[2023-06-08 00:16:15,135] [INFO] DFAST_QC pipeline started.
[2023-06-08 00:16:15,138] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 00:16:15,138] [INFO] DQC Reference Directory: /var/lib/cwl/stg834bebbf-8a16-404e-b3d7-fc19e02ce126/dqc_reference
[2023-06-08 00:16:16,618] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 00:16:16,618] [INFO] Task started: Prodigal
[2023-06-08 00:16:16,619] [INFO] Running command: gunzip -c /var/lib/cwl/stg94600796-516d-4828-b937-68aabfe0d3af/GCA_945993095.1_SRR12203226_bin.1_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945993095.1_SRR12203226_bin.1_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945993095.1_SRR12203226_bin.1_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 00:16:18,084] [INFO] Task succeeded: Prodigal
[2023-06-08 00:16:18,084] [INFO] Task started: HMMsearch
[2023-06-08 00:16:18,084] [INFO] Running command: hmmsearch --tblout GCA_945993095.1_SRR12203226_bin.1_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg834bebbf-8a16-404e-b3d7-fc19e02ce126/dqc_reference/reference_markers.hmm GCA_945993095.1_SRR12203226_bin.1_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 00:16:18,379] [INFO] Task succeeded: HMMsearch
[2023-06-08 00:16:18,380] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg94600796-516d-4828-b937-68aabfe0d3af/GCA_945993095.1_SRR12203226_bin.1_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-08 00:16:18,394] [INFO] Query marker FASTA was written to GCA_945993095.1_SRR12203226_bin.1_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 00:16:18,394] [INFO] Task started: Blastn
[2023-06-08 00:16:18,394] [INFO] Running command: blastn -query GCA_945993095.1_SRR12203226_bin.1_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg834bebbf-8a16-404e-b3d7-fc19e02ce126/dqc_reference/reference_markers.fasta -out GCA_945993095.1_SRR12203226_bin.1_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 00:16:21,047] [INFO] Task succeeded: Blastn
[2023-06-08 00:16:21,052] [INFO] Selected 16 target genomes.
[2023-06-08 00:16:21,053] [INFO] Target genome list was writen to GCA_945993095.1_SRR12203226_bin.1_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 00:16:21,056] [INFO] Task started: fastANI
[2023-06-08 00:16:21,056] [INFO] Running command: fastANI --query /var/lib/cwl/stg94600796-516d-4828-b937-68aabfe0d3af/GCA_945993095.1_SRR12203226_bin.1_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945993095.1_SRR12203226_bin.1_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945993095.1_SRR12203226_bin.1_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 00:16:27,956] [INFO] Task succeeded: fastANI
[2023-06-08 00:16:27,956] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg834bebbf-8a16-404e-b3d7-fc19e02ce126/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 00:16:27,957] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg834bebbf-8a16-404e-b3d7-fc19e02ce126/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 00:16:27,966] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 00:16:27,966] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 00:16:27,966] [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
Fusobacterium necrogenes	strain=NCTC10723	GCA_900450765.1	858	858	type	True	89.5676	181	228	95	below_threshold
Fusobacterium ulcerans	strain=ATCC 49185	GCA_000158315.2	861	861	type	True	79.6355	136	228	95	below_threshold
Fusobacterium ulcerans	strain=ATCC 49185	GCA_003019675.1	861	861	type	True	79.6126	135	228	95	below_threshold
Fusobacterium varium	strain=NCTC10560	GCA_900637705.1	856	856	type	True	79.401	139	228	95	below_threshold
Fusobacterium perfoetens	strain=ATCC 29250	GCA_000622245.1	852	852	type	True	78.1103	100	228	95	below_threshold
Cetobacterium ceti	strain=ATCC 700028	GCA_900167275.1	180163	180163	type	True	78.0048	75	228	95	below_threshold
Cetobacterium somerae	strain=ATCC BAA-474	GCA_000479045.1	188913	188913	type	True	77.6036	67	228	95	below_threshold
Fusobacterium canifelinum	strain=FDAARGOS_1126	GCA_016724785.1	285729	285729	type	True	77.5064	66	228	95	below_threshold
