[2024-01-24 14:11:47,984] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:11:47,988] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:11:47,988] [INFO] DQC Reference Directory: /var/lib/cwl/stg2148f608-039f-426a-9f16-be7f34b1f661/dqc_reference
[2024-01-24 14:11:49,335] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:11:49,335] [INFO] Task started: Prodigal
[2024-01-24 14:11:49,336] [INFO] Running command: gunzip -c /var/lib/cwl/stge77fd745-e4ec-477a-8431-8d1319a0ed14/GCF_002162355.1_ASM216235v1_genomic.fna.gz | prodigal -d GCF_002162355.1_ASM216235v1_genomic.fna/cds.fna -a GCF_002162355.1_ASM216235v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:22,600] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:22,600] [INFO] Task started: HMMsearch
[2024-01-24 14:12:22,600] [INFO] Running command: hmmsearch --tblout GCF_002162355.1_ASM216235v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2148f608-039f-426a-9f16-be7f34b1f661/dqc_reference/reference_markers.hmm GCF_002162355.1_ASM216235v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:22,954] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:22,955] [INFO] Found 6/6 markers.
[2024-01-24 14:12:23,003] [INFO] Query marker FASTA was written to GCF_002162355.1_ASM216235v1_genomic.fna/markers.fasta
[2024-01-24 14:12:23,004] [INFO] Task started: Blastn
[2024-01-24 14:12:23,004] [INFO] Running command: blastn -query GCF_002162355.1_ASM216235v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2148f608-039f-426a-9f16-be7f34b1f661/dqc_reference/reference_markers.fasta -out GCF_002162355.1_ASM216235v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:23,898] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:23,902] [INFO] Selected 13 target genomes.
[2024-01-24 14:12:23,902] [INFO] Target genome list was writen to GCF_002162355.1_ASM216235v1_genomic.fna/target_genomes.txt
[2024-01-24 14:12:23,983] [INFO] Task started: fastANI
[2024-01-24 14:12:23,984] [INFO] Running command: fastANI --query /var/lib/cwl/stge77fd745-e4ec-477a-8431-8d1319a0ed14/GCF_002162355.1_ASM216235v1_genomic.fna.gz --refList GCF_002162355.1_ASM216235v1_genomic.fna/target_genomes.txt --output GCF_002162355.1_ASM216235v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:12:41,811] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:41,812] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2148f608-039f-426a-9f16-be7f34b1f661/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:12:41,813] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2148f608-039f-426a-9f16-be7f34b1f661/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:12:41,872] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:12:41,873] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:12:41,873] [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
Tumebacillus avium	strain=AR23208	GCA_002162355.1	1903704	1903704	type	True	100.0	1748	1749	95	conclusive
Tumebacillus algifaecis	strain=THMBR28	GCA_002243515.1	1214604	1214604	type	True	82.7132	953	1749	95	below_threshold
Tumebacillus flagellatus	strain=GST4	GCA_000714935.1	1157490	1157490	type	True	78.5281	442	1749	95	below_threshold
Tumebacillus amylolyticus	strain=ITR2	GCA_016722965.1	2801339	2801339	type	True	78.0769	411	1749	95	below_threshold
Tumebacillus permanentifrigoris	strain=DSM 18773	GCA_003148565.1	378543	378543	type	True	78.0571	371	1749	95	below_threshold
Cohnella fermenti	strain=CC-MHH1044	GCA_004801405.1	2565925	2565925	type	True	76.34	74	1749	95	below_threshold
Cohnella nanjingensis	strain=DSM 28246	GCA_014212125.1	1387779	1387779	type	True	76.3244	70	1749	95	below_threshold
Cohnella xylanilytica	strain=DSM 25239	GCA_014212175.1	557555	557555	type	True	76.1267	82	1749	95	below_threshold
Cohnella thermotolerans	strain=DSM 17683	GCA_000429825.1	329858	329858	type	True	75.8455	55	1749	95	below_threshold
Paenibacillus flagellatus	strain=DXL2	GCA_003217775.1	2211139	2211139	type	True	75.8363	71	1749	95	below_threshold
Paenibacillus glycinis	strain=T1	GCA_009909185.1	2697035	2697035	type	True	75.4809	63	1749	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:12:41,942] [INFO] DFAST Taxonomy check result was written to GCF_002162355.1_ASM216235v1_genomic.fna/tc_result.tsv
