[2024-01-25 19:11:05,698] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:11:05,708] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:11:05,708] [INFO] DQC Reference Directory: /var/lib/cwl/stg32b890fe-3ed0-4f0b-baa0-d5ee3ed0b6bc/dqc_reference
[2024-01-25 19:11:06,855] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:11:06,856] [INFO] Task started: Prodigal
[2024-01-25 19:11:06,856] [INFO] Running command: gunzip -c /var/lib/cwl/stg8a54b5d3-6e10-4974-b473-ec7e397b9fb8/GCF_001310975.1_ASM131097v1_genomic.fna.gz | prodigal -d GCF_001310975.1_ASM131097v1_genomic.fna/cds.fna -a GCF_001310975.1_ASM131097v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:11:10,796] [INFO] Task succeeded: Prodigal
[2024-01-25 19:11:10,797] [INFO] Task started: HMMsearch
[2024-01-25 19:11:10,797] [INFO] Running command: hmmsearch --tblout GCF_001310975.1_ASM131097v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg32b890fe-3ed0-4f0b-baa0-d5ee3ed0b6bc/dqc_reference/reference_markers.hmm GCF_001310975.1_ASM131097v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:11:11,030] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:11:11,031] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg8a54b5d3-6e10-4974-b473-ec7e397b9fb8/GCF_001310975.1_ASM131097v1_genomic.fna.gz]
[2024-01-25 19:11:11,058] [INFO] Query marker FASTA was written to GCF_001310975.1_ASM131097v1_genomic.fna/markers.fasta
[2024-01-25 19:11:11,058] [INFO] Task started: Blastn
[2024-01-25 19:11:11,058] [INFO] Running command: blastn -query GCF_001310975.1_ASM131097v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg32b890fe-3ed0-4f0b-baa0-d5ee3ed0b6bc/dqc_reference/reference_markers.fasta -out GCF_001310975.1_ASM131097v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:11:11,565] [INFO] Task succeeded: Blastn
[2024-01-25 19:11:11,569] [INFO] Selected 6 target genomes.
[2024-01-25 19:11:11,570] [INFO] Target genome list was writen to GCF_001310975.1_ASM131097v1_genomic.fna/target_genomes.txt
[2024-01-25 19:11:11,574] [INFO] Task started: fastANI
[2024-01-25 19:11:11,575] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a54b5d3-6e10-4974-b473-ec7e397b9fb8/GCF_001310975.1_ASM131097v1_genomic.fna.gz --refList GCF_001310975.1_ASM131097v1_genomic.fna/target_genomes.txt --output GCF_001310975.1_ASM131097v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:11:15,187] [INFO] Task succeeded: fastANI
[2024-01-25 19:11:15,188] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg32b890fe-3ed0-4f0b-baa0-d5ee3ed0b6bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:11:15,188] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg32b890fe-3ed0-4f0b-baa0-d5ee3ed0b6bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:11:15,193] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:11:15,194] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:11:15,194] [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
Thermoanaerobacter thermocopriae	strain=JCM 7501	GCA_001310975.1	29350	29350	suspected-type	True	100.0	779	780	95	conclusive
Thermoanaerobacter thermocopriae	strain=ATCC 51646	GCA_000518565.1	29350	29350	suspected-type	True	99.9193	765	780	95	conclusive
Thermoanaerobacter siderophilus	strain=SR4	GCA_000262445.1	106578	106578	type	True	90.9145	605	780	95	below_threshold
Thermoanaerobacter wiegelii	strain=Rt8.B1	GCA_000147695.3	46354	46354	type	True	90.6101	606	780	95	below_threshold
Thermoanaerobacter uzonensis	strain=DSM 18761	GCA_900129115.1	447593	447593	type	True	90.0879	568	780	95	below_threshold
Thermoanaerobacter kivui	strain=DSM 2030; LKT-1	GCA_000763575.1	2325	2325	type	True	86.2216	505	780	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:11:15,195] [INFO] DFAST Taxonomy check result was written to GCF_001310975.1_ASM131097v1_genomic.fna/tc_result.tsv
[2024-01-25 19:11:15,196] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:11:15,196] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:11:15,196] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg32b890fe-3ed0-4f0b-baa0-d5ee3ed0b6bc/dqc_reference/checkm_data
[2024-01-25 19:11:15,197] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:11:15,226] [INFO] Task started: CheckM
[2024-01-25 19:11:15,227] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001310975.1_ASM131097v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001310975.1_ASM131097v1_genomic.fna/checkm_input GCF_001310975.1_ASM131097v1_genomic.fna/checkm_result
[2024-01-25 19:11:32,981] [INFO] Task succeeded: CheckM
[2024-01-25 19:11:32,982] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.79%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:11:32,999] [INFO] ===== Completeness check finished =====
[2024-01-25 19:11:32,999] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:11:32,999] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001310975.1_ASM131097v1_genomic.fna/markers.fasta)
[2024-01-25 19:11:33,000] [INFO] Task started: Blastn
[2024-01-25 19:11:33,000] [INFO] Running command: blastn -query GCF_001310975.1_ASM131097v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg32b890fe-3ed0-4f0b-baa0-d5ee3ed0b6bc/dqc_reference/reference_markers_gtdb.fasta -out GCF_001310975.1_ASM131097v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:11:33,674] [INFO] Task succeeded: Blastn
[2024-01-25 19:11:33,677] [INFO] Selected 8 target genomes.
