[2023-06-28 23:39:16,573] [INFO] DFAST_QC pipeline started.
[2023-06-28 23:39:16,575] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 23:39:16,576] [INFO] DQC Reference Directory: /var/lib/cwl/stg73a094a7-9081-4cb8-a9e6-f28f8d0de4ce/dqc_reference
[2023-06-28 23:39:18,353] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 23:39:18,353] [INFO] Task started: Prodigal
[2023-06-28 23:39:18,354] [INFO] Running command: gunzip -c /var/lib/cwl/stge696d679-4176-42b7-baa4-562f2efc7334/GCA_017459485.1_ASM1745948v1_genomic.fna.gz | prodigal -d GCA_017459485.1_ASM1745948v1_genomic.fna/cds.fna -a GCA_017459485.1_ASM1745948v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 23:39:24,660] [INFO] Task succeeded: Prodigal
[2023-06-28 23:39:24,661] [INFO] Task started: HMMsearch
[2023-06-28 23:39:24,661] [INFO] Running command: hmmsearch --tblout GCA_017459485.1_ASM1745948v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg73a094a7-9081-4cb8-a9e6-f28f8d0de4ce/dqc_reference/reference_markers.hmm GCA_017459485.1_ASM1745948v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 23:39:24,819] [INFO] Task succeeded: HMMsearch
[2023-06-28 23:39:24,820] [WARNING] Found 3/6 markers. [/var/lib/cwl/stge696d679-4176-42b7-baa4-562f2efc7334/GCA_017459485.1_ASM1745948v1_genomic.fna.gz]
[2023-06-28 23:39:24,843] [INFO] Query marker FASTA was written to GCA_017459485.1_ASM1745948v1_genomic.fna/markers.fasta
[2023-06-28 23:39:24,844] [INFO] Task started: Blastn
[2023-06-28 23:39:24,844] [INFO] Running command: blastn -query GCA_017459485.1_ASM1745948v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg73a094a7-9081-4cb8-a9e6-f28f8d0de4ce/dqc_reference/reference_markers.fasta -out GCA_017459485.1_ASM1745948v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:39:25,330] [INFO] Task succeeded: Blastn
[2023-06-28 23:39:25,334] [INFO] Selected 13 target genomes.
[2023-06-28 23:39:25,334] [INFO] Target genome list was writen to GCA_017459485.1_ASM1745948v1_genomic.fna/target_genomes.txt
[2023-06-28 23:39:25,338] [INFO] Task started: fastANI
[2023-06-28 23:39:25,338] [INFO] Running command: fastANI --query /var/lib/cwl/stge696d679-4176-42b7-baa4-562f2efc7334/GCA_017459485.1_ASM1745948v1_genomic.fna.gz --refList GCA_017459485.1_ASM1745948v1_genomic.fna/target_genomes.txt --output GCA_017459485.1_ASM1745948v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 23:39:30,600] [INFO] Task succeeded: fastANI
[2023-06-28 23:39:30,600] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg73a094a7-9081-4cb8-a9e6-f28f8d0de4ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 23:39:30,601] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg73a094a7-9081-4cb8-a9e6-f28f8d0de4ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 23:39:30,610] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 23:39:30,610] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 23:39:30,610] [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
Gordonibacter pamelaeae	strain=7-10-1-bT	GCA_000210055.1	471189	471189	type	True	77.2363	58	536	95	below_threshold
Xiamenia xianingshaonis	strain=zg-886	GCA_011392455.1	2682776	2682776	type	True	77.1103	51	536	95	below_threshold
Senegalimassilia faecalis	strain=KGMB04484	GCA_004135645.1	2509433	2509433	type	True	76.8264	55	536	95	below_threshold
Eggerthella guodeyinii	strain=HF-1101	GCA_009834925.2	2690837	2690837	type	True	76.5783	61	536	95	below_threshold
Eggerthella sinensis	strain=DSM 16107	GCA_003725965.1	242230	242230	type	True	76.5644	67	536	95	below_threshold
Eggerthella sinensis	strain=DSM 16107	GCA_003339815.1	242230	242230	type	True	76.4857	70	536	95	below_threshold
Eggerthella lenta	strain=DSM 2243	GCA_003339975.1	84112	84112	type	True	76.4417	63	536	95	below_threshold
Eggerthella lenta	strain=ATCC 25559	GCA_003340105.1	84112	84112	type	True	76.4163	64	536	95	below_threshold
Eggerthella lenta	strain=UCSF2243	GCA_003339945.1	84112	84112	type	True	76.4163	64	536	95	below_threshold
Eggerthella lenta	strain=DSM 2243	GCA_000024265.1	84112	84112	type	True	76.4116	64	536	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 23:39:30,612] [INFO] DFAST Taxonomy check result was written to GCA_017459485.1_ASM1745948v1_genomic.fna/tc_result.tsv
