[2024-01-24 14:19:03,176] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:03,178] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:03,179] [INFO] DQC Reference Directory: /var/lib/cwl/stg2af531cf-8f4a-4f16-9e95-2ea5d8305ee9/dqc_reference
[2024-01-24 14:19:04,394] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:04,395] [INFO] Task started: Prodigal
[2024-01-24 14:19:04,395] [INFO] Running command: gunzip -c /var/lib/cwl/stg973b43a6-b1cf-4fd9-acd7-18414e2e859f/GCF_007668225.1_ASM766822v1_genomic.fna.gz | prodigal -d GCF_007668225.1_ASM766822v1_genomic.fna/cds.fna -a GCF_007668225.1_ASM766822v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:15,978] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:15,978] [INFO] Task started: HMMsearch
[2024-01-24 14:19:15,978] [INFO] Running command: hmmsearch --tblout GCF_007668225.1_ASM766822v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2af531cf-8f4a-4f16-9e95-2ea5d8305ee9/dqc_reference/reference_markers.hmm GCF_007668225.1_ASM766822v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:16,272] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:16,274] [INFO] Found 6/6 markers.
[2024-01-24 14:19:16,314] [INFO] Query marker FASTA was written to GCF_007668225.1_ASM766822v1_genomic.fna/markers.fasta
[2024-01-24 14:19:16,315] [INFO] Task started: Blastn
[2024-01-24 14:19:16,315] [INFO] Running command: blastn -query GCF_007668225.1_ASM766822v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2af531cf-8f4a-4f16-9e95-2ea5d8305ee9/dqc_reference/reference_markers.fasta -out GCF_007668225.1_ASM766822v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:17,313] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:17,323] [INFO] Selected 11 target genomes.
[2024-01-24 14:19:17,323] [INFO] Target genome list was writen to GCF_007668225.1_ASM766822v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:17,331] [INFO] Task started: fastANI
[2024-01-24 14:19:17,331] [INFO] Running command: fastANI --query /var/lib/cwl/stg973b43a6-b1cf-4fd9-acd7-18414e2e859f/GCF_007668225.1_ASM766822v1_genomic.fna.gz --refList GCF_007668225.1_ASM766822v1_genomic.fna/target_genomes.txt --output GCF_007668225.1_ASM766822v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:28,392] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:28,392] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2af531cf-8f4a-4f16-9e95-2ea5d8305ee9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:28,393] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2af531cf-8f4a-4f16-9e95-2ea5d8305ee9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:28,403] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:19:28,404] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:19:28,404] [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
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	100.0	1326	1331	95	inconclusive
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	95.6372	1180	1331	95	inconclusive
[Luteovulum] sphaeroides subsp. megalophilum	strain=DSM 18937	GCA_900188265.1	418630	1063	type	True	87.2235	1013	1331	95	below_threshold
Cereibacter johrii	strain=JA192	GCA_001720585.1	445629	445629	type	True	87.1951	910	1331	95	below_threshold
Cereibacter sphaeroides	strain=2.4.1	GCA_000273405.1	1063	1063	type	True	87.186	999	1331	95	below_threshold
Cereibacter sphaeroides	strain=2.4.1	GCA_003324715.1	1063	1063	type	True	87.1575	1001	1331	95	below_threshold
Cereibacter sphaeroides	strain=NBRC 12203	GCA_007991035.1	1063	1063	type	True	87.1165	998	1331	95	below_threshold
Cereibacter johrii	strain=JA192	GCA_003046325.1	445629	445629	type	True	87.0626	1025	1331	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	83.8879	834	1331	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	79.519	545	1331	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	79.4915	548	1331	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:28,406] [INFO] DFAST Taxonomy check result was written to GCF_007668225.1_ASM766822v1_genomic.fna/tc_result.tsv
[2024-01-24 14:19:28,406] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:28,407] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:28,407] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2af531cf-8f4a-4f16-9e95-2ea5d8305ee9/dqc_reference/checkm_data
[2024-01-24 14:19:28,408] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:28,454] [INFO] Task started: CheckM
[2024-01-24 14:19:28,454] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007668225.1_ASM766822v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007668225.1_ASM766822v1_genomic.fna/checkm_input GCF_007668225.1_ASM766822v1_genomic.fna/checkm_result
[2024-01-24 14:20:31,201] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:31,202] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:31,232] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:31,233] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:31,233] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007668225.1_ASM766822v1_genomic.fna/markers.fasta)
[2024-01-24 14:20:31,234] [INFO] Task started: Blastn
[2024-01-24 14:20:31,234] [INFO] Running command: blastn -query GCF_007668225.1_ASM766822v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2af531cf-8f4a-4f16-9e95-2ea5d8305ee9/dqc_reference/reference_markers_gtdb.fasta -out GCF_007668225.1_ASM766822v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:33,213] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:33,216] [INFO] Selected 6 target genomes.
[2024-01-24 14:20:33,217] [INFO] Target genome list was writen to GCF_007668225.1_ASM766822v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:33,223] [INFO] Task started: fastANI
[2024-01-24 14:20:33,224] [INFO] Running command: fastANI --query /var/lib/cwl/stg973b43a6-b1cf-4fd9-acd7-18414e2e859f/GCF_007668225.1_ASM766822v1_genomic.fna.gz --refList GCF_007668225.1_ASM766822v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007668225.1_ASM766822v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:39,324] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:39,331] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:20:39,331] [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
GCA_017599285.1	s__Cereibacter_A azotoformans	95.5649	890	1331	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter_A	95.0	98.54	95.54	0.92	0.86	6	conclusive
GCF_001720585.1	s__Cereibacter_A johrii	87.2006	909	1331	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter_A	95.1736	98.42	97.86	0.94	0.91	6	-
GCF_000012905.2	s__Cereibacter_A sphaeroides	87.1789	1002	1331	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter_A	95.1736	98.82	96.57	0.94	0.87	24	-
GCF_002407205.1	s__Cereibacter_A sp002407205	85.6309	980	1331	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900207575.1	s__Cereibacter_A ovatus	83.9207	830	1331	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003034985.1	s__Cereibacter changlensis	82.2496	766	1331	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter	95.0	98.07	96.18	0.89	0.78	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:20:39,333] [INFO] GTDB search result was written to GCF_007668225.1_ASM766822v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:39,334] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:39,337] [INFO] DFAST_QC result json was written to GCF_007668225.1_ASM766822v1_genomic.fna/dqc_result.json
[2024-01-24 14:20:39,337] [INFO] DFAST_QC completed!
[2024-01-24 14:20:39,337] [INFO] Total running time: 0h1m36s