[2023-06-28 22:52:04,091] [INFO] DFAST_QC pipeline started.
[2023-06-28 22:52:04,093] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 22:52:04,094] [INFO] DQC Reference Directory: /var/lib/cwl/stg7c59506a-2b23-4fad-b24b-e3ccf72cf86c/dqc_reference
[2023-06-28 22:52:05,459] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 22:52:05,460] [INFO] Task started: Prodigal
[2023-06-28 22:52:05,460] [INFO] Running command: gunzip -c /var/lib/cwl/stg6ab51f1b-d336-4ff4-8688-8df91fb5ebc7/GCA_017454065.1_ASM1745406v1_genomic.fna.gz | prodigal -d GCA_017454065.1_ASM1745406v1_genomic.fna/cds.fna -a GCA_017454065.1_ASM1745406v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 22:52:13,103] [INFO] Task succeeded: Prodigal
[2023-06-28 22:52:13,103] [INFO] Task started: HMMsearch
[2023-06-28 22:52:13,103] [INFO] Running command: hmmsearch --tblout GCA_017454065.1_ASM1745406v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7c59506a-2b23-4fad-b24b-e3ccf72cf86c/dqc_reference/reference_markers.hmm GCA_017454065.1_ASM1745406v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 22:52:13,363] [INFO] Task succeeded: HMMsearch
[2023-06-28 22:52:13,365] [INFO] Found 6/6 markers.
[2023-06-28 22:52:13,400] [INFO] Query marker FASTA was written to GCA_017454065.1_ASM1745406v1_genomic.fna/markers.fasta
[2023-06-28 22:52:13,400] [INFO] Task started: Blastn
[2023-06-28 22:52:13,400] [INFO] Running command: blastn -query GCA_017454065.1_ASM1745406v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c59506a-2b23-4fad-b24b-e3ccf72cf86c/dqc_reference/reference_markers.fasta -out GCA_017454065.1_ASM1745406v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 22:52:13,991] [INFO] Task succeeded: Blastn
[2023-06-28 22:52:13,994] [INFO] Selected 22 target genomes.
[2023-06-28 22:52:13,995] [INFO] Target genome list was writen to GCA_017454065.1_ASM1745406v1_genomic.fna/target_genomes.txt
[2023-06-28 22:52:13,999] [INFO] Task started: fastANI
[2023-06-28 22:52:13,999] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ab51f1b-d336-4ff4-8688-8df91fb5ebc7/GCA_017454065.1_ASM1745406v1_genomic.fna.gz --refList GCA_017454065.1_ASM1745406v1_genomic.fna/target_genomes.txt --output GCA_017454065.1_ASM1745406v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 22:52:28,546] [INFO] Task succeeded: fastANI
[2023-06-28 22:52:28,547] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7c59506a-2b23-4fad-b24b-e3ccf72cf86c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 22:52:28,547] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7c59506a-2b23-4fad-b24b-e3ccf72cf86c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 22:52:28,556] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 22:52:28,556] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 22:52:28,556] [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	78.9562	259	1031	95	below_threshold
Butyrivibrio proteoclasticus	strain=B316	GCA_000145035.1	43305	43305	type	True	78.759	270	1031	95	below_threshold
Butyrivibrio fibrisolvens	strain=DSM 3071	GCA_900129945.1	831	831	suspected-type	True	77.1159	107	1031	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 22:52:28,559] [INFO] DFAST Taxonomy check result was written to GCA_017454065.1_ASM1745406v1_genomic.fna/tc_result.tsv
[2023-06-28 22:52:28,560] [INFO] ===== Taxonomy check completed =====
[2023-06-28 22:52:28,560] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 22:52:28,560] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7c59506a-2b23-4fad-b24b-e3ccf72cf86c/dqc_reference/checkm_data
[2023-06-28 22:52:28,563] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 22:52:28,604] [INFO] Task started: CheckM
[2023-06-28 22:52:28,604] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017454065.1_ASM1745406v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017454065.1_ASM1745406v1_genomic.fna/checkm_input GCA_017454065.1_ASM1745406v1_genomic.fna/checkm_result
