[2024-01-24 13:57:31,205] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:31,207] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:31,207] [INFO] DQC Reference Directory: /var/lib/cwl/stg03bd2f9e-a8b5-4b5c-aac0-f6deb3a61735/dqc_reference
[2024-01-24 13:57:32,575] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:32,576] [INFO] Task started: Prodigal
[2024-01-24 13:57:32,576] [INFO] Running command: gunzip -c /var/lib/cwl/stg3269196d-4119-4d47-b2df-7e4c738e648e/GCF_000479045.1_ASM47904v1_genomic.fna.gz | prodigal -d GCF_000479045.1_ASM47904v1_genomic.fna/cds.fna -a GCF_000479045.1_ASM47904v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:37,021] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:37,022] [INFO] Task started: HMMsearch
[2024-01-24 13:57:37,022] [INFO] Running command: hmmsearch --tblout GCF_000479045.1_ASM47904v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg03bd2f9e-a8b5-4b5c-aac0-f6deb3a61735/dqc_reference/reference_markers.hmm GCF_000479045.1_ASM47904v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:37,265] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:37,266] [INFO] Found 6/6 markers.
[2024-01-24 13:57:37,293] [INFO] Query marker FASTA was written to GCF_000479045.1_ASM47904v1_genomic.fna/markers.fasta
[2024-01-24 13:57:37,294] [INFO] Task started: Blastn
[2024-01-24 13:57:37,294] [INFO] Running command: blastn -query GCF_000479045.1_ASM47904v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg03bd2f9e-a8b5-4b5c-aac0-f6deb3a61735/dqc_reference/reference_markers.fasta -out GCF_000479045.1_ASM47904v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:37,985] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:37,988] [INFO] Selected 14 target genomes.
[2024-01-24 13:57:37,989] [INFO] Target genome list was writen to GCF_000479045.1_ASM47904v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:37,995] [INFO] Task started: fastANI
[2024-01-24 13:57:37,995] [INFO] Running command: fastANI --query /var/lib/cwl/stg3269196d-4119-4d47-b2df-7e4c738e648e/GCF_000479045.1_ASM47904v1_genomic.fna.gz --refList GCF_000479045.1_ASM47904v1_genomic.fna/target_genomes.txt --output GCF_000479045.1_ASM47904v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:44,615] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:44,615] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg03bd2f9e-a8b5-4b5c-aac0-f6deb3a61735/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:44,616] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg03bd2f9e-a8b5-4b5c-aac0-f6deb3a61735/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:44,626] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:57:44,627] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:44,627] [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
Cetobacterium somerae	strain=ATCC BAA-474	GCA_000479045.1	188913	188913	type	True	100.0	926	932	95	conclusive
Cetobacterium ceti	strain=ATCC 700028	GCA_900167275.1	180163	180163	type	True	77.8318	275	932	95	below_threshold
Fusobacterium ulcerans	strain=ATCC 49185	GCA_003019675.1	861	861	type	True	76.6863	168	932	95	below_threshold
Fusobacterium necrogenes	strain=NCTC10723	GCA_900450765.1	858	858	type	True	76.4801	163	932	95	below_threshold
Fusobacterium perfoetens	strain=ATCC 29250	GCA_000622245.1	852	852	type	True	76.4265	177	932	95	below_threshold
Fusobacterium varium	strain=NCTC10560	GCA_900637705.1	856	856	type	True	76.3544	208	932	95	below_threshold
Psychrilyobacter atlanticus	strain=DSM 19335	GCA_000426625.1	271091	271091	type	True	75.7185	95	932	95	below_threshold
Fusobacterium hwasookii	strain=KCOM 1249	GCA_014217355.1	1583098	1583098	type	True	75.6707	123	932	95	below_threshold
Fusobacterium hwasookii	strain=ChDC F128	GCA_000292935.1	1583098	1583098	type	True	75.646	121	932	95	below_threshold
Clostridium saccharoperbutylacetonicum	strain=N1-4(HMT)	GCA_000340885.1	36745	36745	type	True	74.8715	74	932	95	below_threshold
Terrisporobacter glycolicus	strain=DSM 1288	GCA_000439105.1	36841	36841	suspected-type	True	74.8413	83	932	95	below_threshold
Clostridium massiliamazoniense	strain=ND2	GCA_001403635.1	1347366	1347366	type	True	74.6893	61	932	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:44,629] [INFO] DFAST Taxonomy check result was written to GCF_000479045.1_ASM47904v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:44,629] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:44,629] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:44,629] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg03bd2f9e-a8b5-4b5c-aac0-f6deb3a61735/dqc_reference/checkm_data
[2024-01-24 13:57:44,630] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:44,661] [INFO] Task started: CheckM
[2024-01-24 13:57:44,661] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000479045.1_ASM47904v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000479045.1_ASM47904v1_genomic.fna/checkm_input GCF_000479045.1_ASM47904v1_genomic.fna/checkm_result
[2024-01-24 13:58:04,453] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:04,454] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:04,473] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:04,473] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:04,474] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000479045.1_ASM47904v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:04,474] [INFO] Task started: Blastn
[2024-01-24 13:58:04,474] [INFO] Running command: blastn -query GCF_000479045.1_ASM47904v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg03bd2f9e-a8b5-4b5c-aac0-f6deb3a61735/dqc_reference/reference_markers_gtdb.fasta -out GCF_000479045.1_ASM47904v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:05,305] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:05,311] [INFO] Selected 6 target genomes.
[2024-01-24 13:58:05,311] [INFO] Target genome list was writen to GCF_000479045.1_ASM47904v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:05,317] [INFO] Task started: fastANI
[2024-01-24 13:58:05,317] [INFO] Running command: fastANI --query /var/lib/cwl/stg3269196d-4119-4d47-b2df-7e4c738e648e/GCF_000479045.1_ASM47904v1_genomic.fna.gz --refList GCF_000479045.1_ASM47904v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000479045.1_ASM47904v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:09,207] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:09,215] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:09,215] [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_000479045.1	s__Cetobacterium_A somerae	100.0	926	932	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Cetobacterium_A	95.0	99.23	98.47	0.92	0.85	3	conclusive
GCA_905216205.1	s__Cetobacterium_A sp905216205	94.2792	702	932	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Cetobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000799075.1	s__Cetobacterium_A sp000799075	83.3465	572	932	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Cetobacterium_A	95.0	98.72	98.42	0.82	0.77	3	-
GCA_002428805.1	s__Cetobacterium_A sp002428805	82.6218	402	932	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Cetobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014250675.1	s__Cetobacterium_A sp014250675	81.5362	508	932	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Cetobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900766645.1	s__Cetobacterium_A sp900766645	80.4567	337	932	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Cetobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:09,217] [INFO] GTDB search result was written to GCF_000479045.1_ASM47904v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:09,217] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:09,220] [INFO] DFAST_QC result json was written to GCF_000479045.1_ASM47904v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:09,221] [INFO] DFAST_QC completed!
[2024-01-24 13:58:09,221] [INFO] Total running time: 0h0m38s