[2024-01-24 11:26:38,948] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:38,949] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:38,950] [INFO] DQC Reference Directory: /var/lib/cwl/stgf21f4ef9-0604-45e1-9f02-2e78e685fc32/dqc_reference
[2024-01-24 11:26:40,278] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:40,279] [INFO] Task started: Prodigal
[2024-01-24 11:26:40,279] [INFO] Running command: gunzip -c /var/lib/cwl/stg6a19de24-f03a-4c3f-8845-248c6c6a8af9/GCF_016586375.1_ASM1658637v1_genomic.fna.gz | prodigal -d GCF_016586375.1_ASM1658637v1_genomic.fna/cds.fna -a GCF_016586375.1_ASM1658637v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:48,554] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:48,555] [INFO] Task started: HMMsearch
[2024-01-24 11:26:48,555] [INFO] Running command: hmmsearch --tblout GCF_016586375.1_ASM1658637v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf21f4ef9-0604-45e1-9f02-2e78e685fc32/dqc_reference/reference_markers.hmm GCF_016586375.1_ASM1658637v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:48,837] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:48,838] [INFO] Found 6/6 markers.
[2024-01-24 11:26:48,868] [INFO] Query marker FASTA was written to GCF_016586375.1_ASM1658637v1_genomic.fna/markers.fasta
[2024-01-24 11:26:48,869] [INFO] Task started: Blastn
[2024-01-24 11:26:48,869] [INFO] Running command: blastn -query GCF_016586375.1_ASM1658637v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf21f4ef9-0604-45e1-9f02-2e78e685fc32/dqc_reference/reference_markers.fasta -out GCF_016586375.1_ASM1658637v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:49,572] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:49,576] [INFO] Selected 16 target genomes.
[2024-01-24 11:26:49,577] [INFO] Target genome list was writen to GCF_016586375.1_ASM1658637v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:49,617] [INFO] Task started: fastANI
[2024-01-24 11:26:49,618] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a19de24-f03a-4c3f-8845-248c6c6a8af9/GCF_016586375.1_ASM1658637v1_genomic.fna.gz --refList GCF_016586375.1_ASM1658637v1_genomic.fna/target_genomes.txt --output GCF_016586375.1_ASM1658637v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:58,886] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:58,887] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf21f4ef9-0604-45e1-9f02-2e78e685fc32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:58,887] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf21f4ef9-0604-45e1-9f02-2e78e685fc32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:58,899] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:26:58,899] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:26:58,899] [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
Butyricicoccus faecihominis	strain=JCM 31056	GCA_016586375.1	1712515	1712515	type	True	100.0	940	949	95	conclusive
Butyricicoccus faecihominis	strain=JCM 31056	GCA_014648015.1	1712515	1712515	type	True	99.9675	940	949	95	conclusive
Faecalibacterium hattorii	strain=APC922/41-1	GCA_003287455.1	2935520	2935520	type	True	80.6595	72	949	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	79.6302	60	949	95	below_threshold
Agathobaculum desmolans	strain=ATCC 43058	GCA_000701665.1	39484	39484	type	True	79.601	313	949	95	below_threshold
Butyricicoccus intestinisimiae	strain=MSJd-7	GCA_018918345.1	2841509	2841509	type	True	78.8782	136	949	95	below_threshold
Butyricicoccus pullicaecorum	strain=DSM 23266	GCA_900167005.1	501571	501571	type	True	78.6205	196	949	95	below_threshold
Intestinibacillus massiliensis	strain=type strain: Marseille-P3216	GCA_900155735.1	1871029	1871029	type	True	78.3647	190	949	95	below_threshold
Butyricicoccus porcorum	strain=BB10	GCA_002157465.1	1945634	1945634	type	True	77.7311	132	949	95	below_threshold
Ligaoa zhengdingensis	strain=NSJ-31	GCA_014384885.1	2763658	2763658	type	True	76.9853	53	949	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:58,901] [INFO] DFAST Taxonomy check result was written to GCF_016586375.1_ASM1658637v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:58,902] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:58,902] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:58,902] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf21f4ef9-0604-45e1-9f02-2e78e685fc32/dqc_reference/checkm_data
[2024-01-24 11:26:58,904] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:58,935] [INFO] Task started: CheckM
[2024-01-24 11:26:58,936] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016586375.1_ASM1658637v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016586375.1_ASM1658637v1_genomic.fna/checkm_input GCF_016586375.1_ASM1658637v1_genomic.fna/checkm_result
[2024-01-24 11:27:28,729] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:28,730] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:28,750] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:28,750] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:28,750] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016586375.1_ASM1658637v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:28,751] [INFO] Task started: Blastn
[2024-01-24 11:27:28,751] [INFO] Running command: blastn -query GCF_016586375.1_ASM1658637v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf21f4ef9-0604-45e1-9f02-2e78e685fc32/dqc_reference/reference_markers_gtdb.fasta -out GCF_016586375.1_ASM1658637v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:29,990] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:29,994] [INFO] Selected 12 target genomes.
[2024-01-24 11:27:29,994] [INFO] Target genome list was writen to GCF_016586375.1_ASM1658637v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:30,036] [INFO] Task started: fastANI
[2024-01-24 11:27:30,036] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a19de24-f03a-4c3f-8845-248c6c6a8af9/GCF_016586375.1_ASM1658637v1_genomic.fna.gz --refList GCF_016586375.1_ASM1658637v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016586375.1_ASM1658637v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:36,280] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:36,291] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:36,291] [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_003096535.1	s__Agathobaculum butyriciproducens	95.7024	725	949	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	96.66	95.68	0.85	0.79	34	conclusive
GCF_003481705.1	s__Agathobaculum sp003481705	84.4411	509	949	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	98.33	96.26	0.92	0.82	8	-
GCA_900544475.1	s__Agathobaculum sp900544475	83.5417	351	949	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	97.90	97.82	0.89	0.86	3	-
GCA_900555465.1	s__Agathobaculum intestinigallinarum	81.05	239	949	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	97.06	97.06	0.83	0.83	2	-
GCF_900625105.1	s__Agathobaculum sp900625105	80.6855	413	949	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019113065.1	s__Agathobaculum stercoravium	80.5154	320	949	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	98.25	98.25	0.89	0.89	2	-
GCA_019115615.1	s__Agathobaculum merdavium	80.2062	306	949	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900557315.1	s__Agathobaculum sp900557315	80.16	208	949	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	100.00	100.00	0.98	0.98	2	-
GCA_019115185.1	s__Agathobaculum merdipullorum	80.0514	258	949	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019115425.1	s__Agathobaculum merdigallinarum	79.999	277	949	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019114345.1	s__Agathobaculum pullistercoris	79.8841	305	949	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	98.72	98.13	0.86	0.78	4	-
GCF_000701665.1	s__Agathobaculum desmolans	79.6107	312	949	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	98.85	98.85	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:36,293] [INFO] GTDB search result was written to GCF_016586375.1_ASM1658637v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:36,294] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:36,297] [INFO] DFAST_QC result json was written to GCF_016586375.1_ASM1658637v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:36,297] [INFO] DFAST_QC completed!
[2024-01-24 11:27:36,298] [INFO] Total running time: 0h0m57s