[2023-06-30 00:10:40,590] [INFO] DFAST_QC pipeline started.
[2023-06-30 00:10:40,593] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 00:10:40,593] [INFO] DQC Reference Directory: /var/lib/cwl/stg96110471-f8f3-4a6c-a587-c3a57f6bc53f/dqc_reference
[2023-06-30 00:10:41,889] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 00:10:41,890] [INFO] Task started: Prodigal
[2023-06-30 00:10:41,891] [INFO] Running command: gunzip -c /var/lib/cwl/stg0c02ec0b-9822-4771-aae0-eeb498752059/GCA_024694855.1_ASM2469485v1_genomic.fna.gz | prodigal -d GCA_024694855.1_ASM2469485v1_genomic.fna/cds.fna -a GCA_024694855.1_ASM2469485v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 00:10:48,635] [INFO] Task succeeded: Prodigal
[2023-06-30 00:10:48,636] [INFO] Task started: HMMsearch
[2023-06-30 00:10:48,636] [INFO] Running command: hmmsearch --tblout GCA_024694855.1_ASM2469485v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg96110471-f8f3-4a6c-a587-c3a57f6bc53f/dqc_reference/reference_markers.hmm GCA_024694855.1_ASM2469485v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 00:10:48,883] [INFO] Task succeeded: HMMsearch
[2023-06-30 00:10:48,884] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0c02ec0b-9822-4771-aae0-eeb498752059/GCA_024694855.1_ASM2469485v1_genomic.fna.gz]
[2023-06-30 00:10:48,915] [INFO] Query marker FASTA was written to GCA_024694855.1_ASM2469485v1_genomic.fna/markers.fasta
[2023-06-30 00:10:48,915] [INFO] Task started: Blastn
[2023-06-30 00:10:48,915] [INFO] Running command: blastn -query GCA_024694855.1_ASM2469485v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg96110471-f8f3-4a6c-a587-c3a57f6bc53f/dqc_reference/reference_markers.fasta -out GCA_024694855.1_ASM2469485v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 00:10:49,527] [INFO] Task succeeded: Blastn
[2023-06-30 00:10:49,532] [INFO] Selected 22 target genomes.
[2023-06-30 00:10:49,533] [INFO] Target genome list was writen to GCA_024694855.1_ASM2469485v1_genomic.fna/target_genomes.txt
[2023-06-30 00:10:49,534] [INFO] Task started: fastANI
[2023-06-30 00:10:49,535] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c02ec0b-9822-4771-aae0-eeb498752059/GCA_024694855.1_ASM2469485v1_genomic.fna.gz --refList GCA_024694855.1_ASM2469485v1_genomic.fna/target_genomes.txt --output GCA_024694855.1_ASM2469485v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 00:11:00,690] [INFO] Task succeeded: fastANI
[2023-06-30 00:11:00,690] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg96110471-f8f3-4a6c-a587-c3a57f6bc53f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 00:11:00,690] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg96110471-f8f3-4a6c-a587-c3a57f6bc53f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 00:11:00,698] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 00:11:00,698] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 00:11:00,698] [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
Butyrivibrio hungatei	strain=DSM 14810	GCA_900143205.1	185008	185008	type	True	77.7971	166	1015	95	below_threshold
Butyrivibrio proteoclasticus	strain=B316	GCA_000145035.1	43305	43305	type	True	77.6683	170	1015	95	below_threshold
Butyrivibrio fibrisolvens	strain=DSM 3071	GCA_900129945.1	831	831	suspected-type	True	77.4521	131	1015	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 00:11:00,700] [INFO] DFAST Taxonomy check result was written to GCA_024694855.1_ASM2469485v1_genomic.fna/tc_result.tsv
[2023-06-30 00:11:00,701] [INFO] ===== Taxonomy check completed =====
[2023-06-30 00:11:00,701] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 00:11:00,701] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg96110471-f8f3-4a6c-a587-c3a57f6bc53f/dqc_reference/checkm_data
[2023-06-30 00:11:00,703] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 00:11:00,735] [INFO] Task started: CheckM
[2023-06-30 00:11:00,735] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024694855.1_ASM2469485v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024694855.1_ASM2469485v1_genomic.fna/checkm_input GCA_024694855.1_ASM2469485v1_genomic.fna/checkm_result
