[2023-06-19 08:35:12,296] [INFO] DFAST_QC pipeline started.
[2023-06-19 08:35:12,298] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 08:35:12,298] [INFO] DQC Reference Directory: /var/lib/cwl/stg4862850c-01f0-4501-b858-3c9598739c75/dqc_reference
[2023-06-19 08:35:13,591] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 08:35:13,592] [INFO] Task started: Prodigal
[2023-06-19 08:35:13,592] [INFO] Running command: gunzip -c /var/lib/cwl/stgafc504c1-3331-47b7-8547-33621a17e1fb/GCA_018264405.1_ASM1826440v1_genomic.fna.gz | prodigal -d GCA_018264405.1_ASM1826440v1_genomic.fna/cds.fna -a GCA_018264405.1_ASM1826440v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 08:35:15,678] [INFO] Task succeeded: Prodigal
[2023-06-19 08:35:15,678] [INFO] Task started: HMMsearch
[2023-06-19 08:35:15,678] [INFO] Running command: hmmsearch --tblout GCA_018264405.1_ASM1826440v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4862850c-01f0-4501-b858-3c9598739c75/dqc_reference/reference_markers.hmm GCA_018264405.1_ASM1826440v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 08:35:15,846] [INFO] Task succeeded: HMMsearch
[2023-06-19 08:35:15,848] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgafc504c1-3331-47b7-8547-33621a17e1fb/GCA_018264405.1_ASM1826440v1_genomic.fna.gz]
[2023-06-19 08:35:15,867] [INFO] Query marker FASTA was written to GCA_018264405.1_ASM1826440v1_genomic.fna/markers.fasta
[2023-06-19 08:35:15,868] [INFO] Task started: Blastn
[2023-06-19 08:35:15,868] [INFO] Running command: blastn -query GCA_018264405.1_ASM1826440v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4862850c-01f0-4501-b858-3c9598739c75/dqc_reference/reference_markers.fasta -out GCA_018264405.1_ASM1826440v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:35:16,393] [INFO] Task succeeded: Blastn
[2023-06-19 08:35:16,397] [INFO] Selected 7 target genomes.
[2023-06-19 08:35:16,397] [INFO] Target genome list was writen to GCA_018264405.1_ASM1826440v1_genomic.fna/target_genomes.txt
[2023-06-19 08:35:16,398] [INFO] Task started: fastANI
[2023-06-19 08:35:16,398] [INFO] Running command: fastANI --query /var/lib/cwl/stgafc504c1-3331-47b7-8547-33621a17e1fb/GCA_018264405.1_ASM1826440v1_genomic.fna.gz --refList GCA_018264405.1_ASM1826440v1_genomic.fna/target_genomes.txt --output GCA_018264405.1_ASM1826440v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 08:35:18,799] [INFO] Task succeeded: fastANI
[2023-06-19 08:35:18,799] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4862850c-01f0-4501-b858-3c9598739c75/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 08:35:18,799] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4862850c-01f0-4501-b858-3c9598739c75/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 08:35:18,806] [INFO] Found 6 fastANI hits (3 hits with ANI > threshold)
[2023-06-19 08:35:18,807] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-19 08:35:18,807] [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
Collinsella aerofaciens	strain=ATCC 25986	GCA_000169035.1	74426	74426	type	True	95.5739	121	126	95	conclusive
Collinsella aerofaciens	strain=NCTC11838	GCA_900461335.1	74426	74426	type	True	95.5275	123	126	95	conclusive
Collinsella aerofaciens	strain=JCM 10188	GCA_010509075.1	74426	74426	type	True	95.5009	123	126	95	conclusive
Collinsella bouchesdurhonensis	strain=Marseille-P3296	GCA_900155365.1	1907654	1907654	type	True	80.2135	52	126	95	below_threshold
Enorma burkinafasonensis	strain=Marseille-P9525	GCA_902150035.1	2590867	2590867	type	True	78.9016	50	126	95	below_threshold
Collinsella tanakaei	strain=YIT 12063	GCA_000225705.1	626935	626935	suspected-type	True	78.3327	50	126	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 08:35:18,809] [INFO] DFAST Taxonomy check result was written to GCA_018264405.1_ASM1826440v1_genomic.fna/tc_result.tsv
[2023-06-19 08:35:18,810] [INFO] ===== Taxonomy check completed =====
