[2024-01-24 15:02:18,171] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:18,179] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:18,180] [INFO] DQC Reference Directory: /var/lib/cwl/stg25daf740-ce7d-4a35-8c02-cc47cb7e15a5/dqc_reference
[2024-01-24 15:02:20,834] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:20,835] [INFO] Task started: Prodigal
[2024-01-24 15:02:20,836] [INFO] Running command: gunzip -c /var/lib/cwl/stg76420232-cd57-47dd-b450-f37232d13788/GCF_900637705.1_52451_E01_genomic.fna.gz | prodigal -d GCF_900637705.1_52451_E01_genomic.fna/cds.fna -a GCF_900637705.1_52451_E01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:26,848] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:26,848] [INFO] Task started: HMMsearch
[2024-01-24 15:02:26,849] [INFO] Running command: hmmsearch --tblout GCF_900637705.1_52451_E01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg25daf740-ce7d-4a35-8c02-cc47cb7e15a5/dqc_reference/reference_markers.hmm GCF_900637705.1_52451_E01_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:27,110] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:27,111] [INFO] Found 6/6 markers.
[2024-01-24 15:02:27,143] [INFO] Query marker FASTA was written to GCF_900637705.1_52451_E01_genomic.fna/markers.fasta
[2024-01-24 15:02:27,144] [INFO] Task started: Blastn
[2024-01-24 15:02:27,144] [INFO] Running command: blastn -query GCF_900637705.1_52451_E01_genomic.fna/markers.fasta -db /var/lib/cwl/stg25daf740-ce7d-4a35-8c02-cc47cb7e15a5/dqc_reference/reference_markers.fasta -out GCF_900637705.1_52451_E01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:28,011] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:28,014] [INFO] Selected 12 target genomes.
[2024-01-24 15:02:28,015] [INFO] Target genome list was writen to GCF_900637705.1_52451_E01_genomic.fna/target_genomes.txt
[2024-01-24 15:02:28,058] [INFO] Task started: fastANI
[2024-01-24 15:02:28,058] [INFO] Running command: fastANI --query /var/lib/cwl/stg76420232-cd57-47dd-b450-f37232d13788/GCF_900637705.1_52451_E01_genomic.fna.gz --refList GCF_900637705.1_52451_E01_genomic.fna/target_genomes.txt --output GCF_900637705.1_52451_E01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:02:36,202] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:36,203] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg25daf740-ce7d-4a35-8c02-cc47cb7e15a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:02:36,203] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg25daf740-ce7d-4a35-8c02-cc47cb7e15a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:02:36,214] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:02:36,215] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:02:36,215] [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 varium	strain=NCTC10560	GCA_900637705.1	856	856	type	True	100.0	1100	1100	95	conclusive
Fusobacterium ulcerans	strain=ATCC 49185	GCA_003019675.1	861	861	type	True	88.1534	874	1100	95	below_threshold
Fusobacterium ulcerans	strain=ATCC 49185	GCA_000158315.2	861	861	type	True	87.9832	863	1100	95	below_threshold
Fusobacterium necrogenes	strain=NCTC10723	GCA_900450765.1	858	858	type	True	78.9939	273	1100	95	below_threshold
Fusobacterium pseudoperiodonticum	strain=KCOM 1259	GCA_002761955.1	2663009	2663009	type	True	77.5991	169	1100	95	below_threshold
Fusobacterium periodonticum	strain=ATCC 33693	GCA_000160475.1	860	860	suspected-type	True	76.9851	166	1100	95	below_threshold
Fusobacterium perfoetens	strain=ATCC 29250	GCA_000622245.1	852	852	type	True	76.8732	217	1100	95	below_threshold
Cetobacterium ceti	strain=ATCC 700028	GCA_900167275.1	180163	180163	type	True	76.7963	193	1100	95	below_threshold
Cetobacterium somerae	strain=ATCC BAA-474	GCA_000479045.1	188913	188913	type	True	76.6249	195	1100	95	below_threshold
Streptobacillus ratti	strain=OGS16	GCA_001891165.1	1720557	1720557	type	True	75.3952	54	1100	95	below_threshold
