[2023-06-18 17:26:55,311] [INFO] DFAST_QC pipeline started.
[2023-06-18 17:26:55,313] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 17:26:55,313] [INFO] DQC Reference Directory: /var/lib/cwl/stg0e6bfa9f-4656-4625-980f-b23737e8dfaf/dqc_reference
[2023-06-18 17:26:56,562] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 17:26:56,563] [INFO] Task started: Prodigal
[2023-06-18 17:26:56,563] [INFO] Running command: gunzip -c /var/lib/cwl/stg915a4537-f293-4627-8840-44f93bc4608b/GCA_018433765.1_SM3_genomic.fna.gz | prodigal -d GCA_018433765.1_SM3_genomic.fna/cds.fna -a GCA_018433765.1_SM3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 17:27:03,157] [INFO] Task succeeded: Prodigal
[2023-06-18 17:27:03,158] [INFO] Task started: HMMsearch
[2023-06-18 17:27:03,158] [INFO] Running command: hmmsearch --tblout GCA_018433765.1_SM3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0e6bfa9f-4656-4625-980f-b23737e8dfaf/dqc_reference/reference_markers.hmm GCA_018433765.1_SM3_genomic.fna/protein.faa > /dev/null
[2023-06-18 17:27:03,454] [INFO] Task succeeded: HMMsearch
[2023-06-18 17:27:03,455] [INFO] Found 6/6 markers.
[2023-06-18 17:27:03,504] [INFO] Query marker FASTA was written to GCA_018433765.1_SM3_genomic.fna/markers.fasta
[2023-06-18 17:27:03,505] [INFO] Task started: Blastn
[2023-06-18 17:27:03,505] [INFO] Running command: blastn -query GCA_018433765.1_SM3_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e6bfa9f-4656-4625-980f-b23737e8dfaf/dqc_reference/reference_markers.fasta -out GCA_018433765.1_SM3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 17:27:04,103] [INFO] Task succeeded: Blastn
[2023-06-18 17:27:04,111] [INFO] Selected 19 target genomes.
[2023-06-18 17:27:04,112] [INFO] Target genome list was writen to GCA_018433765.1_SM3_genomic.fna/target_genomes.txt
[2023-06-18 17:27:04,117] [INFO] Task started: fastANI
[2023-06-18 17:27:04,117] [INFO] Running command: fastANI --query /var/lib/cwl/stg915a4537-f293-4627-8840-44f93bc4608b/GCA_018433765.1_SM3_genomic.fna.gz --refList GCA_018433765.1_SM3_genomic.fna/target_genomes.txt --output GCA_018433765.1_SM3_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 17:27:12,304] [INFO] Task succeeded: fastANI
[2023-06-18 17:27:12,304] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0e6bfa9f-4656-4625-980f-b23737e8dfaf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 17:27:12,305] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0e6bfa9f-4656-4625-980f-b23737e8dfaf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 17:27:12,324] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 17:27:12,324] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 17:27:12,324] [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
Sedimentibacter acidaminivorans	strain=DSM 24004	GCA_017873955.1	913099	913099	type	True	75.8187	132	1376	95	below_threshold
Senegalia massiliensis	strain=SIT17	GCA_900626135.1	1720316	1720316	type	True	75.748	116	1376	95	below_threshold
Caminicella sporogenes	strain=DSM 14501	GCA_900142285.1	166485	166485	type	True	75.5925	80	1376	95	below_threshold
Caminicella sporogenes	strain=AM 1114	GCA_003609595.1	166485	166485	type	True	75.5877	83	1376	95	below_threshold
Anaeromonas gelatinilytica	strain=D2Q-14	GCA_016820635.1	2683194	2683194	type	True	75.5214	103	1376	95	below_threshold
Caloranaerobacter ferrireducens	strain=DY22619	GCA_001730685.1	1323370	1323370	type	True	75.3216	86	1376	95	below_threshold
Caldisalinibacter kiritimatiensis	strain=L21-TH-D2	GCA_000387765.1	1304284	1304284	type	True	75.305	82	1376	95	below_threshold
Clostridium scatologenes	strain=ATCC 25775	GCA_000968375.1	1548	1548	type	True	75.1829	109	1376	95	below_threshold
Thermohalobacter berrensis	strain=CTT3	GCA_003609645.1	99594	99594	type	True	75.1033	81	1376	95	below_threshold
Clostridium formicaceticum	strain=DSM 92	GCA_002080475.1	1497	1497	type	True	75.0897	51	1376	95	below_threshold
Clostridium formicaceticum	strain=ATCC 27076	GCA_001854185.1	1497	1497	type	True	75.0786	52	1376	95	below_threshold
Clostridium tepidum	strain=IEH 97212	GCA_002008345.1	1962263	1962263	type	True	74.923	106	1376	95	below_threshold
Clostridium botulinum	strain=ATCC 25763	GCA_011017965.1	1491	1491	type	True	74.7712	111	1376	95	below_threshold
Clostridium botulinum	strain=ATCC 25763	GCA_001276985.1	1491	1491	type	True	74.7414	114	1376	95	below_threshold
Cetobacterium somerae	strain=ATCC BAA-474	GCA_000479045.1	188913	188913	type	True	74.6628	52	1376	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 17:27:12,326] [INFO] DFAST Taxonomy check result was written to GCA_018433765.1_SM3_genomic.fna/tc_result.tsv
[2023-06-18 17:27:12,330] [INFO] ===== Taxonomy check completed =====
