	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	78.271	312	1395	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014274685.1	s__Edaphobacter sp014274685	78.0106	226	1395	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114625.1	s__Granulicella_C pectinivorans	77.9182	267	1395	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_003133205.1	s__Palsa-288 sp003133205	77.9138	278	1395	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_009765785.1	s__UBA5172 sp009765785	77.6569	188	1395	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__UBA5172	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003151155.1	s__Koribacter sp003151155	76.3819	53	1395	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Koribacteraceae;g__Koribacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:28:00,476] [INFO] GTDB search result was written to GCF_014642855.1_ASM1464285v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:00,477] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:00,481] [INFO] DFAST_QC result json was written to GCF_014642855.1_ASM1464285v1_genomic.fna/dqc_result.json
[2024-01-24 11:28:00,481] [INFO] DFAST_QC completed!
[2024-01-24 11:28:00,481] [INFO] Total running time: 0h1m32s