[2024-01-25 20:17:05,512] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:17:05,514] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:17:05,514] [INFO] DQC Reference Directory: /var/lib/cwl/stgabd3de55-5844-4c56-b945-e275f5bc2934/dqc_reference
[2024-01-25 20:17:06,661] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:17:06,662] [INFO] Task started: Prodigal
[2024-01-25 20:17:06,662] [INFO] Running command: gunzip -c /var/lib/cwl/stga139a991-e9d5-49f8-847b-488a7f8c3b37/GCF_030295325.1_ASM3029532v1_genomic.fna.gz | prodigal -d GCF_030295325.1_ASM3029532v1_genomic.fna/cds.fna -a GCF_030295325.1_ASM3029532v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:17:10,459] [INFO] Task succeeded: Prodigal
[2024-01-25 20:17:10,459] [INFO] Task started: HMMsearch
[2024-01-25 20:17:10,459] [INFO] Running command: hmmsearch --tblout GCF_030295325.1_ASM3029532v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgabd3de55-5844-4c56-b945-e275f5bc2934/dqc_reference/reference_markers.hmm GCF_030295325.1_ASM3029532v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:17:10,665] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:17:10,666] [INFO] Found 6/6 markers.
[2024-01-25 20:17:10,690] [INFO] Query marker FASTA was written to GCF_030295325.1_ASM3029532v1_genomic.fna/markers.fasta
[2024-01-25 20:17:10,690] [INFO] Task started: Blastn
[2024-01-25 20:17:10,690] [INFO] Running command: blastn -query GCF_030295325.1_ASM3029532v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgabd3de55-5844-4c56-b945-e275f5bc2934/dqc_reference/reference_markers.fasta -out GCF_030295325.1_ASM3029532v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:17:11,216] [INFO] Task succeeded: Blastn
[2024-01-25 20:17:11,220] [INFO] Selected 21 target genomes.
[2024-01-25 20:17:11,220] [INFO] Target genome list was writen to GCF_030295325.1_ASM3029532v1_genomic.fna/target_genomes.txt
[2024-01-25 20:17:11,249] [INFO] Task started: fastANI
[2024-01-25 20:17:11,249] [INFO] Running command: fastANI --query /var/lib/cwl/stga139a991-e9d5-49f8-847b-488a7f8c3b37/GCF_030295325.1_ASM3029532v1_genomic.fna.gz --refList GCF_030295325.1_ASM3029532v1_genomic.fna/target_genomes.txt --output GCF_030295325.1_ASM3029532v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:17:19,759] [INFO] Task succeeded: fastANI
[2024-01-25 20:17:19,760] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgabd3de55-5844-4c56-b945-e275f5bc2934/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:17:19,760] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgabd3de55-5844-4c56-b945-e275f5bc2934/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:17:19,772] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:17:19,772] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:17:19,772] [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
Oceanivirga miroungae	strain=ES3154-GLU	GCA_902505095.1	1130046	1130046	type	True	75.779	65	908	95	below_threshold
Fusobacterium hwasookii	strain=KCOM 1249	GCA_014217355.1	1583098	1583098	type	True	75.7482	123	908	95	below_threshold
Fusobacterium canifelinum	strain=FDAARGOS_1126	GCA_016724785.1	285729	285729	type	True	75.6977	104	908	95	below_threshold
Leptotrichia wadei	strain=JCM16777	GCA_007990545.2	157687	157687	type	True	75.6888	103	908	95	below_threshold
Fusobacterium ulcerans	strain=ATCC 49185	GCA_003019675.1	861	861	type	True	75.6873	100	908	95	below_threshold
Fusobacterium massiliense	strain=Marseille-P2749	GCA_900095705.1	1852365	1852365	type	True	75.5532	104	908	95	below_threshold
Crassaminicella thermophila	strain=SY095	GCA_008152325.1	2599308	2599308	type	True	75.4917	75	908	95	below_threshold
Caviibacter abscessus	strain=CCUG 39713	GCA_001517835.1	1766719	1766719	type	True	75.3496	68	908	95	below_threshold
Sneathia sanguinegens	strain=CCUG41628	GCA_001517935.1	40543	40543	type	True	75.3108	56	908	95	below_threshold
Fusobacterium hwasookii	strain=ChDC F128	GCA_000292935.1	1583098	1583098	type	True	75.2712	115	908	95	below_threshold
Fusobacterium perfoetens	strain=ATCC 29250	GCA_000622245.1	852	852	type	True	75.2339	144	908	95	below_threshold
Cetobacterium somerae	strain=ATCC BAA-474	GCA_000479045.1	188913	188913	type	True	75.0451	105	908	95	below_threshold
Leptotrichia wadei	strain=DSM 19758	GCA_000373345.1	157687	157687	type	True	75.0042	95	908	95	below_threshold
Hydrogenothermus marinus	strain=VM1	GCA_003688665.1	133270	133270	type	True	74.8478	69	908	95	below_threshold
Terrisporobacter mayombei	strain=DSM 6539	GCA_020748465.1	1541	1541	type	True	74.7969	95	908	95	below_threshold
Clostridium puniceum	strain=DSM 2619	GCA_002006345.1	29367	29367	type	True	74.7878	115	908	95	below_threshold
Clostridium prolinivorans	strain=PYR-10	GCA_004011155.1	2769420	2769420	type	True	74.7874	93	908	95	below_threshold
Tepidibacter formicigenes	strain=DSM 15518	GCA_900142235.1	227138	227138	type	True	74.7605	93	908	95	below_threshold
Terrisporobacter glycolicus	strain=DSM 1288	GCA_000439105.1	36841	36841	suspected-type	True	74.739	99	908	95	below_threshold
Marinitoga hydrogenitolerans	strain=DSM 16785	GCA_900129175.1	287990	287990	type	True	74.6925	84	908	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:17:19,773] [INFO] DFAST Taxonomy check result was written to GCF_030295325.1_ASM3029532v1_genomic.fna/tc_result.tsv