[2024-01-25 19:11:33,677] [INFO] Target genome list was writen to GCF_001310975.1_ASM131097v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:11:33,688] [INFO] Task started: fastANI
[2024-01-25 19:11:33,688] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a54b5d3-6e10-4974-b473-ec7e397b9fb8/GCF_001310975.1_ASM131097v1_genomic.fna.gz --refList GCF_001310975.1_ASM131097v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001310975.1_ASM131097v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:11:38,573] [INFO] Task succeeded: fastANI
[2024-01-25 19:11:38,579] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:11:38,579] [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_001310975.1	s__Thermoanaerobacter thermocopriae	100.0	779	780	d__Bacteria;p__Firmicutes_A;c__Thermoanaerobacteria;o__Thermoanaerobacterales;f__Thermoanaerobacteraceae;g__Thermoanaerobacter	95.0	98.14	96.24	0.87	0.83	5	conclusive
GCF_000019085.1	s__Thermoanaerobacter pseudethanolicus	91.6375	580	780	d__Bacteria;p__Firmicutes_A;c__Thermoanaerobacteria;o__Thermoanaerobacterales;f__Thermoanaerobacteraceae;g__Thermoanaerobacter	95.1128	98.35	97.55	0.89	0.81	10	-
GCA_000445185.1	s__Thermoanaerobacter sp000445185	90.9546	537	780	d__Bacteria;p__Firmicutes_A;c__Thermoanaerobacteria;o__Thermoanaerobacterales;f__Thermoanaerobacteraceae;g__Thermoanaerobacter	95.9754	N/A	N/A	N/A	N/A	1	-
GCA_003722315.1	s__Thermoanaerobacter ethanolicus	90.6706	613	780	d__Bacteria;p__Firmicutes_A;c__Thermoanaerobacteria;o__Thermoanaerobacterales;f__Thermoanaerobacteraceae;g__Thermoanaerobacter	96.9409	98.23	97.61	0.86	0.74	8	-
GCF_000147695.2	s__Thermoanaerobacter wiegelii	90.5918	607	780	d__Bacteria;p__Firmicutes_A;c__Thermoanaerobacteria;o__Thermoanaerobacterales;f__Thermoanaerobacteraceae;g__Thermoanaerobacter	96.9409	N/A	N/A	N/A	N/A	1	-
GCF_900129115.1	s__Thermoanaerobacter uzonensis	90.109	567	780	d__Bacteria;p__Firmicutes_A;c__Thermoanaerobacteria;o__Thermoanaerobacterales;f__Thermoanaerobacteraceae;g__Thermoanaerobacter	95.0	96.59	96.59	0.87	0.87	2	-
GCA_014896455.1	s__Thermoanaerobacter sp014896455	89.156	506	780	d__Bacteria;p__Firmicutes_A;c__Thermoanaerobacteria;o__Thermoanaerobacterales;f__Thermoanaerobacteraceae;g__Thermoanaerobacter	95.6271	N/A	N/A	N/A	N/A	1	-
GCF_000763575.1	s__Thermoanaerobacter kivui	86.2577	503	780	d__Bacteria;p__Firmicutes_A;c__Thermoanaerobacteria;o__Thermoanaerobacterales;f__Thermoanaerobacteraceae;g__Thermoanaerobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:11:38,581] [INFO] GTDB search result was written to GCF_001310975.1_ASM131097v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:11:38,581] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:11:38,586] [INFO] DFAST_QC result json was written to GCF_001310975.1_ASM131097v1_genomic.fna/dqc_result.json
[2024-01-25 19:11:38,586] [INFO] DFAST_QC completed!
[2024-01-25 19:11:38,586] [INFO] Total running time: 0h0m33s