[2024-01-24 13:30:12,628] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:30:12,630] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:30:12,631] [INFO] DQC Reference Directory: /var/lib/cwl/stgef1fbf44-1fd0-4488-89d9-a6e87af515de/dqc_reference
[2024-01-24 13:30:13,826] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:30:13,827] [INFO] Task started: Prodigal
[2024-01-24 13:30:13,827] [INFO] Running command: gunzip -c /var/lib/cwl/stga84c03b8-da7b-405a-a87d-6e41dcfeb375/GCF_001486445.1_Hugonella_massiliensis_genomic.fna.gz | prodigal -d GCF_001486445.1_Hugonella_massiliensis_genomic.fna/cds.fna -a GCF_001486445.1_Hugonella_massiliensis_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:30:20,196] [INFO] Task succeeded: Prodigal
[2024-01-24 13:30:20,197] [INFO] Task started: HMMsearch
[2024-01-24 13:30:20,197] [INFO] Running command: hmmsearch --tblout GCF_001486445.1_Hugonella_massiliensis_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgef1fbf44-1fd0-4488-89d9-a6e87af515de/dqc_reference/reference_markers.hmm GCF_001486445.1_Hugonella_massiliensis_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:30:20,419] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:30:20,421] [INFO] Found 6/6 markers.
[2024-01-24 13:30:20,443] [INFO] Query marker FASTA was written to GCF_001486445.1_Hugonella_massiliensis_genomic.fna/markers.fasta
[2024-01-24 13:30:20,444] [INFO] Task started: Blastn
[2024-01-24 13:30:20,444] [INFO] Running command: blastn -query GCF_001486445.1_Hugonella_massiliensis_genomic.fna/markers.fasta -db /var/lib/cwl/stgef1fbf44-1fd0-4488-89d9-a6e87af515de/dqc_reference/reference_markers.fasta -out GCF_001486445.1_Hugonella_massiliensis_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:30:21,083] [INFO] Task succeeded: Blastn
[2024-01-24 13:30:21,086] [INFO] Selected 14 target genomes.
[2024-01-24 13:30:21,087] [INFO] Target genome list was writen to GCF_001486445.1_Hugonella_massiliensis_genomic.fna/target_genomes.txt
[2024-01-24 13:30:21,252] [INFO] Task started: fastANI
[2024-01-24 13:30:21,252] [INFO] Running command: fastANI --query /var/lib/cwl/stga84c03b8-da7b-405a-a87d-6e41dcfeb375/GCF_001486445.1_Hugonella_massiliensis_genomic.fna.gz --refList GCF_001486445.1_Hugonella_massiliensis_genomic.fna/target_genomes.txt --output GCF_001486445.1_Hugonella_massiliensis_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:30:27,446] [INFO] Task succeeded: fastANI
[2024-01-24 13:30:27,446] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgef1fbf44-1fd0-4488-89d9-a6e87af515de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:30:27,447] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgef1fbf44-1fd0-4488-89d9-a6e87af515de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:30:27,463] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:30:27,464] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:30:27,464] [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
Denitrobacterium detoxificans	strain=NPOH1	GCA_001643775.1	79604	79604	type	True	79.2197	169	693	95	below_threshold
Denitrobacterium detoxificans	strain=DSM 21843	GCA_900110565.1	79604	79604	type	True	78.6434	162	693	95	below_threshold
Slackia faecicanis	strain=DSM 17537	GCA_003725295.1	255723	255723	type	True	78.3965	127	693	95	below_threshold
Gordonibacter pamelaeae	strain=7-10-1-bT	GCA_000210055.1	471189	471189	type	True	78.1875	172	693	95	below_threshold
Eggerthella guodeyinii	strain=HF-1101	GCA_009834925.2	2690837	2690837	type	True	78.1075	201	693	95	below_threshold
Senegalimassilia anaerobia	strain=type strain: JC110	GCA_000236865.1	1473216	1473216	type	True	77.9887	165	693	95	below_threshold
Eggerthella sinensis	strain=DSM 16107	GCA_003339815.1	242230	242230	type	True	77.9171	184	693	95	below_threshold
Eggerthella sinensis	strain=DSM 16107	GCA_003725965.1	242230	242230	type	True	77.7891	186	693	95	below_threshold
Eggerthella lenta	strain=DSM 2243	GCA_000024265.1	84112	84112	type	True	77.7862	187	693	95	below_threshold
Slackia equolifaciens	strain=DSM 24851	GCA_003725995.1	498718	498718	type	True	77.5059	104	693	95	below_threshold
Eggerthella lenta	strain=DSM 2243	GCA_003339975.1	84112	84112	type	True	77.5005	175	693	95	below_threshold
Eggerthella lenta	strain=UCSF2243	GCA_003339945.1	84112	84112	type	True	77.4774	174	693	95	below_threshold
Eggerthella lenta	strain=ATCC 25559	GCA_003340105.1	84112	84112	type	True	77.4719	172	693	95	below_threshold
Raoultibacter massiliensis	strain=Marseille-P2849	GCA_900199545.1	1852371	1852371	type	True	77.0915	124	693	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:30:27,466] [INFO] DFAST Taxonomy check result was written to GCF_001486445.1_Hugonella_massiliensis_genomic.fna/tc_result.tsv
[2024-01-24 13:30:27,466] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:30:27,467] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:30:27,467] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgef1fbf44-1fd0-4488-89d9-a6e87af515de/dqc_reference/checkm_data
[2024-01-24 13:30:27,468] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:30:27,501] [INFO] Task started: CheckM
[2024-01-24 13:30:27,501] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001486445.1_Hugonella_massiliensis_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001486445.1_Hugonella_massiliensis_genomic.fna/checkm_input GCF_001486445.1_Hugonella_massiliensis_genomic.fna/checkm_result
[2024-01-24 13:30:50,988] [INFO] Task succeeded: CheckM
[2024-01-24 13:30:50,990] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:30:51,012] [INFO] ===== Completeness check finished =====
[2024-01-24 13:30:51,012] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:30:51,013] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001486445.1_Hugonella_massiliensis_genomic.fna/markers.fasta)
[2024-01-24 13:30:51,013] [INFO] Task started: Blastn
[2024-01-24 13:30:51,013] [INFO] Running command: blastn -query GCF_001486445.1_Hugonella_massiliensis_genomic.fna/markers.fasta -db /var/lib/cwl/stgef1fbf44-1fd0-4488-89d9-a6e87af515de/dqc_reference/reference_markers_gtdb.fasta -out GCF_001486445.1_Hugonella_massiliensis_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:30:51,953] [INFO] Task succeeded: Blastn
[2024-01-24 13:30:51,956] [INFO] Selected 20 target genomes.
