[2024-01-25 19:38:20,462] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:38:20,464] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:38:20,464] [INFO] DQC Reference Directory: /var/lib/cwl/stg528c2b6c-8036-4e4b-8961-b5b3904a7da4/dqc_reference
[2024-01-25 19:38:21,635] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:38:21,636] [INFO] Task started: Prodigal
[2024-01-25 19:38:21,636] [INFO] Running command: gunzip -c /var/lib/cwl/stgbe53a1fb-1e7f-41f3-be0e-c1c44728bb02/GCF_031191795.1_ASM3119179v1_genomic.fna.gz | prodigal -d GCF_031191795.1_ASM3119179v1_genomic.fna/cds.fna -a GCF_031191795.1_ASM3119179v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:38:24,655] [INFO] Task succeeded: Prodigal
[2024-01-25 19:38:24,655] [INFO] Task started: HMMsearch
[2024-01-25 19:38:24,655] [INFO] Running command: hmmsearch --tblout GCF_031191795.1_ASM3119179v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg528c2b6c-8036-4e4b-8961-b5b3904a7da4/dqc_reference/reference_markers.hmm GCF_031191795.1_ASM3119179v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:38:24,837] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:38:24,840] [INFO] Found 6/6 markers.
[2024-01-25 19:38:24,860] [INFO] Query marker FASTA was written to GCF_031191795.1_ASM3119179v1_genomic.fna/markers.fasta
[2024-01-25 19:38:24,860] [INFO] Task started: Blastn
[2024-01-25 19:38:24,860] [INFO] Running command: blastn -query GCF_031191795.1_ASM3119179v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg528c2b6c-8036-4e4b-8961-b5b3904a7da4/dqc_reference/reference_markers.fasta -out GCF_031191795.1_ASM3119179v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:38:25,403] [INFO] Task succeeded: Blastn
[2024-01-25 19:38:25,405] [INFO] Selected 5 target genomes.
[2024-01-25 19:38:25,406] [INFO] Target genome list was writen to GCF_031191795.1_ASM3119179v1_genomic.fna/target_genomes.txt
[2024-01-25 19:38:25,411] [INFO] Task started: fastANI
[2024-01-25 19:38:25,411] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe53a1fb-1e7f-41f3-be0e-c1c44728bb02/GCF_031191795.1_ASM3119179v1_genomic.fna.gz --refList GCF_031191795.1_ASM3119179v1_genomic.fna/target_genomes.txt --output GCF_031191795.1_ASM3119179v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:38:28,570] [INFO] Task succeeded: fastANI
[2024-01-25 19:38:28,571] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg528c2b6c-8036-4e4b-8961-b5b3904a7da4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:38:28,571] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg528c2b6c-8036-4e4b-8961-b5b3904a7da4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:38:28,576] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:38:28,576] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:38:28,577] [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 canifelinum	strain=FDAARGOS_1126	GCA_016724785.1	285729	285729	type	True	92.3191	615	727	95	below_threshold
Fusobacterium nucleatum subsp. polymorphum	strain=NCTC10562	GCA_001457555.1	76857	851	type	True	91.645	598	727	95	below_threshold
Fusobacterium nucleatum subsp. polymorphum	strain=ATCC 10953	GCA_000153625.1	76857	851	type	True	91.4962	594	727	95	below_threshold
Fusobacterium hwasookii	strain=KCOM 1249	GCA_014217355.1	1583098	1583098	type	True	90.8063	582	727	95	below_threshold
Fusobacterium hwasookii	strain=ChDC F128	GCA_000292935.1	1583098	1583098	type	True	90.7014	571	727	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:38:28,578] [INFO] DFAST Taxonomy check result was written to GCF_031191795.1_ASM3119179v1_genomic.fna/tc_result.tsv
[2024-01-25 19:38:28,578] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:38:28,578] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:38:28,578] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg528c2b6c-8036-4e4b-8961-b5b3904a7da4/dqc_reference/checkm_data
[2024-01-25 19:38:28,579] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:38:28,604] [INFO] Task started: CheckM
[2024-01-25 19:38:28,604] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_031191795.1_ASM3119179v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_031191795.1_ASM3119179v1_genomic.fna/checkm_input GCF_031191795.1_ASM3119179v1_genomic.fna/checkm_result
[2024-01-25 19:38:43,933] [INFO] Task succeeded: CheckM
[2024-01-25 19:38:43,934] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:38:43,954] [INFO] ===== Completeness check finished =====
[2024-01-25 19:38:43,954] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:38:43,954] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_031191795.1_ASM3119179v1_genomic.fna/markers.fasta)
[2024-01-25 19:38:43,955] [INFO] Task started: Blastn
[2024-01-25 19:38:43,955] [INFO] Running command: blastn -query GCF_031191795.1_ASM3119179v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg528c2b6c-8036-4e4b-8961-b5b3904a7da4/dqc_reference/reference_markers_gtdb.fasta -out GCF_031191795.1_ASM3119179v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:38:44,720] [INFO] Task succeeded: Blastn
[2024-01-25 19:38:44,723] [INFO] Selected 8 target genomes.
[2024-01-25 19:38:44,723] [INFO] Target genome list was writen to GCF_031191795.1_ASM3119179v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:38:44,732] [INFO] Task started: fastANI
[2024-01-25 19:38:44,732] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe53a1fb-1e7f-41f3-be0e-c1c44728bb02/GCF_031191795.1_ASM3119179v1_genomic.fna.gz --refList GCF_031191795.1_ASM3119179v1_genomic.fna/target_genomes_gtdb.txt --output GCF_031191795.1_ASM3119179v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:38:49,957] [INFO] Task succeeded: fastANI
[2024-01-25 19:38:49,963] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:38:49,963] [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_000007325.1	s__Fusobacterium nucleatum	99.9952	723	727	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium	95.0	98.30	95.23	0.93	0.85	13	conclusive
GCF_016724785.1	s__Fusobacterium canifelinum	92.3191	615	727	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium	95.0	98.22	98.13	0.90	0.87	3	-
GCA_000182945.1	s__Fusobacterium vincentii	92.0306	462	727	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium	95.0	97.44	96.10	0.85	0.73	18	-
GCF_001457555.1	s__Fusobacterium polymorphum	91.645	598	727	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium	95.0	96.55	95.37	0.85	0.79	30	-
GCF_008633215.1	s__Fusobacterium nucleatum_J	91.4837	554	727	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium	95.0	98.47	98.47	0.86	0.86	2	-
GCF_000158275.2	s__Fusobacterium animalis	91.1857	596	727	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium	95.0	97.57	95.72	0.88	0.80	29	-
GCF_014217355.1	s__Fusobacterium hwasookii	90.822	580	727	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium	95.0	97.78	97.42	0.89	0.85	10	-
GCF_002573625.1	s__Fusobacterium nucleatum_D	90.7467	560	727	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:38:49,965] [INFO] GTDB search result was written to GCF_031191795.1_ASM3119179v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:38:49,965] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:38:49,972] [INFO] DFAST_QC result json was written to GCF_031191795.1_ASM3119179v1_genomic.fna/dqc_result.json
[2024-01-25 19:38:49,972] [INFO] DFAST_QC completed!
[2024-01-25 19:38:49,972] [INFO] Total running time: 0h0m30s