[2024-01-24 14:30:46,931] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:46,933] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:46,933] [INFO] DQC Reference Directory: /var/lib/cwl/stg392460db-e2ea-47aa-96e1-8feec0d29268/dqc_reference
[2024-01-24 14:30:48,215] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:48,216] [INFO] Task started: Prodigal
[2024-01-24 14:30:48,216] [INFO] Running command: gunzip -c /var/lib/cwl/stg198d9f51-968c-485c-9d7f-f8a3b7054099/GCF_007991035.1_ASM799103v1_genomic.fna.gz | prodigal -d GCF_007991035.1_ASM799103v1_genomic.fna/cds.fna -a GCF_007991035.1_ASM799103v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:01,113] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:01,114] [INFO] Task started: HMMsearch
[2024-01-24 14:31:01,114] [INFO] Running command: hmmsearch --tblout GCF_007991035.1_ASM799103v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg392460db-e2ea-47aa-96e1-8feec0d29268/dqc_reference/reference_markers.hmm GCF_007991035.1_ASM799103v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:01,439] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:01,441] [INFO] Found 6/6 markers.
[2024-01-24 14:31:01,489] [INFO] Query marker FASTA was written to GCF_007991035.1_ASM799103v1_genomic.fna/markers.fasta
[2024-01-24 14:31:01,490] [INFO] Task started: Blastn
[2024-01-24 14:31:01,490] [INFO] Running command: blastn -query GCF_007991035.1_ASM799103v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg392460db-e2ea-47aa-96e1-8feec0d29268/dqc_reference/reference_markers.fasta -out GCF_007991035.1_ASM799103v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:02,633] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:02,636] [INFO] Selected 10 target genomes.
[2024-01-24 14:31:02,636] [INFO] Target genome list was writen to GCF_007991035.1_ASM799103v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:02,658] [INFO] Task started: fastANI
[2024-01-24 14:31:02,659] [INFO] Running command: fastANI --query /var/lib/cwl/stg198d9f51-968c-485c-9d7f-f8a3b7054099/GCF_007991035.1_ASM799103v1_genomic.fna.gz --refList GCF_007991035.1_ASM799103v1_genomic.fna/target_genomes.txt --output GCF_007991035.1_ASM799103v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:13,592] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:13,593] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg392460db-e2ea-47aa-96e1-8feec0d29268/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:13,593] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg392460db-e2ea-47aa-96e1-8feec0d29268/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:13,603] [INFO] Found 10 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 14:31:13,603] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:13,603] [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 sphaeroides	strain=NBRC 12203	GCA_007991035.1	1063	1063	type	True	100.0	1521	1529	95	conclusive
Cereibacter sphaeroides	strain=2.4.1	GCA_000269625.2	1063	1063	type	True	99.9848	1456	1529	95	conclusive
Cereibacter sphaeroides	strain=2.4.1	GCA_000273405.1	1063	1063	type	True	99.9781	1459	1529	95	conclusive
Cereibacter sphaeroides	strain=2.4.1	GCA_003324715.1	1063	1063	type	True	99.978	1459	1529	95	conclusive
Cereibacter sphaeroides	strain=2.4.1	GCA_000012905.2	1063	1063	type	True	99.9778	1458	1529	95	conclusive
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	87.0456	1001	1529	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	87.0095	1047	1529	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	82.7962	828	1529	95	below_threshold
Rhodobacter calidifons	strain=M37P	GCA_011174775.1	2715277	2715277	type	True	79.1469	561	1529	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	78.4635	509	1529	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:13,605] [INFO] DFAST Taxonomy check result was written to GCF_007991035.1_ASM799103v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:13,606] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:13,606] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:13,606] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg392460db-e2ea-47aa-96e1-8feec0d29268/dqc_reference/checkm_data
[2024-01-24 14:31:13,608] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:13,661] [INFO] Task started: CheckM
[2024-01-24 14:31:13,661] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007991035.1_ASM799103v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007991035.1_ASM799103v1_genomic.fna/checkm_input GCF_007991035.1_ASM799103v1_genomic.fna/checkm_result
[2024-01-24 14:32:03,515] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:03,516] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:03,541] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:03,541] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:03,541] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007991035.1_ASM799103v1_genomic.fna/markers.fasta)
[2024-01-24 14:32:03,542] [INFO] Task started: Blastn
[2024-01-24 14:32:03,542] [INFO] Running command: blastn -query GCF_007991035.1_ASM799103v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg392460db-e2ea-47aa-96e1-8feec0d29268/dqc_reference/reference_markers_gtdb.fasta -out GCF_007991035.1_ASM799103v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:05,881] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:05,884] [INFO] Selected 6 target genomes.
[2024-01-24 14:32:05,884] [INFO] Target genome list was writen to GCF_007991035.1_ASM799103v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:05,889] [INFO] Task started: fastANI
[2024-01-24 14:32:05,890] [INFO] Running command: fastANI --query /var/lib/cwl/stg198d9f51-968c-485c-9d7f-f8a3b7054099/GCF_007991035.1_ASM799103v1_genomic.fna.gz --refList GCF_007991035.1_ASM799103v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007991035.1_ASM799103v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:12,788] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:12,798] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:12,799] [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_000012905.2	s__Cereibacter_A sphaeroides	99.9778	1458	1529	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter_A	95.1736	98.82	96.57	0.94	0.87	24	conclusive
GCF_001720585.1	s__Cereibacter_A johrii	95.0012	1206	1529	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter_A	95.1736	98.42	97.86	0.94	0.91	6	-
GCA_017599285.1	s__Cereibacter_A azotoformans	87.4924	879	1529	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter_A	95.0	98.54	95.54	0.92	0.86	6	-
GCF_002407205.1	s__Cereibacter_A sp002407205	84.8756	995	1529	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	82.8164	826	1529	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	82.4876	829	1529	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 14:32:12,800] [INFO] GTDB search result was written to GCF_007991035.1_ASM799103v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:12,801] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:12,804] [INFO] DFAST_QC result json was written to GCF_007991035.1_ASM799103v1_genomic.fna/dqc_result.json
[2024-01-24 14:32:12,804] [INFO] DFAST_QC completed!
[2024-01-24 14:32:12,804] [INFO] Total running time: 0h1m26s