[2024-01-24 13:30:51,957] [INFO] Target genome list was writen to GCF_001486445.1_Hugonella_massiliensis_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:30:52,215] [INFO] Task started: fastANI
[2024-01-24 13:30:52,216] [INFO] Running command: fastANI --query /var/lib/cwl/stga84c03b8-da7b-405a-a87d-6e41dcfeb375/GCF_001486445.1_Hugonella_massiliensis_genomic.fna.gz --refList GCF_001486445.1_Hugonella_massiliensis_genomic.fna/target_genomes_gtdb.txt --output GCF_001486445.1_Hugonella_massiliensis_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:31:00,118] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:00,133] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:31:00,133] [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_001486445.1	s__RUG013 sp001486445	100.0	691	693	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__RUG013	95.0	98.36	97.63	0.92	0.89	7	conclusive
GCF_001643775.1	s__Denitrobacterium detoxificans	79.2137	170	693	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Denitrobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCA_015062615.1	s__Denitrobacterium detoxificans_A	78.6168	173	693	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Denitrobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003725295.1	s__Slackia_A faecicanis	78.3457	128	693	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Slackia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009834925.2	s__Eggerthella sp014287365	78.1612	203	693	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Eggerthella	95.0	97.74	96.91	0.89	0.85	3	-
GCA_900550385.1	s__Aphodovivens sp900550385	78.0419	122	693	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Aphodovivens	95.0	99.66	99.66	0.86	0.86	2	-
GCF_011038975.1	s__CAAEEV01 sp011038975	78.0331	187	693	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__CAAEEV01	95.0	99.99	99.99	0.98	0.98	2	-
GCA_905215325.1	s__Senegalimassilia sp905215325	77.9317	151	693	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Senegalimassilia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900754495.1	s__Aphodovivens avicola	77.8915	123	693	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Aphodovivens	95.0	96.28	95.91	0.79	0.73	3	-
GCF_003339815.1	s__Eggerthella sinensis	77.8638	187	693	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Eggerthella	95.0	99.07	98.15	0.94	0.88	3	-
GCA_905234785.1	s__UBA9715 sp905234785	77.8435	140	693	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__UBA9715	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000024265.1	s__Eggerthella lenta	77.8434	188	693	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Eggerthella	95.0	98.39	97.51	0.89	0.82	72	-
GCA_900754955.1	s__CAAEEV01 sp900754955	77.7939	130	693	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__CAAEEV01	95.0	99.85	99.85	0.86	0.86	2	-
GCA_018715725.1	s__Aveggerthella excrementigallinarum	77.4699	145	693	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Aveggerthella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004555335.1	s__W1P20-047 sp004555335	77.441	95	693	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__W1P20-047	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910589165.1	s__Adlercreutzia sp910589165	77.4049	165	693	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Adlercreutzia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902767025.1	s__CACXMZ01 sp902767025	77.2955	105	693	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__CACXMZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900540955.1	s__Paratractidigestivibacter sp900540955	77.2891	72	693	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Paratractidigestivibacter	95.0	96.08	96.08	0.89	0.89	2	-
GCA_900553775.1	s__Slackia_A sp900553775	77.2224	93	693	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Slackia_A	95.0	98.24	98.24	0.77	0.77	2	-
GCA_900555495.1	s__Slackia_A sp900555495	77.0151	73	693	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Slackia_A	95.0	100.00	100.00	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:31:00,135] [INFO] GTDB search result was written to GCF_001486445.1_Hugonella_massiliensis_genomic.fna/result_gtdb.tsv
[2024-01-24 13:31:00,136] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:31:00,140] [INFO] DFAST_QC result json was written to GCF_001486445.1_Hugonella_massiliensis_genomic.fna/dqc_result.json
[2024-01-24 13:31:00,140] [INFO] DFAST_QC completed!
[2024-01-24 13:31:00,140] [INFO] Total running time: 0h0m48s