[2024-01-25 19:43:50,342] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:43:50,343] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:43:50,343] [INFO] DQC Reference Directory: /var/lib/cwl/stg2382cba3-124a-4f4a-ae04-b7a3f8c81096/dqc_reference
[2024-01-25 19:43:51,487] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:43:51,488] [INFO] Task started: Prodigal
[2024-01-25 19:43:51,488] [INFO] Running command: gunzip -c /var/lib/cwl/stgbc304083-3799-4e13-bfe2-91462dabf846/GCF_025685705.1_ASM2568570v1_genomic.fna.gz | prodigal -d GCF_025685705.1_ASM2568570v1_genomic.fna/cds.fna -a GCF_025685705.1_ASM2568570v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:44:03,094] [INFO] Task succeeded: Prodigal
[2024-01-25 19:44:03,094] [INFO] Task started: HMMsearch
[2024-01-25 19:44:03,094] [INFO] Running command: hmmsearch --tblout GCF_025685705.1_ASM2568570v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2382cba3-124a-4f4a-ae04-b7a3f8c81096/dqc_reference/reference_markers.hmm GCF_025685705.1_ASM2568570v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:44:03,349] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:44:03,350] [INFO] Found 6/6 markers.
[2024-01-25 19:44:03,390] [INFO] Query marker FASTA was written to GCF_025685705.1_ASM2568570v1_genomic.fna/markers.fasta
[2024-01-25 19:44:03,391] [INFO] Task started: Blastn
[2024-01-25 19:44:03,391] [INFO] Running command: blastn -query GCF_025685705.1_ASM2568570v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2382cba3-124a-4f4a-ae04-b7a3f8c81096/dqc_reference/reference_markers.fasta -out GCF_025685705.1_ASM2568570v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:44:03,988] [INFO] Task succeeded: Blastn
[2024-01-25 19:44:03,991] [INFO] Selected 13 target genomes.
[2024-01-25 19:44:03,991] [INFO] Target genome list was writen to GCF_025685705.1_ASM2568570v1_genomic.fna/target_genomes.txt
[2024-01-25 19:44:03,996] [INFO] Task started: fastANI
[2024-01-25 19:44:03,996] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc304083-3799-4e13-bfe2-91462dabf846/GCF_025685705.1_ASM2568570v1_genomic.fna.gz --refList GCF_025685705.1_ASM2568570v1_genomic.fna/target_genomes.txt --output GCF_025685705.1_ASM2568570v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:44:17,371] [INFO] Task succeeded: fastANI
[2024-01-25 19:44:17,372] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2382cba3-124a-4f4a-ae04-b7a3f8c81096/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:44:17,372] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2382cba3-124a-4f4a-ae04-b7a3f8c81096/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:44:17,381] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:44:17,381] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:44:17,381] [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 dinghuensis	strain=CGMCC 1.12997	GCA_014640335.1	1560005	1560005	type	True	99.9997	1506	1507	95	conclusive
Edaphobacter aggregans	strain=DSM 19364	GCA_000745965.1	570835	570835	type	True	78.8344	428	1507	95	below_threshold
Edaphobacter lichenicola	strain=DSM 104462	GCA_025264645.1	2051959	2051959	suspected-type	True	78.7805	389	1507	95	below_threshold
Edaphobacter flagellatus	strain=HZ411	GCA_025264665.1	1933044	1933044	type	True	78.3829	316	1507	95	below_threshold
Edaphobacter acidisoli	strain=CGMCC 1.15447	GCA_014642855.1	2040573	2040573	type	True	78.3301	404	1507	95	below_threshold
Edaphobacter modestus	strain=DSM 18101	GCA_004217555.1	388466	388466	type	True	78.3008	336	1507	95	below_threshold
Granulicella mallensis	strain=MP5ACTX8	GCA_000178955.2	940614	940614	type	True	78.2266	289	1507	95	below_threshold
Granulicella rosea	strain=DSM 18704	GCA_900188085.1	474952	474952	type	True	77.7862	331	1507	95	below_threshold
Granulicella sibirica	strain=AF10	GCA_004115155.1	2479048	2479048	type	True	77.7649	275	1507	95	below_threshold
Granulicella pectinivorans	strain=DSM 21001	GCA_900114625.1	474950	474950	type	True	77.7613	292	1507	95	below_threshold