[2024-01-25 20:17:19,774] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:17:19,774] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:17:19,774] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgabd3de55-5844-4c56-b945-e275f5bc2934/dqc_reference/checkm_data
[2024-01-25 20:17:19,775] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:17:19,820] [INFO] Task started: CheckM
[2024-01-25 20:17:19,820] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030295325.1_ASM3029532v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030295325.1_ASM3029532v1_genomic.fna/checkm_input GCF_030295325.1_ASM3029532v1_genomic.fna/checkm_result
[2024-01-25 20:17:37,011] [INFO] Task succeeded: CheckM
[2024-01-25 20:17:37,012] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:17:37,033] [INFO] ===== Completeness check finished =====
[2024-01-25 20:17:37,033] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:17:37,033] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030295325.1_ASM3029532v1_genomic.fna/markers.fasta)
[2024-01-25 20:17:37,034] [INFO] Task started: Blastn
[2024-01-25 20:17:37,034] [INFO] Running command: blastn -query GCF_030295325.1_ASM3029532v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgabd3de55-5844-4c56-b945-e275f5bc2934/dqc_reference/reference_markers_gtdb.fasta -out GCF_030295325.1_ASM3029532v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:17:37,732] [INFO] Task succeeded: Blastn
[2024-01-25 20:17:37,735] [INFO] Selected 22 target genomes.
[2024-01-25 20:17:37,735] [INFO] Target genome list was writen to GCF_030295325.1_ASM3029532v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:17:37,775] [INFO] Task started: fastANI
[2024-01-25 20:17:37,775] [INFO] Running command: fastANI --query /var/lib/cwl/stga139a991-e9d5-49f8-847b-488a7f8c3b37/GCF_030295325.1_ASM3029532v1_genomic.fna.gz --refList GCF_030295325.1_ASM3029532v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030295325.1_ASM3029532v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:17:45,908] [INFO] Task succeeded: fastANI
[2024-01-25 20:17:45,919] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:17:45,920] [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_004365575.1	s__Hypnocyclicus thermotrophus	75.9621	215	908	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Hypnocyclicus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014337255.1	s__Fusobacterium_A sp900015295	75.9577	104	908	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium_A	95.0	99.50	99.45	0.93	0.92	5	-
GCF_001559795.1	s__Streptobacillus hongkongensis	75.5886	69	908	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Streptobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016938425.1	s__JAFGUR01 sp016938425	75.559	83	908	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__JAFGUR01	95.0	99.62	99.62	0.87	0.87	2	-
GCA_012519615.1	s__JAAYPW01 sp012519615	75.5482	131	908	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__JAAYPW01;g__JAAYPW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000007325.1	s__Fusobacterium nucleatum	75.5344	119	908	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium	95.0	98.30	95.23	0.93	0.85	13	-
GCF_900095705.1	s__Fusobacterium massiliense	75.5302	107	908	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000158275.2	s__Fusobacterium animalis	75.5091	125	908	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium	95.0	97.57	95.72	0.88	0.80	29	-
GCA_905193685.1	s__Fusobacterium_A sp900555485	75.4165	105	908	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium_A	95.0	100.00	100.00	0.99	0.99	2	-
GCA_018058425.1	s__Sebaldella sp018058425	75.343	106	908	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Sebaldella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010367435.1	s__Fusobacterium_B sp010367435	75.3103	88	908	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002342785.1	s__Psychrilyobacter sp002342785	75.2268	114	908	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Psychrilyobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905216205.1	s__Cetobacterium_A sp905216205	75.2189	100	908	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_900545035.1	s__Fusobacterium_B sp900545035	75.1286	52	908	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000479045.1	s__Cetobacterium_A somerae	75.0247	109	908	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Cetobacterium_A	95.0	99.23	98.47	0.92	0.85	3	-
GCF_003391055.1	s__Psychrilyobacter sp003391055	74.9059	55	908	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Psychrilyobacter	95.0	100.00	100.00	0.99	0.99	3	-
GCF_003688665.1	s__Hydrogenothermus marinus	74.8478	69	908	d__Bacteria;p__Aquificota;c__Aquificae;o__Hydrogenothermales;f__Hydrogenothermaceae;g__Hydrogenothermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002006345.1	s__Clostridium puniceum	74.7834	117	908	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:17:45,921] [INFO] GTDB search result was written to GCF_030295325.1_ASM3029532v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:17:45,924] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:17:45,928] [INFO] DFAST_QC result json was written to GCF_030295325.1_ASM3029532v1_genomic.fna/dqc_result.json
[2024-01-25 20:17:45,928] [INFO] DFAST_QC completed!
[2024-01-25 20:17:45,928] [INFO] Total running time: 0h0m40s