[2024-01-24 14:03:08,503] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:03:08,505] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:03:08,505] [INFO] DQC Reference Directory: /var/lib/cwl/stg9b68be3b-fd28-48c7-9bfb-b3c3b4804679/dqc_reference
[2024-01-24 14:03:09,774] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:03:09,775] [INFO] Task started: Prodigal
[2024-01-24 14:03:09,775] [INFO] Running command: gunzip -c /var/lib/cwl/stg9a6a7894-3d93-4927-82b4-5a2f5c98eff1/GCF_014201455.1_ASM1420145v1_genomic.fna.gz | prodigal -d GCF_014201455.1_ASM1420145v1_genomic.fna/cds.fna -a GCF_014201455.1_ASM1420145v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:03:29,510] [INFO] Task succeeded: Prodigal
[2024-01-24 14:03:29,511] [INFO] Task started: HMMsearch
[2024-01-24 14:03:29,511] [INFO] Running command: hmmsearch --tblout GCF_014201455.1_ASM1420145v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9b68be3b-fd28-48c7-9bfb-b3c3b4804679/dqc_reference/reference_markers.hmm GCF_014201455.1_ASM1420145v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:03:29,909] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:03:29,910] [INFO] Found 6/6 markers.
[2024-01-24 14:03:29,963] [INFO] Query marker FASTA was written to GCF_014201455.1_ASM1420145v1_genomic.fna/markers.fasta
[2024-01-24 14:03:29,964] [INFO] Task started: Blastn
[2024-01-24 14:03:29,964] [INFO] Running command: blastn -query GCF_014201455.1_ASM1420145v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b68be3b-fd28-48c7-9bfb-b3c3b4804679/dqc_reference/reference_markers.fasta -out GCF_014201455.1_ASM1420145v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:03:30,617] [INFO] Task succeeded: Blastn
[2024-01-24 14:03:30,622] [INFO] Selected 14 target genomes.
[2024-01-24 14:03:30,623] [INFO] Target genome list was writen to GCF_014201455.1_ASM1420145v1_genomic.fna/target_genomes.txt
[2024-01-24 14:03:30,647] [INFO] Task started: fastANI
[2024-01-24 14:03:30,647] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a6a7894-3d93-4927-82b4-5a2f5c98eff1/GCF_014201455.1_ASM1420145v1_genomic.fna.gz --refList GCF_014201455.1_ASM1420145v1_genomic.fna/target_genomes.txt --output GCF_014201455.1_ASM1420145v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:03:44,946] [INFO] Task succeeded: fastANI
[2024-01-24 14:03:44,947] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9b68be3b-fd28-48c7-9bfb-b3c3b4804679/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:03:44,948] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9b68be3b-fd28-48c7-9bfb-b3c3b4804679/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:03:44,959] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:03:44,960] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:03:44,960] [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
Silvibacterium bohemicum	strain=DSM 103733	GCA_014201455.1	1577686	1577686	type	True	100.0	2139	2141	95	conclusive
Silvibacterium bohemicum	strain=S15	GCA_001006305.1	1577686	1577686	type	True	99.9993	2137	2141	95	conclusive
Silvibacterium dinghuense	strain=DHOF10	GCA_004123295.1	1560006	1560006	type	True	78.451	551	2141	95	below_threshold
Silvibacterium dinghuense	strain=CGMCC 1.13007	GCA_014640355.1	1560006	1560006	type	True	78.4097	556	2141	95	below_threshold
Paracidobacterium acidisoli	strain=4G-K13	GCA_003428625.2	2303751	2303751	type	True	78.0272	389	2141	95	below_threshold
Acidobacterium capsulatum	strain=ATCC 51196	GCA_000022565.1	33075	33075	type	True	77.6224	249	2141	95	below_threshold
Granulicella rosea	strain=DSM 18704	GCA_900188085.1	474952	474952	type	True	76.895	202	2141	95	below_threshold
Granulicella pectinivorans	strain=DSM 21001	GCA_900114625.1	474950	474950	type	True	76.6093	162	2141	95	below_threshold
Bradyrhizobium quebecense	strain=66S1MB, /ecotype=symbiovar septentrionalis	GCA_013373795.3	2748629	2748629	type	True	75.195	65	2141	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:03:44,962] [INFO] DFAST Taxonomy check result was written to GCF_014201455.1_ASM1420145v1_genomic.fna/tc_result.tsv
[2024-01-24 14:03:44,962] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:03:44,963] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:03:44,963] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9b68be3b-fd28-48c7-9bfb-b3c3b4804679/dqc_reference/checkm_data
[2024-01-24 14:03:44,965] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:03:45,029] [INFO] Task started: CheckM
[2024-01-24 14:03:45,030] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014201455.1_ASM1420145v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014201455.1_ASM1420145v1_genomic.fna/checkm_input GCF_014201455.1_ASM1420145v1_genomic.fna/checkm_result
[2024-01-24 14:04:39,238] [INFO] Task succeeded: CheckM
