[2024-01-24 12:53:50,910] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:50,913] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:50,913] [INFO] DQC Reference Directory: /var/lib/cwl/stgedd116ae-2071-4af5-878c-bfd2f2e730d9/dqc_reference
[2024-01-24 12:53:52,107] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:52,110] [INFO] Task started: Prodigal
[2024-01-24 12:53:52,111] [INFO] Running command: gunzip -c /var/lib/cwl/stgb0889941-ca73-4c5f-8a3b-3ca30cf3b481/GCF_900095705.1_PRJEB15286_genomic.fna.gz | prodigal -d GCF_900095705.1_PRJEB15286_genomic.fna/cds.fna -a GCF_900095705.1_PRJEB15286_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:53:54,787] [INFO] Task succeeded: Prodigal
[2024-01-24 12:53:54,788] [INFO] Task started: HMMsearch
[2024-01-24 12:53:54,788] [INFO] Running command: hmmsearch --tblout GCF_900095705.1_PRJEB15286_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgedd116ae-2071-4af5-878c-bfd2f2e730d9/dqc_reference/reference_markers.hmm GCF_900095705.1_PRJEB15286_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:53:54,967] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:53:54,970] [INFO] Found 6/6 markers.
[2024-01-24 12:53:54,998] [INFO] Query marker FASTA was written to GCF_900095705.1_PRJEB15286_genomic.fna/markers.fasta
[2024-01-24 12:53:54,999] [INFO] Task started: Blastn
[2024-01-24 12:53:54,999] [INFO] Running command: blastn -query GCF_900095705.1_PRJEB15286_genomic.fna/markers.fasta -db /var/lib/cwl/stgedd116ae-2071-4af5-878c-bfd2f2e730d9/dqc_reference/reference_markers.fasta -out GCF_900095705.1_PRJEB15286_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:53:55,558] [INFO] Task succeeded: Blastn
[2024-01-24 12:53:55,563] [INFO] Selected 9 target genomes.
[2024-01-24 12:53:55,563] [INFO] Target genome list was writen to GCF_900095705.1_PRJEB15286_genomic.fna/target_genomes.txt
[2024-01-24 12:53:55,651] [INFO] Task started: fastANI
[2024-01-24 12:53:55,651] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0889941-ca73-4c5f-8a3b-3ca30cf3b481/GCF_900095705.1_PRJEB15286_genomic.fna.gz --refList GCF_900095705.1_PRJEB15286_genomic.fna/target_genomes.txt --output GCF_900095705.1_PRJEB15286_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:02,768] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:02,768] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgedd116ae-2071-4af5-878c-bfd2f2e730d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:02,769] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgedd116ae-2071-4af5-878c-bfd2f2e730d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:02,784] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:54:02,784] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:02,784] [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 massiliense	strain=Marseille-P2749	GCA_900095705.1	1852365	1852365	type	True	100.0	600	600	95	conclusive
Fusobacterium nucleatum subsp. polymorphum	strain=NCTC10562	GCA_001457555.1	76857	851	type	True	82.2193	390	600	95	below_threshold
Fusobacterium nucleatum subsp. polymorphum	strain=ATCC 10953	GCA_000153625.1	76857	851	type	True	82.0853	389	600	95	below_threshold
Fusobacterium hwasookii	strain=ChDC F128	GCA_000292935.1	1583098	1583098	type	True	81.9919	388	600	95	below_threshold
Fusobacterium hwasookii	strain=KCOM 1249	GCA_014217355.1	1583098	1583098	type	True	81.9299	398	600	95	below_threshold
Fusobacterium periodonticum	strain=ATCC 33693	GCA_000160475.1	860	860	suspected-type	True	81.7786	369	600	95	below_threshold
Fusobacterium pseudoperiodonticum	strain=KCOM 1259	GCA_002761955.1	2663009	2663009	type	True	81.6673	363	600	95	below_threshold
Fusobacterium canifelinum	strain=FDAARGOS_1126	GCA_016724785.1	285729	285729	type	True	81.5535	381	600	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:02,790] [INFO] DFAST Taxonomy check result was written to GCF_900095705.1_PRJEB15286_genomic.fna/tc_result.tsv
