[2024-01-24 13:01:26,623] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:26,629] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:26,630] [INFO] DQC Reference Directory: /var/lib/cwl/stg47e89eb0-68e4-493e-a0dd-ac88229012d3/dqc_reference
[2024-01-24 13:01:27,911] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:27,912] [INFO] Task started: Prodigal
[2024-01-24 13:01:27,912] [INFO] Running command: gunzip -c /var/lib/cwl/stgfb257ed2-489d-4396-adb3-cb2d7dbc7c0a/GCF_001457555.1_NCTC10562_genomic.fna.gz | prodigal -d GCF_001457555.1_NCTC10562_genomic.fna/cds.fna -a GCF_001457555.1_NCTC10562_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:31,874] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:31,874] [INFO] Task started: HMMsearch
[2024-01-24 13:01:31,874] [INFO] Running command: hmmsearch --tblout GCF_001457555.1_NCTC10562_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg47e89eb0-68e4-493e-a0dd-ac88229012d3/dqc_reference/reference_markers.hmm GCF_001457555.1_NCTC10562_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:32,155] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:32,156] [INFO] Found 6/6 markers.
[2024-01-24 13:01:32,185] [INFO] Query marker FASTA was written to GCF_001457555.1_NCTC10562_genomic.fna/markers.fasta
[2024-01-24 13:01:32,185] [INFO] Task started: Blastn
[2024-01-24 13:01:32,185] [INFO] Running command: blastn -query GCF_001457555.1_NCTC10562_genomic.fna/markers.fasta -db /var/lib/cwl/stg47e89eb0-68e4-493e-a0dd-ac88229012d3/dqc_reference/reference_markers.fasta -out GCF_001457555.1_NCTC10562_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:32,827] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:32,830] [INFO] Selected 5 target genomes.
[2024-01-24 13:01:32,830] [INFO] Target genome list was writen to GCF_001457555.1_NCTC10562_genomic.fna/target_genomes.txt
[2024-01-24 13:01:32,851] [INFO] Task started: fastANI
[2024-01-24 13:01:32,851] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb257ed2-489d-4396-adb3-cb2d7dbc7c0a/GCF_001457555.1_NCTC10562_genomic.fna.gz --refList GCF_001457555.1_NCTC10562_genomic.fna/target_genomes.txt --output GCF_001457555.1_NCTC10562_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:37,380] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:37,381] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg47e89eb0-68e4-493e-a0dd-ac88229012d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:37,381] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg47e89eb0-68e4-493e-a0dd-ac88229012d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:37,387] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:01:37,387] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:01:37,387] [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 nucleatum subsp. polymorphum	strain=NCTC10562	GCA_001457555.1	76857	851	type	True	100.0	816	817	95	conclusive
Fusobacterium nucleatum subsp. polymorphum	strain=ATCC 10953	GCA_000153625.1	76857	851	type	True	99.9568	809	817	95	conclusive
Fusobacterium hwasookii	strain=KCOM 1249	GCA_014217355.1	1583098	1583098	type	True	92.9989	661	817	95	below_threshold
Fusobacterium hwasookii	strain=ChDC F128	GCA_000292935.1	1583098	1583098	type	True	92.8125	653	817	95	below_threshold
Fusobacterium canifelinum	strain=FDAARGOS_1126	GCA_016724785.1	285729	285729	type	True	92.627	639	817	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:37,389] [INFO] DFAST Taxonomy check result was written to GCF_001457555.1_NCTC10562_genomic.fna/tc_result.tsv
[2024-01-24 13:01:37,390] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:37,390] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:37,391] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg47e89eb0-68e4-493e-a0dd-ac88229012d3/dqc_reference/checkm_data
[2024-01-24 13:01:37,392] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:37,422] [INFO] Task started: CheckM
[2024-01-24 13:01:37,422] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001457555.1_NCTC10562_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001457555.1_NCTC10562_genomic.fna/checkm_input GCF_001457555.1_NCTC10562_genomic.fna/checkm_result
[2024-01-24 13:01:57,348] [INFO] Task succeeded: CheckM
[2024-01-24 13:01:57,350] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:01:57,374] [INFO] ===== Completeness check finished =====
[2024-01-24 13:01:57,375] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:01:57,375] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001457555.1_NCTC10562_genomic.fna/markers.fasta)
[2024-01-24 13:01:57,375] [INFO] Task started: Blastn
[2024-01-24 13:01:57,376] [INFO] Running command: blastn -query GCF_001457555.1_NCTC10562_genomic.fna/markers.fasta -db /var/lib/cwl/stg47e89eb0-68e4-493e-a0dd-ac88229012d3/dqc_reference/reference_markers_gtdb.fasta -out GCF_001457555.1_NCTC10562_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:58,188] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:58,191] [INFO] Selected 8 target genomes.
[2024-01-24 13:01:58,192] [INFO] Target genome list was writen to GCF_001457555.1_NCTC10562_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:01:58,198] [INFO] Task started: fastANI
[2024-01-24 13:01:58,198] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb257ed2-489d-4396-adb3-cb2d7dbc7c0a/GCF_001457555.1_NCTC10562_genomic.fna.gz --refList GCF_001457555.1_NCTC10562_genomic.fna/target_genomes_gtdb.txt --output GCF_001457555.1_NCTC10562_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:04,323] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:04,338] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:02:04,338] [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_001457555.1	s__Fusobacterium polymorphum	100.0	816	817	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium	95.0	96.55	95.37	0.85	0.79	30	conclusive
GCF_002573625.1	s__Fusobacterium nucleatum_D	94.6529	660	817	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014217355.1	s__Fusobacterium hwasookii	92.9989	661	817	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium	95.0	97.78	97.42	0.89	0.85	10	-
GCF_016724785.1	s__Fusobacterium canifelinum	92.5743	641	817	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium	95.0	98.22	98.13	0.90	0.87	3	-
GCA_000007325.1	s__Fusobacterium nucleatum	91.3034	602	817	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium	95.0	98.30	95.23	0.93	0.85	13	-
GCA_000182945.1	s__Fusobacterium vincentii	90.681	454	817	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium	95.0	97.44	96.10	0.85	0.73	18	-
GCF_000158275.2	s__Fusobacterium animalis	90.2822	628	817	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium	95.0	97.57	95.72	0.88	0.80	29	-
GCF_008633215.1	s__Fusobacterium nucleatum_J	89.8642	522	817	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium	95.0	98.47	98.47	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:02:04,342] [INFO] GTDB search result was written to GCF_001457555.1_NCTC10562_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:04,344] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:04,347] [INFO] DFAST_QC result json was written to GCF_001457555.1_NCTC10562_genomic.fna/dqc_result.json
[2024-01-24 13:02:04,347] [INFO] DFAST_QC completed!
[2024-01-24 13:02:04,347] [INFO] Total running time: 0h0m38s