[2023-06-30 00:11:27,452] [INFO] Task succeeded: CheckM
[2023-06-30 00:11:27,454] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.04%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 00:11:27,476] [INFO] ===== Completeness check finished =====
[2023-06-30 00:11:27,476] [INFO] ===== Start GTDB Search =====
[2023-06-30 00:11:27,477] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024694855.1_ASM2469485v1_genomic.fna/markers.fasta)
[2023-06-30 00:11:27,477] [INFO] Task started: Blastn
[2023-06-30 00:11:27,477] [INFO] Running command: blastn -query GCA_024694855.1_ASM2469485v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg96110471-f8f3-4a6c-a587-c3a57f6bc53f/dqc_reference/reference_markers_gtdb.fasta -out GCA_024694855.1_ASM2469485v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 00:11:28,424] [INFO] Task succeeded: Blastn
[2023-06-30 00:11:28,429] [INFO] Selected 18 target genomes.
[2023-06-30 00:11:28,429] [INFO] Target genome list was writen to GCA_024694855.1_ASM2469485v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 00:11:28,439] [INFO] Task started: fastANI
[2023-06-30 00:11:28,439] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c02ec0b-9822-4771-aae0-eeb498752059/GCA_024694855.1_ASM2469485v1_genomic.fna.gz --refList GCA_024694855.1_ASM2469485v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024694855.1_ASM2469485v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 00:11:40,643] [INFO] Task succeeded: fastANI
[2023-06-30 00:11:40,659] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 00:11:40,659] [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_000423945.1	s__Butyrivibrio sp000423945	97.7317	917	1015	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio	95.0	98.50	98.50	0.88	0.88	2	conclusive
GCF_000424145.1	s__Butyrivibrio sp000424145	82.945	623	1015	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423925.1	s__Butyrivibrio sp000423925	81.044	489	1015	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104155.1	s__Butyrivibrio sp900104155	81.0029	459	1015	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio	95.0	96.52	96.36	0.79	0.75	4	-
GCF_000703165.1	s__Butyrivibrio sp000703165	80.5075	439	1015	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000424385.1	s__Butyrivibrio sp000424385	80.2991	466	1015	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio	95.0	98.60	98.60	0.88	0.88	2	-
GCF_000424285.1	s__Butyrivibrio sp000424285	80.24	394	1015	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio	95.0	97.82	97.82	0.87	0.87	2	-
GCF_000424265.1	s__Butyrivibrio sp000424265	80.2201	401	1015	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015056655.1	s__Butyrivibrio sp015056655	79.9936	381	1015	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003625485.1	s__Butyrivibrio sp003625485	78.0907	175	1015	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017433805.1	s__Butyrivibrio sp017433805	78.0143	193	1015	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015056625.1	s__Butyrivibrio sp015056625	77.5165	157	1015	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129945.1	s__Butyrivibrio fibrisolvens	77.4331	131	1015	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003175155.1	s__Butyrivibrio fibrisolvens_C	77.2374	110	1015	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio	95.0	96.87	96.32	0.83	0.76	12	-
--------------------------------------------------------------------------------
[2023-06-30 00:11:40,661] [INFO] GTDB search result was written to GCA_024694855.1_ASM2469485v1_genomic.fna/result_gtdb.tsv
[2023-06-30 00:11:40,662] [INFO] ===== GTDB Search completed =====
[2023-06-30 00:11:40,665] [INFO] DFAST_QC result json was written to GCA_024694855.1_ASM2469485v1_genomic.fna/dqc_result.json
[2023-06-30 00:11:40,665] [INFO] DFAST_QC completed!
[2023-06-30 00:11:40,665] [INFO] Total running time: 0h1m0s