[2023-06-18 17:27:12,330] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 17:27:12,331] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0e6bfa9f-4656-4625-980f-b23737e8dfaf/dqc_reference/checkm_data
[2023-06-18 17:27:12,332] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 17:27:12,379] [INFO] Task started: CheckM
[2023-06-18 17:27:12,380] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018433765.1_SM3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018433765.1_SM3_genomic.fna/checkm_input GCA_018433765.1_SM3_genomic.fna/checkm_result
[2023-06-18 17:27:39,011] [INFO] Task succeeded: CheckM
[2023-06-18 17:27:39,012] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 17:27:39,050] [INFO] ===== Completeness check finished =====
[2023-06-18 17:27:39,050] [INFO] ===== Start GTDB Search =====
[2023-06-18 17:27:39,051] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018433765.1_SM3_genomic.fna/markers.fasta)
[2023-06-18 17:27:39,051] [INFO] Task started: Blastn
[2023-06-18 17:27:39,051] [INFO] Running command: blastn -query GCA_018433765.1_SM3_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e6bfa9f-4656-4625-980f-b23737e8dfaf/dqc_reference/reference_markers_gtdb.fasta -out GCA_018433765.1_SM3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 17:27:39,804] [INFO] Task succeeded: Blastn
[2023-06-18 17:27:39,809] [INFO] Selected 18 target genomes.
[2023-06-18 17:27:39,809] [INFO] Target genome list was writen to GCA_018433765.1_SM3_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 17:27:39,823] [INFO] Task started: fastANI
[2023-06-18 17:27:39,823] [INFO] Running command: fastANI --query /var/lib/cwl/stg915a4537-f293-4627-8840-44f93bc4608b/GCA_018433765.1_SM3_genomic.fna.gz --refList GCA_018433765.1_SM3_genomic.fna/target_genomes_gtdb.txt --output GCA_018433765.1_SM3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 17:27:49,454] [INFO] Task succeeded: fastANI
[2023-06-18 17:27:49,472] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 17:27:49,473] [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
GCA_018433765.1	s__SM3-B41 sp018433765	100.0	1376	1376	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sedimentibacteraceae;g__SM3-B41	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017352195.1	s__UBA1535 sp017352195	76.0788	121	1376	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sedimentibacteraceae;g__UBA1535	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017873955.1	s__Sedimentibacter acidaminivorans	75.8187	132	1376	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sedimentibacteraceae;g__Sedimentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142285.1	s__Caminicella sporogenes	75.5925	80	1376	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Caminicellaceae;g__Caminicella	95.0	99.99	99.99	0.99	0.99	2	-
GCA_002332905.1	s__UBA1535 sp002332905	75.5463	108	1376	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sedimentibacteraceae;g__UBA1535	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002479485.1	s__UBA1535 sp002479485	75.5447	114	1376	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sedimentibacteraceae;g__UBA1535	95.0	98.88	98.88	0.91	0.91	2	-
GCF_000387765.1	s__Caldisalinibacter kiritimatiensis	75.305	82	1376	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Caldisalinibacteraceae;g__Caldisalinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009711785.1	s__MES13 sp009711785	75.2908	115	1376	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__MES13;g__MES13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009711765.1	s__MES13 sp009711765	75.1851	117	1376	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__MES13;g__MES13	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003609645.1	s__Thermohalobacter berrensis	75.0952	82	1376	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Thermohalobacteraceae;g__Thermohalobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001675165.1	s__Clostridium_B ragsdalei	75.0673	50	1376	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_B	95.0	98.18	98.18	0.88	0.88	2	-
GCF_001636845.1	s__Clostridium_B ljungdahlii_A	74.9661	65	1376	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002008345.1	s__Clostridium_F tepidum	74.9185	107	1376	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	99.70	99.54	0.93	0.92	5	-
--------------------------------------------------------------------------------
[2023-06-18 17:27:49,477] [INFO] GTDB search result was written to GCA_018433765.1_SM3_genomic.fna/result_gtdb.tsv
[2023-06-18 17:27:49,481] [INFO] ===== GTDB Search completed =====
[2023-06-18 17:27:49,486] [INFO] DFAST_QC result json was written to GCA_018433765.1_SM3_genomic.fna/dqc_result.json
[2023-06-18 17:27:49,487] [INFO] DFAST_QC completed!
[2023-06-18 17:27:49,487] [INFO] Total running time: 0h0m54s