Fusobacterium hwasookii	strain=ChDC F128	GCA_000292935.1	1583098	1583098	type	True	77.1918	73	228	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 00:16:27,969] [INFO] DFAST Taxonomy check result was written to GCA_945993095.1_SRR12203226_bin.1_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 00:16:27,970] [INFO] ===== Taxonomy check completed =====
[2023-06-08 00:16:27,970] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 00:16:27,970] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg834bebbf-8a16-404e-b3d7-fc19e02ce126/dqc_reference/checkm_data
[2023-06-08 00:16:27,971] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 00:16:27,990] [INFO] Task started: CheckM
[2023-06-08 00:16:27,990] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945993095.1_SRR12203226_bin.1_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945993095.1_SRR12203226_bin.1_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945993095.1_SRR12203226_bin.1_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 00:16:41,460] [INFO] Task succeeded: CheckM
[2023-06-08 00:16:41,461] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 1.50%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-08 00:16:41,483] [INFO] ===== Completeness check finished =====
[2023-06-08 00:16:41,483] [INFO] ===== Start GTDB Search =====
[2023-06-08 00:16:41,484] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945993095.1_SRR12203226_bin.1_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 00:16:41,484] [INFO] Task started: Blastn
[2023-06-08 00:16:41,485] [INFO] Running command: blastn -query GCA_945993095.1_SRR12203226_bin.1_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg834bebbf-8a16-404e-b3d7-fc19e02ce126/dqc_reference/reference_markers_gtdb.fasta -out GCA_945993095.1_SRR12203226_bin.1_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 00:16:42,393] [INFO] Task succeeded: Blastn
[2023-06-08 00:16:42,397] [INFO] Selected 8 target genomes.
[2023-06-08 00:16:42,398] [INFO] Target genome list was writen to GCA_945993095.1_SRR12203226_bin.1_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 00:16:42,403] [INFO] Task started: fastANI
[2023-06-08 00:16:42,403] [INFO] Running command: fastANI --query /var/lib/cwl/stg94600796-516d-4828-b937-68aabfe0d3af/GCA_945993095.1_SRR12203226_bin.1_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945993095.1_SRR12203226_bin.1_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945993095.1_SRR12203226_bin.1_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 00:16:45,612] [INFO] Task succeeded: fastANI
[2023-06-08 00:16:45,619] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 00:16:45,620] [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_000158195.2	s__Fusobacterium_A mortiferum	99.2141	227	228	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium_A	95.0	99.16	98.67	0.92	0.88	9	conclusive
GCF_900450765.1	s__Fusobacterium_A necrogenes	89.5676	181	228	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905193685.1	s__Fusobacterium_A sp900555485	86.5576	193	228	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium_A	95.0	100.00	100.00	0.99	0.99	2	-
GCF_016900045.1	s__Fusobacterium_A sp900549465	85.7865	190	228	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium_A	95.0	98.59	98.37	0.86	0.84	6	-
GCA_900764925.1	s__Fusobacterium_A sp900764925	85.2748	163	228	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium_A	95.0	99.98	99.98	0.98	0.98	2	-
GCA_019012925.1	s__Fusobacterium_A sp019012925	82.9952	165	228	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014337255.1	s__Fusobacterium_A sp900015295	80.4378	138	228	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium_A	95.0	99.50	99.45	0.93	0.92	5	-
GCF_900637705.1	s__Fusobacterium_A varium	79.401	139	228	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium_A	95.0	99.17	98.59	0.93	0.87	10	-
--------------------------------------------------------------------------------
[2023-06-08 00:16:45,622] [INFO] GTDB search result was written to GCA_945993095.1_SRR12203226_bin.1_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 00:16:45,622] [INFO] ===== GTDB Search completed =====
[2023-06-08 00:16:45,625] [INFO] DFAST_QC result json was written to GCA_945993095.1_SRR12203226_bin.1_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 00:16:45,626] [INFO] DFAST_QC completed!
[2023-06-08 00:16:45,626] [INFO] Total running time: 0h0m30s