[2024-01-24 14:46:35,496] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:35,498] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:35,498] [INFO] DQC Reference Directory: /var/lib/cwl/stg133fcfc9-2e80-4e4b-9ecb-43d0a281d811/dqc_reference
[2024-01-24 14:46:37,187] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:37,188] [INFO] Task started: Prodigal
[2024-01-24 14:46:37,189] [INFO] Running command: gunzip -c /var/lib/cwl/stg0adf99d0-a411-4d89-b061-f45f619fd162/GCF_017874545.1_ASM1787454v1_genomic.fna.gz | prodigal -d GCF_017874545.1_ASM1787454v1_genomic.fna/cds.fna -a GCF_017874545.1_ASM1787454v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:46:42,723] [INFO] Task succeeded: Prodigal
[2024-01-24 14:46:42,723] [INFO] Task started: HMMsearch
[2024-01-24 14:46:42,723] [INFO] Running command: hmmsearch --tblout GCF_017874545.1_ASM1787454v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg133fcfc9-2e80-4e4b-9ecb-43d0a281d811/dqc_reference/reference_markers.hmm GCF_017874545.1_ASM1787454v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:46:42,922] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:46:42,923] [INFO] Found 6/6 markers.
[2024-01-24 14:46:42,948] [INFO] Query marker FASTA was written to GCF_017874545.1_ASM1787454v1_genomic.fna/markers.fasta
[2024-01-24 14:46:42,948] [INFO] Task started: Blastn
[2024-01-24 14:46:42,948] [INFO] Running command: blastn -query GCF_017874545.1_ASM1787454v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg133fcfc9-2e80-4e4b-9ecb-43d0a281d811/dqc_reference/reference_markers.fasta -out GCF_017874545.1_ASM1787454v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:46:43,507] [INFO] Task succeeded: Blastn
[2024-01-24 14:46:43,510] [INFO] Selected 16 target genomes.
[2024-01-24 14:46:43,510] [INFO] Target genome list was writen to GCF_017874545.1_ASM1787454v1_genomic.fna/target_genomes.txt
[2024-01-24 14:46:43,626] [INFO] Task started: fastANI
[2024-01-24 14:46:43,626] [INFO] Running command: fastANI --query /var/lib/cwl/stg0adf99d0-a411-4d89-b061-f45f619fd162/GCF_017874545.1_ASM1787454v1_genomic.fna.gz --refList GCF_017874545.1_ASM1787454v1_genomic.fna/target_genomes.txt --output GCF_017874545.1_ASM1787454v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:46:53,147] [INFO] Task succeeded: fastANI
[2024-01-24 14:46:53,147] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg133fcfc9-2e80-4e4b-9ecb-43d0a281d811/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:46:53,147] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg133fcfc9-2e80-4e4b-9ecb-43d0a281d811/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:46:53,152] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:46:53,153] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:46:53,153] [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
Thermoanaerobacterium butyriciformans	strain=DSM 101588	GCA_017874545.1	1702242	1702242	type	True	100.0	942	944	95	conclusive
Thermoanaerobacterium thermosaccharolyticum	strain=DSM 571	GCA_000145615.1	1517	1517	type	True	92.2502	743	944	95	below_threshold
Thermoanaerobacterium xylanolyticum	strain=LX-11	GCA_000189775.3	29329	29329	type	True	84.1889	604	944	95	below_threshold
Thermoanaerobacter uzonensis	strain=DSM 18761	GCA_900129115.1	447593	447593	type	True	77.1002	81	944	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:46:53,154] [INFO] DFAST Taxonomy check result was written to GCF_017874545.1_ASM1787454v1_genomic.fna/tc_result.tsv
[2024-01-24 14:46:53,155] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:46:53,155] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:46:53,155] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg133fcfc9-2e80-4e4b-9ecb-43d0a281d811/dqc_reference/checkm_data
[2024-01-24 14:46:53,156] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:46:53,185] [INFO] Task started: CheckM
[2024-01-24 14:46:53,185] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017874545.1_ASM1787454v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017874545.1_ASM1787454v1_genomic.fna/checkm_input GCF_017874545.1_ASM1787454v1_genomic.fna/checkm_result
[2024-01-24 14:47:15,206] [INFO] Task succeeded: CheckM
[2024-01-24 14:47:15,207] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:47:15,221] [INFO] ===== Completeness check finished =====
[2024-01-24 14:47:15,221] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:47:15,222] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017874545.1_ASM1787454v1_genomic.fna/markers.fasta)
[2024-01-24 14:47:15,222] [INFO] Task started: Blastn
[2024-01-24 14:47:15,222] [INFO] Running command: blastn -query GCF_017874545.1_ASM1787454v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg133fcfc9-2e80-4e4b-9ecb-43d0a281d811/dqc_reference/reference_markers_gtdb.fasta -out GCF_017874545.1_ASM1787454v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:15,983] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:15,986] [INFO] Selected 14 target genomes.