[2024-01-24 14:04:39,240] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:04:39,261] [INFO] ===== Completeness check finished =====
[2024-01-24 14:04:39,262] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:04:39,262] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014201455.1_ASM1420145v1_genomic.fna/markers.fasta)
[2024-01-24 14:04:39,263] [INFO] Task started: Blastn
[2024-01-24 14:04:39,263] [INFO] Running command: blastn -query GCF_014201455.1_ASM1420145v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b68be3b-fd28-48c7-9bfb-b3c3b4804679/dqc_reference/reference_markers_gtdb.fasta -out GCF_014201455.1_ASM1420145v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:04:40,091] [INFO] Task succeeded: Blastn
[2024-01-24 14:04:40,096] [INFO] Selected 20 target genomes.
[2024-01-24 14:04:40,096] [INFO] Target genome list was writen to GCF_014201455.1_ASM1420145v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:04:40,121] [INFO] Task started: fastANI
[2024-01-24 14:04:40,122] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a6a7894-3d93-4927-82b4-5a2f5c98eff1/GCF_014201455.1_ASM1420145v1_genomic.fna.gz --refList GCF_014201455.1_ASM1420145v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014201455.1_ASM1420145v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:04:56,112] [INFO] Task succeeded: fastANI
[2024-01-24 14:04:56,131] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:04:56,131] [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_001006305.1	s__Silvibacterium bohemicum	99.9993	2137	2141	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Silvibacterium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_004123295.1	s__Silvibacterium dinghuense	78.4582	550	2141	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Silvibacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003428625.2	s__Palsa-343 sp003428625	78.0362	388	2141	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Palsa-343	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765825.1	s__Edaphobacter sp009765825	77.8591	207	2141	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765985.1	s__Acidobacterium_A sp009765985	77.6747	274	2141	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Acidobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014274465.1	s__Acidobacterium_A sp014274465	77.6516	253	2141	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Acidobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000022565.1	s__Acidobacterium capsulatum	77.6226	249	2141	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Acidobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_013289875.1	s__Silvibacterium sp013289875	77.5417	350	2141	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Silvibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011333575.1	s__Acidobacterium capsulatum_A	77.5351	223	2141	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Acidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019234945.1	s__Silvibacterium sp019234945	77.4999	236	2141	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Silvibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013285705.1	s__Acidobacterium_A sp013285705	77.3635	204	2141	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Acidobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188085.1	s__Granulicella_C rosea	76.9191	200	2141	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_018268855.1	s__Terriglobus sp018268855	76.8554	119	2141	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terriglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015655315.1	s__Acidobacterium_A sp015655315	76.7491	203	2141	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Acidobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003131625.1	s__Palsa-343 sp003131625	76.6123	253	2141	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Palsa-343	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003159355.1	s__Terracidiphilus sp003159355	76.4027	132	2141	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	99.48	99.30	0.83	0.80	7	-
GCA_003142215.1	s__Palsa-288 sp003142215	76.3188	126	2141	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Palsa-288	95.0	99.59	99.59	0.84	0.84	2	-
GCF_013373795.1	s__Bradyrhizobium quebecense	75.2005	64	2141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.1616	96.90	95.60	0.87	0.83	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:04:56,133] [INFO] GTDB search result was written to GCF_014201455.1_ASM1420145v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:04:56,133] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:04:56,137] [INFO] DFAST_QC result json was written to GCF_014201455.1_ASM1420145v1_genomic.fna/dqc_result.json
[2024-01-24 14:04:56,137] [INFO] DFAST_QC completed!
[2024-01-24 14:04:56,137] [INFO] Total running time: 0h1m48s