[2024-01-24 14:19:14,939] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:14,944] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:14,945] [INFO] DQC Reference Directory: /var/lib/cwl/stga8cec587-798f-4a05-bfbf-4acfc138d596/dqc_reference
[2024-01-24 14:19:16,125] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:16,126] [INFO] Task started: Prodigal
[2024-01-24 14:19:16,126] [INFO] Running command: gunzip -c /var/lib/cwl/stg5d8148ec-a81c-4f1e-8fb8-b7c75d5927bc/GCF_008831035.1_ASM883103v1_genomic.fna.gz | prodigal -d GCF_008831035.1_ASM883103v1_genomic.fna/cds.fna -a GCF_008831035.1_ASM883103v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:23,343] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:23,343] [INFO] Task started: HMMsearch
[2024-01-24 14:19:23,343] [INFO] Running command: hmmsearch --tblout GCF_008831035.1_ASM883103v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga8cec587-798f-4a05-bfbf-4acfc138d596/dqc_reference/reference_markers.hmm GCF_008831035.1_ASM883103v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:23,519] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:23,520] [INFO] Found 6/6 markers.
[2024-01-24 14:19:23,542] [INFO] Query marker FASTA was written to GCF_008831035.1_ASM883103v1_genomic.fna/markers.fasta
[2024-01-24 14:19:23,542] [INFO] Task started: Blastn
[2024-01-24 14:19:23,542] [INFO] Running command: blastn -query GCF_008831035.1_ASM883103v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga8cec587-798f-4a05-bfbf-4acfc138d596/dqc_reference/reference_markers.fasta -out GCF_008831035.1_ASM883103v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:24,181] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:24,186] [INFO] Selected 20 target genomes.
[2024-01-24 14:19:24,186] [INFO] Target genome list was writen to GCF_008831035.1_ASM883103v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:24,193] [INFO] Task started: fastANI
[2024-01-24 14:19:24,193] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d8148ec-a81c-4f1e-8fb8-b7c75d5927bc/GCF_008831035.1_ASM883103v1_genomic.fna.gz --refList GCF_008831035.1_ASM883103v1_genomic.fna/target_genomes.txt --output GCF_008831035.1_ASM883103v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:34,019] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:34,020] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga8cec587-798f-4a05-bfbf-4acfc138d596/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:34,020] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga8cec587-798f-4a05-bfbf-4acfc138d596/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:34,035] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:19:34,035] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:19:34,035] [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
Senegalimassilia anaerobia	strain=type strain: JC110	GCA_000236865.1	1473216	1473216	type	True	80.1658	285	782	95	below_threshold
Senegalimassilia faecalis	strain=KGMB04484	GCA_004135645.1	2509433	2509433	type	True	79.6689	277	782	95	below_threshold
Gordonibacter pamelaeae	strain=7-10-1-bT	GCA_000210055.1	471189	471189	type	True	79.2843	301	782	95	below_threshold
Eggerthella lenta	strain=DSM 2243	GCA_003339975.1	84112	84112	type	True	78.8784	254	782	95	below_threshold
Eggerthella guodeyinii	strain=HF-1101	GCA_009834925.2	2690837	2690837	type	True	78.852	273	782	95	below_threshold
Eggerthella lenta	strain=ATCC 25559	GCA_003340105.1	84112	84112	type	True	78.8308	254	782	95	below_threshold
Eggerthella lenta	strain=UCSF2243	GCA_003339945.1	84112	84112	type	True	78.7864	254	782	95	below_threshold
Eggerthella lenta	strain=DSM 2243	GCA_000024265.1	84112	84112	type	True	78.7662	255	782	95	below_threshold
Eggerthella sinensis	strain=DSM 16107	GCA_003725965.1	242230	242230	type	True	78.6094	266	782	95	below_threshold
Eggerthella sinensis	strain=DSM 16107	GCA_003339815.1	242230	242230	type	True	78.6006	268	782	95	below_threshold
Gordonibacter urolithinfaciens	strain=DSM 27213	GCA_003788975.1	1335613	1335613	type	True	78.5851	283	782	95	below_threshold
Eggerthella timonensis	strain=Marseille-P3135	GCA_900184265.1	1871008	1871008	type	True	78.5365	269	782	95	below_threshold
Gordonibacter urolithinfaciens	strain=DSM 27213T	GCA_900199375.1	1335613	1335613	type	True	78.4829	290	782	95	below_threshold
Adlercreutzia hattorii	strain=8CFCBH1	GCA_011405655.1	2707299	2707299	type	True	78.381	207	782	95	below_threshold
Adlercreutzia mucosicola	strain=DSM 19490	GCA_024623255.1	580026	580026	type	True	78.1919	166	782	95	below_threshold
Slackia faecicanis	strain=DSM 17537	GCA_003725295.1	255723	255723	type	True	78.1402	145	782	95	below_threshold
Adlercreutzia caecimuris	strain=B7	GCA_000403355.2	671266	671266	type	True	78.0987	183	782	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_025149625.1	147206	147206	type	True	77.5655	75	782	95	below_threshold
Slackia piriformis	strain=YIT 12062	GCA_000296445.1	626934	626934	type	True	77.3144	104	782	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:34,037] [INFO] DFAST Taxonomy check result was written to GCF_008831035.1_ASM883103v1_genomic.fna/tc_result.tsv
[2024-01-24 14:19:34,038] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:34,038] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:34,038] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga8cec587-798f-4a05-bfbf-4acfc138d596/dqc_reference/checkm_data
[2024-01-24 14:19:34,039] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:34,065] [INFO] Task started: CheckM
[2024-01-24 14:19:34,065] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008831035.1_ASM883103v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008831035.1_ASM883103v1_genomic.fna/checkm_input GCF_008831035.1_ASM883103v1_genomic.fna/checkm_result
[2024-01-24 14:20:01,562] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:01,564] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:01,589] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:01,589] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:01,589] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008831035.1_ASM883103v1_genomic.fna/markers.fasta)
[2024-01-24 14:20:01,590] [INFO] Task started: Blastn
[2024-01-24 14:20:01,590] [INFO] Running command: blastn -query GCF_008831035.1_ASM883103v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga8cec587-798f-4a05-bfbf-4acfc138d596/dqc_reference/reference_markers_gtdb.fasta -out GCF_008831035.1_ASM883103v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:02,731] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:02,735] [INFO] Selected 19 target genomes.