[2023-06-19 08:35:18,810] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 08:35:18,810] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4862850c-01f0-4501-b858-3c9598739c75/dqc_reference/checkm_data
[2023-06-19 08:35:18,811] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 08:35:18,829] [INFO] Task started: CheckM
[2023-06-19 08:35:18,829] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018264405.1_ASM1826440v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018264405.1_ASM1826440v1_genomic.fna/checkm_input GCA_018264405.1_ASM1826440v1_genomic.fna/checkm_result
[2023-06-19 08:35:34,098] [INFO] Task succeeded: CheckM
[2023-06-19 08:35:34,099] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.34%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 08:35:34,121] [INFO] ===== Completeness check finished =====
[2023-06-19 08:35:34,122] [INFO] ===== Start GTDB Search =====
[2023-06-19 08:35:34,122] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018264405.1_ASM1826440v1_genomic.fna/markers.fasta)
[2023-06-19 08:35:34,123] [INFO] Task started: Blastn
[2023-06-19 08:35:34,123] [INFO] Running command: blastn -query GCA_018264405.1_ASM1826440v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4862850c-01f0-4501-b858-3c9598739c75/dqc_reference/reference_markers_gtdb.fasta -out GCA_018264405.1_ASM1826440v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:35:34,717] [INFO] Task succeeded: Blastn
[2023-06-19 08:35:34,723] [INFO] Selected 10 target genomes.
[2023-06-19 08:35:34,723] [INFO] Target genome list was writen to GCA_018264405.1_ASM1826440v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 08:35:34,726] [INFO] Task started: fastANI
[2023-06-19 08:35:34,726] [INFO] Running command: fastANI --query /var/lib/cwl/stgafc504c1-3331-47b7-8547-33621a17e1fb/GCA_018264405.1_ASM1826440v1_genomic.fna.gz --refList GCA_018264405.1_ASM1826440v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018264405.1_ASM1826440v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 08:35:39,086] [INFO] Task succeeded: fastANI
[2023-06-19 08:35:39,098] [INFO] Found 10 fastANI hits (3 hits with ANI > circumscription radius)
[2023-06-19 08:35:39,098] [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_902363125.1	s__Collinsella sp902363125	95.8226	118	126	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	96.02	96.02	0.87	0.87	2	inconclusive
GCA_900752545.1	s__Collinsella sp900752545	95.2651	119	126	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.97	99.97	0.93	0.93	2	inconclusive
GCA_900752215.1	s__Collinsella sp900752215	95.09	111	126	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0875	99.95	99.95	0.94	0.94	2	inconclusive
GCA_900542315.1	s__Collinsella sp900542315	94.8766	119	126	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002736145.1	s__Collinsella aerofaciens_A	94.7379	120	126	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	0.99	0.99	2	-
GCA_900542275.1	s__Collinsella sp900542275	94.625	110	126	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.02	95.02	0.82	0.82	2	-
GCA_900545555.1	s__Collinsella sp900545555	94.3146	113	126	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0872	N/A	N/A	N/A	N/A	1	-
GCA_900546825.1	s__Collinsella sp900546825	94.1095	113	126	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900552395.1	s__Collinsella sp900552395	92.9521	100	126	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.15	N/A	N/A	N/A	N/A	1	-
GCA_900756725.1	s__Collinsella sp900756725	92.0411	105	126	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.39	95.39	0.81	0.81	2	-
--------------------------------------------------------------------------------
[2023-06-19 08:35:39,101] [INFO] GTDB search result was written to GCA_018264405.1_ASM1826440v1_genomic.fna/result_gtdb.tsv
[2023-06-19 08:35:39,101] [INFO] ===== GTDB Search completed =====
[2023-06-19 08:35:39,105] [INFO] DFAST_QC result json was written to GCA_018264405.1_ASM1826440v1_genomic.fna/dqc_result.json
[2023-06-19 08:35:39,105] [INFO] DFAST_QC completed!
[2023-06-19 08:35:39,105] [INFO] Total running time: 0h0m27s