[2024-01-24 14:47:15,987] [INFO] Target genome list was writen to GCF_017874545.1_ASM1787454v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:47:16,001] [INFO] Task started: fastANI
[2024-01-24 14:47:16,002] [INFO] Running command: fastANI --query /var/lib/cwl/stg0adf99d0-a411-4d89-b061-f45f619fd162/GCF_017874545.1_ASM1787454v1_genomic.fna.gz --refList GCF_017874545.1_ASM1787454v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017874545.1_ASM1787454v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:47:23,983] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:23,991] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:47:23,991] [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_017874545.1	s__Thermoanaerobacterium butyriciformans	100.0	942	944	d__Bacteria;p__Firmicutes_A;c__Thermoanaerobacteria;o__Thermoanaerobacterales;f__Thermoanaerobacteraceae;g__Thermoanaerobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000145615.1	s__Thermoanaerobacterium thermosaccharolyticum	92.2264	744	944	d__Bacteria;p__Firmicutes_A;c__Thermoanaerobacteria;o__Thermoanaerobacterales;f__Thermoanaerobacteraceae;g__Thermoanaerobacterium	95.0	97.32	96.90	0.85	0.81	9	-
GCF_000747665.1	s__Thermoanaerobacterium saccharolyticum_A	85.529	646	944	d__Bacteria;p__Firmicutes_A;c__Thermoanaerobacteria;o__Thermoanaerobacterales;f__Thermoanaerobacteraceae;g__Thermoanaerobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002102475.1	s__Thermoanaerobacterium sp002102475	85.429	607	944	d__Bacteria;p__Firmicutes_A;c__Thermoanaerobacteria;o__Thermoanaerobacterales;f__Thermoanaerobacteraceae;g__Thermoanaerobacterium	95.0	98.00	98.00	0.86	0.86	2	-
GCF_009905255.1	s__Thermoanaerobacterium aotearoense	84.8908	625	944	d__Bacteria;p__Firmicutes_A;c__Thermoanaerobacteria;o__Thermoanaerobacterales;f__Thermoanaerobacteraceae;g__Thermoanaerobacterium	95.0	99.96	99.95	0.96	0.93	3	-
GCF_000189775.2	s__Thermoanaerobacterium xylanolyticum	84.2121	603	944	d__Bacteria;p__Firmicutes_A;c__Thermoanaerobacteria;o__Thermoanaerobacterales;f__Thermoanaerobacteraceae;g__Thermoanaerobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900205865.1	s__Thermoanaerobacterium sp900205865	82.2311	471	944	d__Bacteria;p__Firmicutes_A;c__Thermoanaerobacteria;o__Thermoanaerobacterales;f__Thermoanaerobacteraceae;g__Thermoanaerobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129115.1	s__Thermoanaerobacter uzonensis	77.1002	81	944	d__Bacteria;p__Firmicutes_A;c__Thermoanaerobacteria;o__Thermoanaerobacterales;f__Thermoanaerobacteraceae;g__Thermoanaerobacter	95.0	96.59	96.59	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:47:23,993] [INFO] GTDB search result was written to GCF_017874545.1_ASM1787454v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:47:23,993] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:47:23,996] [INFO] DFAST_QC result json was written to GCF_017874545.1_ASM1787454v1_genomic.fna/dqc_result.json
[2024-01-24 14:47:23,996] [INFO] DFAST_QC completed!
[2024-01-24 14:47:23,996] [INFO] Total running time: 0h0m48s