[2024-01-24 14:20:02,735] [INFO] Target genome list was writen to GCF_008831035.1_ASM883103v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:02,757] [INFO] Task started: fastANI
[2024-01-24 14:20:02,758] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d8148ec-a81c-4f1e-8fb8-b7c75d5927bc/GCF_008831035.1_ASM883103v1_genomic.fna.gz --refList GCF_008831035.1_ASM883103v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008831035.1_ASM883103v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:14,032] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:14,057] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:20:14,058] [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_008831035.1	s__Ellagibacter isourolithinifaciens	100.0	779	782	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Ellagibacter	95.0	96.52	96.27	0.85	0.76	13	conclusive
GCA_900554945.1	s__Ellagibacter sp900554945	94.1269	358	782	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Ellagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000236865.1	s__Senegalimassilia anaerobia	80.1658	285	782	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Senegalimassilia	95.0	96.57	95.07	0.88	0.81	7	-
GCA_905215325.1	s__Senegalimassilia sp905215325	79.794	240	782	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Senegalimassilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135645.1	s__Senegalimassilia faecalis	79.6689	277	782	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Senegalimassilia	95.0	96.85	96.73	0.92	0.89	4	-
GCA_900550055.1	s__Senegalimassilia sp900550055	79.5093	221	782	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Senegalimassilia	95.0	97.04	96.58	0.76	0.72	3	-
GCF_000210055.1	s__Gordonibacter pamelaeae	79.2923	301	782	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Gordonibacter	95.0	98.65	97.59	0.89	0.82	6	-
GCA_900754955.1	s__CAAEEV01 sp900754955	79.278	214	782	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__CAAEEV01	95.0	99.85	99.85	0.86	0.86	2	-
GCF_011038975.1	s__CAAEEV01 sp011038975	79.1241	279	782	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__CAAEEV01	95.0	99.99	99.99	0.98	0.98	2	-
GCF_013185065.1	s__CAAEEV01 sp013185065	79.0603	276	782	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__CAAEEV01	95.0	97.04	97.04	0.76	0.76	2	-
GCF_009834925.2	s__Eggerthella sp014287365	78.8441	273	782	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Eggerthella	95.0	97.74	96.91	0.89	0.85	3	-
GCF_902386925.1	s__Arabia massiliensis	78.786	259	782	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Arabia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000024265.1	s__Eggerthella lenta	78.7488	256	782	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Eggerthella	95.0	98.39	97.51	0.89	0.82	72	-
GCA_900170005.1	s__Gordonibacter massiliensis	78.7409	266	782	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Gordonibacter	95.0	98.56	97.12	0.94	0.89	3	-
GCF_003339845.1	s__Gordonibacter sp003339845	78.6288	286	782	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Gordonibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003339815.1	s__Eggerthella sinensis	78.6008	268	782	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Eggerthella	95.0	99.07	98.15	0.94	0.88	3	-
GCF_003725955.1	s__Slackia_A isoflavoniconvertens	78.5145	135	782	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Slackia_A	95.0	96.92	96.02	0.86	0.81	13	-
GCF_900184265.1	s__Eggerthella timonensis	78.5067	271	782	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Eggerthella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003726035.1	s__Paraeggerthella hongkongensis	78.4308	181	782	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Paraeggerthella	95.0	99.02	99.02	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:20:14,065] [INFO] GTDB search result was written to GCF_008831035.1_ASM883103v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:14,065] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:14,073] [INFO] DFAST_QC result json was written to GCF_008831035.1_ASM883103v1_genomic.fna/dqc_result.json
[2024-01-24 14:20:14,074] [INFO] DFAST_QC completed!
[2024-01-24 14:20:14,074] [INFO] Total running time: 0h0m59s