Clostridium kluyveri	strain=NBRC 12016	GCA_000010265.1	1534	1534	type	True	75.2521	59	1100	95	below_threshold
Leptotrichia trevisanii	strain=DSM 22070	GCA_000482505.1	109328	109328	type	True	74.7776	75	1100	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:02:36,216] [INFO] DFAST Taxonomy check result was written to GCF_900637705.1_52451_E01_genomic.fna/tc_result.tsv
[2024-01-24 15:02:36,217] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:02:36,217] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:02:36,217] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg25daf740-ce7d-4a35-8c02-cc47cb7e15a5/dqc_reference/checkm_data
[2024-01-24 15:02:36,219] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:02:36,252] [INFO] Task started: CheckM
[2024-01-24 15:02:36,253] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900637705.1_52451_E01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900637705.1_52451_E01_genomic.fna/checkm_input GCF_900637705.1_52451_E01_genomic.fna/checkm_result
[2024-01-24 15:03:01,358] [INFO] Task succeeded: CheckM
[2024-01-24 15:03:01,360] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:03:01,408] [INFO] ===== Completeness check finished =====
[2024-01-24 15:03:01,408] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:03:01,409] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900637705.1_52451_E01_genomic.fna/markers.fasta)
[2024-01-24 15:03:01,409] [INFO] Task started: Blastn
[2024-01-24 15:03:01,409] [INFO] Running command: blastn -query GCF_900637705.1_52451_E01_genomic.fna/markers.fasta -db /var/lib/cwl/stg25daf740-ce7d-4a35-8c02-cc47cb7e15a5/dqc_reference/reference_markers_gtdb.fasta -out GCF_900637705.1_52451_E01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:02,460] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:02,463] [INFO] Selected 6 target genomes.
[2024-01-24 15:03:02,464] [INFO] Target genome list was writen to GCF_900637705.1_52451_E01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:03:02,470] [INFO] Task started: fastANI
[2024-01-24 15:03:02,470] [INFO] Running command: fastANI --query /var/lib/cwl/stg76420232-cd57-47dd-b450-f37232d13788/GCF_900637705.1_52451_E01_genomic.fna.gz --refList GCF_900637705.1_52451_E01_genomic.fna/target_genomes_gtdb.txt --output GCF_900637705.1_52451_E01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:03:08,861] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:08,868] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:03:08,868] [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_900637705.1	s__Fusobacterium_A varium	100.0	1100	1100	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium_A	95.0	99.17	98.59	0.93	0.87	10	conclusive
GCF_002356455.1	s__Fusobacterium_A varium_A	90.0472	929	1100	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium_A	95.0	99.56	99.56	0.92	0.92	2	-
GCF_900683735.1	s__Fusobacterium_A ulcerans_A	88.7609	924	1100	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium_A	95.0	98.86	98.73	0.94	0.93	4	-
GCF_003019675.1	s__Fusobacterium_A ulcerans	88.1721	872	1100	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium_A	95.0	99.20	98.24	0.93	0.85	7	-
GCA_900543175.1	s__Fusobacterium_A sp900543175	80.0144	379	1100	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium_A	95.0	97.42	96.78	0.84	0.75	4	-
GCA_900555845.1	s__Fusobacterium_A sp900555845	79.8612	257	1100	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium_A	95.0	98.55	98.55	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:03:08,870] [INFO] GTDB search result was written to GCF_900637705.1_52451_E01_genomic.fna/result_gtdb.tsv
[2024-01-24 15:03:08,871] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:03:08,876] [INFO] DFAST_QC result json was written to GCF_900637705.1_52451_E01_genomic.fna/dqc_result.json
[2024-01-24 15:03:08,876] [INFO] DFAST_QC completed!
[2024-01-24 15:03:08,877] [INFO] Total running time: 0h0m51s