[2024-01-24 12:22:13,654] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:13,658] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:13,658] [INFO] DQC Reference Directory: /var/lib/cwl/stg9beeb87d-3416-4dfa-a1d8-97557821aa3f/dqc_reference
[2024-01-24 12:22:15,262] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:15,263] [INFO] Task started: Prodigal
[2024-01-24 12:22:15,263] [INFO] Running command: gunzip -c /var/lib/cwl/stg94ffc20e-d480-4512-befc-698fa924ed85/GCF_000189775.2_ASM18977v3_genomic.fna.gz | prodigal -d GCF_000189775.2_ASM18977v3_genomic.fna/cds.fna -a GCF_000189775.2_ASM18977v3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:20,729] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:20,729] [INFO] Task started: HMMsearch
[2024-01-24 12:22:20,729] [INFO] Running command: hmmsearch --tblout GCF_000189775.2_ASM18977v3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9beeb87d-3416-4dfa-a1d8-97557821aa3f/dqc_reference/reference_markers.hmm GCF_000189775.2_ASM18977v3_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:21,026] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:21,028] [INFO] Found 6/6 markers.
[2024-01-24 12:22:21,054] [INFO] Query marker FASTA was written to GCF_000189775.2_ASM18977v3_genomic.fna/markers.fasta
[2024-01-24 12:22:21,055] [INFO] Task started: Blastn
[2024-01-24 12:22:21,055] [INFO] Running command: blastn -query GCF_000189775.2_ASM18977v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg9beeb87d-3416-4dfa-a1d8-97557821aa3f/dqc_reference/reference_markers.fasta -out GCF_000189775.2_ASM18977v3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:21,652] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:21,655] [INFO] Selected 16 target genomes.
[2024-01-24 12:22:21,655] [INFO] Target genome list was writen to GCF_000189775.2_ASM18977v3_genomic.fna/target_genomes.txt
[2024-01-24 12:22:21,702] [INFO] Task started: fastANI
[2024-01-24 12:22:21,702] [INFO] Running command: fastANI --query /var/lib/cwl/stg94ffc20e-d480-4512-befc-698fa924ed85/GCF_000189775.2_ASM18977v3_genomic.fna.gz --refList GCF_000189775.2_ASM18977v3_genomic.fna/target_genomes.txt --output GCF_000189775.2_ASM18977v3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:29,990] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:29,990] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9beeb87d-3416-4dfa-a1d8-97557821aa3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:29,991] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9beeb87d-3416-4dfa-a1d8-97557821aa3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:29,996] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:22:29,996] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:29,996] [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 xylanolyticum	strain=LX-11	GCA_000189775.3	29329	29329	type	True	100.0	843	844	95	conclusive
Thermoanaerobacterium butyriciformans	strain=DSM 101588	GCA_017874545.1	1702242	1702242	type	True	84.4615	581	844	95	below_threshold
Thermoanaerobacterium thermosaccharolyticum	strain=DSM 571	GCA_000145615.1	1517	1517	type	True	82.9473	571	844	95	below_threshold
Thermoanaerobacter uzonensis	strain=DSM 18761	GCA_900129115.1	447593	447593	type	True	77.2073	88	844	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:29,998] [INFO] DFAST Taxonomy check result was written to GCF_000189775.2_ASM18977v3_genomic.fna/tc_result.tsv
[2024-01-24 12:22:29,999] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:29,999] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:29,999] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9beeb87d-3416-4dfa-a1d8-97557821aa3f/dqc_reference/checkm_data
[2024-01-24 12:22:30,000] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:30,027] [INFO] Task started: CheckM
[2024-01-24 12:22:30,027] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000189775.2_ASM18977v3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000189775.2_ASM18977v3_genomic.fna/checkm_input GCF_000189775.2_ASM18977v3_genomic.fna/checkm_result
[2024-01-24 12:22:53,976] [INFO] Task succeeded: CheckM
[2024-01-24 12:22:53,977] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:22:54,018] [INFO] ===== Completeness check finished =====
[2024-01-24 12:22:54,018] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:22:54,019] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000189775.2_ASM18977v3_genomic.fna/markers.fasta)
[2024-01-24 12:22:54,019] [INFO] Task started: Blastn
[2024-01-24 12:22:54,020] [INFO] Running command: blastn -query GCF_000189775.2_ASM18977v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg9beeb87d-3416-4dfa-a1d8-97557821aa3f/dqc_reference/reference_markers_gtdb.fasta -out GCF_000189775.2_ASM18977v3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:54,868] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:54,871] [INFO] Selected 10 target genomes.
[2024-01-24 12:22:54,871] [INFO] Target genome list was writen to GCF_000189775.2_ASM18977v3_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:22:54,922] [INFO] Task started: fastANI
[2024-01-24 12:22:54,922] [INFO] Running command: fastANI --query /var/lib/cwl/stg94ffc20e-d480-4512-befc-698fa924ed85/GCF_000189775.2_ASM18977v3_genomic.fna.gz --refList GCF_000189775.2_ASM18977v3_genomic.fna/target_genomes_gtdb.txt --output GCF_000189775.2_ASM18977v3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:01,269] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:01,276] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:01,277] [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_000189775.2	s__Thermoanaerobacterium xylanolyticum	100.0	843	844	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_002102475.1	s__Thermoanaerobacterium sp002102475	94.2353	686	844	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	91.4576	710	844	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_000747665.1	s__Thermoanaerobacterium saccharolyticum_A	91.3579	668	844	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_017874545.1	s__Thermoanaerobacterium butyriciformans	84.4524	582	844	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_000145615.1	s__Thermoanaerobacterium thermosaccharolyticum	82.9363	572	844	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_900129115.1	s__Thermoanaerobacter uzonensis	77.2091	87	844	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 12:23:01,278] [INFO] GTDB search result was written to GCF_000189775.2_ASM18977v3_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:01,279] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:01,282] [INFO] DFAST_QC result json was written to GCF_000189775.2_ASM18977v3_genomic.fna/dqc_result.json
[2024-01-24 12:23:01,282] [INFO] DFAST_QC completed!
[2024-01-24 12:23:01,282] [INFO] Total running time: 0h0m48s