[2024-01-24 14:12:41,943] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:12:41,944] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:12:41,944] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2148f608-039f-426a-9f16-be7f34b1f661/dqc_reference/checkm_data
[2024-01-24 14:12:41,954] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:12:42,035] [INFO] Task started: CheckM
[2024-01-24 14:12:42,035] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002162355.1_ASM216235v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002162355.1_ASM216235v1_genomic.fna/checkm_input GCF_002162355.1_ASM216235v1_genomic.fna/checkm_result
[2024-01-24 14:14:23,054] [INFO] Task succeeded: CheckM
[2024-01-24 14:14:23,058] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:14:23,086] [INFO] ===== Completeness check finished =====
[2024-01-24 14:14:23,087] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:14:23,087] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002162355.1_ASM216235v1_genomic.fna/markers.fasta)
[2024-01-24 14:14:23,088] [INFO] Task started: Blastn
[2024-01-24 14:14:23,088] [INFO] Running command: blastn -query GCF_002162355.1_ASM216235v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2148f608-039f-426a-9f16-be7f34b1f661/dqc_reference/reference_markers_gtdb.fasta -out GCF_002162355.1_ASM216235v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:26,614] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:26,619] [INFO] Selected 11 target genomes.
[2024-01-24 14:14:26,619] [INFO] Target genome list was writen to GCF_002162355.1_ASM216235v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:14:26,634] [INFO] Task started: fastANI
[2024-01-24 14:14:26,634] [INFO] Running command: fastANI --query /var/lib/cwl/stge77fd745-e4ec-477a-8431-8d1319a0ed14/GCF_002162355.1_ASM216235v1_genomic.fna.gz --refList GCF_002162355.1_ASM216235v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002162355.1_ASM216235v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:14:40,945] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:40,994] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:14:40,995] [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_002162355.1	s__Tumebacillus_A avium	100.0	1748	1749	d__Bacteria;p__Firmicutes;c__Bacilli;o__Tumebacillales;f__Tumebacillaceae;g__Tumebacillus_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004340785.1	s__Tumebacillus_A sp004340785	88.172	1277	1749	d__Bacteria;p__Firmicutes;c__Bacilli;o__Tumebacillales;f__Tumebacillaceae;g__Tumebacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002243515.1	s__Tumebacillus_A algifaecis	82.6931	952	1749	d__Bacteria;p__Firmicutes;c__Bacilli;o__Tumebacillales;f__Tumebacillaceae;g__Tumebacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000714935.1	s__Tumebacillus flagellatus	78.5142	443	1749	d__Bacteria;p__Firmicutes;c__Bacilli;o__Tumebacillales;f__Tumebacillaceae;g__Tumebacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016722965.1	s__Tumebacillus sp016722965	78.0808	410	1749	d__Bacteria;p__Firmicutes;c__Bacilli;o__Tumebacillales;f__Tumebacillaceae;g__Tumebacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148565.1	s__Tumebacillus permanentifrigoris	78.0608	371	1749	d__Bacteria;p__Firmicutes;c__Bacilli;o__Tumebacillales;f__Tumebacillaceae;g__Tumebacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004801405.1	s__Cohnella sp004801405	76.34	74	1749	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014212175.1	s__Cohnella xylanilytica	76.1185	82	1749	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	98.90	98.90	0.93	0.93	2	-
GCF_000429825.1	s__Cohnella thermotolerans	75.8572	55	1749	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:14:40,998] [INFO] GTDB search result was written to GCF_002162355.1_ASM216235v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:14:40,998] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:14:41,009] [INFO] DFAST_QC result json was written to GCF_002162355.1_ASM216235v1_genomic.fna/dqc_result.json
[2024-01-24 14:14:41,009] [INFO] DFAST_QC completed!
[2024-01-24 14:14:41,010] [INFO] Total running time: 0h2m53s