[2024-01-24 12:54:02,791] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:02,791] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:02,791] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgedd116ae-2071-4af5-878c-bfd2f2e730d9/dqc_reference/checkm_data
[2024-01-24 12:54:02,793] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:02,817] [INFO] Task started: CheckM
[2024-01-24 12:54:02,817] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900095705.1_PRJEB15286_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900095705.1_PRJEB15286_genomic.fna/checkm_input GCF_900095705.1_PRJEB15286_genomic.fna/checkm_result
[2024-01-24 12:54:19,163] [INFO] Task succeeded: CheckM
[2024-01-24 12:54:19,164] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:54:19,186] [INFO] ===== Completeness check finished =====
[2024-01-24 12:54:19,186] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:54:19,186] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900095705.1_PRJEB15286_genomic.fna/markers.fasta)
[2024-01-24 12:54:19,187] [INFO] Task started: Blastn
[2024-01-24 12:54:19,187] [INFO] Running command: blastn -query GCF_900095705.1_PRJEB15286_genomic.fna/markers.fasta -db /var/lib/cwl/stgedd116ae-2071-4af5-878c-bfd2f2e730d9/dqc_reference/reference_markers_gtdb.fasta -out GCF_900095705.1_PRJEB15286_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:19,937] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:19,941] [INFO] Selected 11 target genomes.
[2024-01-24 12:54:19,941] [INFO] Target genome list was writen to GCF_900095705.1_PRJEB15286_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:54:19,953] [INFO] Task started: fastANI
[2024-01-24 12:54:19,953] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0889941-ca73-4c5f-8a3b-3ca30cf3b481/GCF_900095705.1_PRJEB15286_genomic.fna.gz --refList GCF_900095705.1_PRJEB15286_genomic.fna/target_genomes_gtdb.txt --output GCF_900095705.1_PRJEB15286_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:54:27,795] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:27,807] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:54:27,808] [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_900095705.1	s__Fusobacterium massiliense	100.0	600	600	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_001457555.1	s__Fusobacterium polymorphum	82.1931	390	600	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium	95.0	96.55	95.37	0.85	0.79	30	-
GCA_000182945.1	s__Fusobacterium vincentii	82.127	324	600	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium	95.0	97.44	96.10	0.85	0.73	18	-
GCF_014217355.1	s__Fusobacterium hwasookii	81.931	397	600	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium	95.0	97.78	97.42	0.89	0.85	10	-
GCA_000007325.1	s__Fusobacterium nucleatum	81.8355	371	600	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium	95.0	98.30	95.23	0.93	0.85	13	-
GCF_000160475.1	s__Fusobacterium periodonticum	81.8313	366	600	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002763915.1	s__Fusobacterium periodonticum_D	81.8093	381	600	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium	95.1543	96.98	95.97	0.86	0.80	11	-
GCF_002761955.1	s__Fusobacterium pseudoperiodonticum	81.6673	363	600	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium	95.1543	96.63	95.97	0.86	0.84	10	-
GCF_016724785.1	s__Fusobacterium canifelinum	81.5827	381	600	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium	95.0	98.22	98.13	0.90	0.87	3	-
GCF_008633215.1	s__Fusobacterium nucleatum_J	81.5562	344	600	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium	95.0	98.47	98.47	0.86	0.86	2	-
GCF_000235465.1	s__Fusobacterium sp000235465	81.2994	320	600	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:54:27,812] [INFO] GTDB search result was written to GCF_900095705.1_PRJEB15286_genomic.fna/result_gtdb.tsv
[2024-01-24 12:54:27,814] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:54:27,821] [INFO] DFAST_QC result json was written to GCF_900095705.1_PRJEB15286_genomic.fna/dqc_result.json
[2024-01-24 12:54:27,821] [INFO] DFAST_QC completed!
[2024-01-24 12:54:27,821] [INFO] Total running time: 0h0m37s