Bryocella elongata	strain=DSM 22489	GCA_900108185.1	863522	863522	type	True	77.6682	222	1507	95	below_threshold
Granulicella tundricola	strain=MP5ACTX9	GCA_000178975.2	940615	940615	type	True	77.653	260	1507	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:44:17,382] [INFO] DFAST Taxonomy check result was written to GCF_025685705.1_ASM2568570v1_genomic.fna/tc_result.tsv
[2024-01-25 19:44:17,383] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:44:17,383] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:44:17,383] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2382cba3-124a-4f4a-ae04-b7a3f8c81096/dqc_reference/checkm_data
[2024-01-25 19:44:17,384] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:44:17,426] [INFO] Task started: CheckM
[2024-01-25 19:44:17,426] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025685705.1_ASM2568570v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025685705.1_ASM2568570v1_genomic.fna/checkm_input GCF_025685705.1_ASM2568570v1_genomic.fna/checkm_result
[2024-01-25 19:44:53,374] [INFO] Task succeeded: CheckM
[2024-01-25 19:44:53,375] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:44:53,410] [INFO] ===== Completeness check finished =====
[2024-01-25 19:44:53,411] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:44:53,411] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025685705.1_ASM2568570v1_genomic.fna/markers.fasta)
[2024-01-25 19:44:53,412] [INFO] Task started: Blastn
[2024-01-25 19:44:53,412] [INFO] Running command: blastn -query GCF_025685705.1_ASM2568570v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2382cba3-124a-4f4a-ae04-b7a3f8c81096/dqc_reference/reference_markers_gtdb.fasta -out GCF_025685705.1_ASM2568570v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:44:54,343] [INFO] Task succeeded: Blastn
[2024-01-25 19:44:54,346] [INFO] Selected 10 target genomes.
[2024-01-25 19:44:54,346] [INFO] Target genome list was writen to GCF_025685705.1_ASM2568570v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:44:54,365] [INFO] Task started: fastANI
[2024-01-25 19:44:54,365] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc304083-3799-4e13-bfe2-91462dabf846/GCF_025685705.1_ASM2568570v1_genomic.fna.gz --refList GCF_025685705.1_ASM2568570v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025685705.1_ASM2568570v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:45:04,322] [INFO] Task succeeded: fastANI
[2024-01-25 19:45:04,329] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:45:04,329] [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_014640335.1	s__Edaphobacter dinghuensis	99.9997	1506	1507	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_009765835.1	s__Edaphobacter sp009765835	85.7575	1068	1507	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	81.387	665	1507	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003633965.1	s__Edaphobacter dinghuensis_A	80.9081	647	1507	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	80.5052	698	1507	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	99.98	99.98	0.99	0.99	2	-
GCF_003945235.1	s__Edaphobacter aggregans_A	79.0076	439	1507	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	78.9943	459	1507	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015655585.1	s__Edaphobacter sp015655585	78.5328	290	1507	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268775.1	s__Edaphobacter sp018268775	78.4498	323	1507	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000421065.1	s__Edaphobacter sp000421065	78.291	347	1507	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:45:04,330] [INFO] GTDB search result was written to GCF_025685705.1_ASM2568570v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:45:04,331] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:45:04,334] [INFO] DFAST_QC result json was written to GCF_025685705.1_ASM2568570v1_genomic.fna/dqc_result.json
[2024-01-25 19:45:04,334] [INFO] DFAST_QC completed!
[2024-01-25 19:45:04,334] [INFO] Total running time: 0h1m14s