[2023-06-28 23:39:30,613] [INFO] ===== Taxonomy check completed =====
[2023-06-28 23:39:30,613] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 23:39:30,613] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg73a094a7-9081-4cb8-a9e6-f28f8d0de4ce/dqc_reference/checkm_data
[2023-06-28 23:39:30,614] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 23:39:30,640] [INFO] Task started: CheckM
[2023-06-28 23:39:30,640] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017459485.1_ASM1745948v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017459485.1_ASM1745948v1_genomic.fna/checkm_input GCA_017459485.1_ASM1745948v1_genomic.fna/checkm_result
[2023-06-28 23:39:54,447] [INFO] Task succeeded: CheckM
[2023-06-28 23:39:54,448] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.05%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 23:39:54,467] [INFO] ===== Completeness check finished =====
[2023-06-28 23:39:54,467] [INFO] ===== Start GTDB Search =====
[2023-06-28 23:39:54,468] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017459485.1_ASM1745948v1_genomic.fna/markers.fasta)
[2023-06-28 23:39:54,468] [INFO] Task started: Blastn
[2023-06-28 23:39:54,468] [INFO] Running command: blastn -query GCA_017459485.1_ASM1745948v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg73a094a7-9081-4cb8-a9e6-f28f8d0de4ce/dqc_reference/reference_markers_gtdb.fasta -out GCA_017459485.1_ASM1745948v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:39:54,936] [INFO] Task succeeded: Blastn
[2023-06-28 23:39:54,940] [INFO] Selected 12 target genomes.
[2023-06-28 23:39:54,940] [INFO] Target genome list was writen to GCA_017459485.1_ASM1745948v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 23:39:54,950] [INFO] Task started: fastANI
[2023-06-28 23:39:54,950] [INFO] Running command: fastANI --query /var/lib/cwl/stge696d679-4176-42b7-baa4-562f2efc7334/GCA_017459485.1_ASM1745948v1_genomic.fna.gz --refList GCA_017459485.1_ASM1745948v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017459485.1_ASM1745948v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 23:39:58,940] [INFO] Task succeeded: fastANI
[2023-06-28 23:39:58,948] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 23:39:58,948] [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_017459485.1	s__CACXMZ01 sp017459485	100.0	525	536	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__CACXMZ01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017459805.1	s__CACXMZ01 sp017459805	83.3443	89	536	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__CACXMZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902768975.1	s__CACXMZ01 sp902768975	77.7612	90	536	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__CACXMZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905234635.1	s__CACXMZ01 sp905234635	77.547	67	536	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__CACXMZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905234785.1	s__UBA9715 sp905234785	77.4442	64	536	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__UBA9715	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018710945.1	s__Aphodovivens avistercoris	77.1016	58	536	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Aphodovivens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001486445.1	s__RUG013 sp001486445	76.6108	50	536	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__RUG013	95.0	98.36	97.63	0.92	0.89	7	-
GCF_000024265.1	s__Eggerthella lenta	76.3812	65	536	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Eggerthella	95.0	98.39	97.51	0.89	0.82	72	-
--------------------------------------------------------------------------------
[2023-06-28 23:39:58,950] [INFO] GTDB search result was written to GCA_017459485.1_ASM1745948v1_genomic.fna/result_gtdb.tsv
[2023-06-28 23:39:58,951] [INFO] ===== GTDB Search completed =====
[2023-06-28 23:39:58,954] [INFO] DFAST_QC result json was written to GCA_017459485.1_ASM1745948v1_genomic.fna/dqc_result.json
[2023-06-28 23:39:58,954] [INFO] DFAST_QC completed!
[2023-06-28 23:39:58,954] [INFO] Total running time: 0h0m42s