[2023-06-28 22:52:57,844] [INFO] Task succeeded: CheckM
[2023-06-28 22:52:57,845] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.37%
Contamintation: 12.50%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 22:52:57,875] [INFO] ===== Completeness check finished =====
[2023-06-28 22:52:57,875] [INFO] ===== Start GTDB Search =====
[2023-06-28 22:52:57,876] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017454065.1_ASM1745406v1_genomic.fna/markers.fasta)
[2023-06-28 22:52:57,876] [INFO] Task started: Blastn
[2023-06-28 22:52:57,876] [INFO] Running command: blastn -query GCA_017454065.1_ASM1745406v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c59506a-2b23-4fad-b24b-e3ccf72cf86c/dqc_reference/reference_markers_gtdb.fasta -out GCA_017454065.1_ASM1745406v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 22:52:58,711] [INFO] Task succeeded: Blastn
[2023-06-28 22:52:58,716] [INFO] Selected 16 target genomes.
[2023-06-28 22:52:58,716] [INFO] Target genome list was writen to GCA_017454065.1_ASM1745406v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 22:52:58,749] [INFO] Task started: fastANI
[2023-06-28 22:52:58,749] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ab51f1b-d336-4ff4-8688-8df91fb5ebc7/GCA_017454065.1_ASM1745406v1_genomic.fna.gz --refList GCA_017454065.1_ASM1745406v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017454065.1_ASM1745406v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 22:53:08,385] [INFO] Task succeeded: fastANI
[2023-06-28 22:53:08,399] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 22:53:08,399] [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_000421405.1	s__Butyrivibrio sp000421405	81.0703	460	1031	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio	95.0	96.36	95.13	0.87	0.84	3	-
GCF_000420865.1	s__Butyrivibrio sp000420865	80.8317	447	1031	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_017634825.1	s__Butyrivibrio sp017634825	80.8016	348	1031	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_002372465.1	s__Butyrivibrio sp002372465	80.4412	383	1031	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	80.1553	401	1031	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_017445665.1	s__Butyrivibrio sp017445665	80.0474	280	1031	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_000526935.1	s__Butyrivibrio sp000526935	79.7631	411	1031	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_015056575.1	s__Butyrivibrio sp015056575	79.67	351	1031	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	79.5961	370	1031	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_015056565.1	s__Butyrivibrio sp015056565	79.5091	372	1031	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio	95.0	96.70	96.70	0.78	0.78	2	-
GCF_000622085.1	s__Butyrivibrio proteoclasticus_A	79.4711	299	1031	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_000420825.1	s__Butyrivibrio sp000420825	78.952	262	1031	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_015056685.1	s__Butyrivibrio sp015056685	78.8073	264	1031	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio	95.0	95.83	95.83	0.67	0.67	2	-
GCF_900108105.1	s__Butyrivibrio sp900108105	78.6771	284	1031	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_000424465.1	s__Butyrivibrio hungatei_A	78.4079	230	1031	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio	95.0	98.43	98.32	0.90	0.90	3	-
GCF_900116865.1	s__Butyrivibrio sp900116865	78.2908	224	1031	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 22:53:08,401] [INFO] GTDB search result was written to GCA_017454065.1_ASM1745406v1_genomic.fna/result_gtdb.tsv
[2023-06-28 22:53:08,402] [INFO] ===== GTDB Search completed =====
[2023-06-28 22:53:08,405] [INFO] DFAST_QC result json was written to GCA_017454065.1_ASM1745406v1_genomic.fna/dqc_result.json
[2023-06-28 22:53:08,405] [INFO] DFAST_QC completed!
[2023-06-28 22:53:08,405] [INFO] Total running time: 0h1m4s