[2024-01-25 19:51:50,779] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:51:50,783] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:51:50,783] [INFO] DQC Reference Directory: /var/lib/cwl/stge8c0431d-1cd9-4a88-99ee-123e6eb7a73f/dqc_reference
[2024-01-25 19:51:51,940] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:51:51,941] [INFO] Task started: Prodigal
[2024-01-25 19:51:51,942] [INFO] Running command: gunzip -c /var/lib/cwl/stg9ba6cc32-7178-455c-b13d-cfb004c4e1a0/GCF_000262445.1_ASM26244v1_genomic.fna.gz | prodigal -d GCF_000262445.1_ASM26244v1_genomic.fna/cds.fna -a GCF_000262445.1_ASM26244v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:51:56,361] [INFO] Task succeeded: Prodigal
[2024-01-25 19:51:56,362] [INFO] Task started: HMMsearch
[2024-01-25 19:51:56,362] [INFO] Running command: hmmsearch --tblout GCF_000262445.1_ASM26244v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge8c0431d-1cd9-4a88-99ee-123e6eb7a73f/dqc_reference/reference_markers.hmm GCF_000262445.1_ASM26244v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:51:56,603] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:51:56,605] [INFO] Found 6/6 markers.
[2024-01-25 19:51:56,630] [INFO] Query marker FASTA was written to GCF_000262445.1_ASM26244v1_genomic.fna/markers.fasta
[2024-01-25 19:51:56,630] [INFO] Task started: Blastn
[2024-01-25 19:51:56,630] [INFO] Running command: blastn -query GCF_000262445.1_ASM26244v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge8c0431d-1cd9-4a88-99ee-123e6eb7a73f/dqc_reference/reference_markers.fasta -out GCF_000262445.1_ASM26244v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:51:57,151] [INFO] Task succeeded: Blastn
[2024-01-25 19:51:57,154] [INFO] Selected 6 target genomes.
[2024-01-25 19:51:57,154] [INFO] Target genome list was writen to GCF_000262445.1_ASM26244v1_genomic.fna/target_genomes.txt
[2024-01-25 19:51:57,159] [INFO] Task started: fastANI
[2024-01-25 19:51:57,159] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ba6cc32-7178-455c-b13d-cfb004c4e1a0/GCF_000262445.1_ASM26244v1_genomic.fna.gz --refList GCF_000262445.1_ASM26244v1_genomic.fna/target_genomes.txt --output GCF_000262445.1_ASM26244v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:52:02,141] [INFO] Task succeeded: fastANI
[2024-01-25 19:52:02,141] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge8c0431d-1cd9-4a88-99ee-123e6eb7a73f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:52:02,142] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge8c0431d-1cd9-4a88-99ee-123e6eb7a73f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:52:02,147] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:52:02,147] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 19:52:02,147] [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 siderophilus	strain=SR4	GCA_000262445.1	106578	106578	type	True	100.0	846	846	95	inconclusive
Thermoanaerobacter wiegelii	strain=Rt8.B1	GCA_000147695.3	46354	46354	type	True	97.2229	741	846	95	inconclusive
Thermoanaerobacter uzonensis	strain=DSM 18761	GCA_900129115.1	447593	447593	type	True	94.4048	652	846	95	below_threshold
Thermoanaerobacter thermocopriae	strain=JCM 7501	GCA_001310975.1	29350	29350	suspected-type	True	90.8671	596	846	95	below_threshold
Thermoanaerobacter thermocopriae	strain=ATCC 51646	GCA_000518565.1	29350	29350	suspected-type	True	90.8575	605	846	95	below_threshold
Thermoanaerobacter kivui	strain=DSM 2030; LKT-1	GCA_000763575.1	2325	2325	type	True	89.7669	567	846	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:52:02,149] [INFO] DFAST Taxonomy check result was written to GCF_000262445.1_ASM26244v1_genomic.fna/tc_result.tsv
[2024-01-25 19:52:02,149] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:52:02,149] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:52:02,149] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge8c0431d-1cd9-4a88-99ee-123e6eb7a73f/dqc_reference/checkm_data
[2024-01-25 19:52:02,150] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:52:02,179] [INFO] Task started: CheckM
[2024-01-25 19:52:02,179] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000262445.1_ASM26244v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000262445.1_ASM26244v1_genomic.fna/checkm_input GCF_000262445.1_ASM26244v1_genomic.fna/checkm_result
[2024-01-25 19:52:21,461] [INFO] Task succeeded: CheckM
[2024-01-25 19:52:21,462] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:52:21,478] [INFO] ===== Completeness check finished =====
[2024-01-25 19:52:21,478] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:52:21,478] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000262445.1_ASM26244v1_genomic.fna/markers.fasta)
[2024-01-25 19:52:21,479] [INFO] Task started: Blastn
[2024-01-25 19:52:21,479] [INFO] Running command: blastn -query GCF_000262445.1_ASM26244v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge8c0431d-1cd9-4a88-99ee-123e6eb7a73f/dqc_reference/reference_markers_gtdb.fasta -out GCF_000262445.1_ASM26244v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:52:22,208] [INFO] Task succeeded: Blastn
[2024-01-25 19:52:22,212] [INFO] Selected 6 target genomes.
[2024-01-25 19:52:22,212] [INFO] Target genome list was writen to GCF_000262445.1_ASM26244v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:52:22,220] [INFO] Task started: fastANI
[2024-01-25 19:52:22,220] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ba6cc32-7178-455c-b13d-cfb004c4e1a0/GCF_000262445.1_ASM26244v1_genomic.fna.gz --refList GCF_000262445.1_ASM26244v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000262445.1_ASM26244v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:52:28,185] [INFO] Task succeeded: fastANI
[2024-01-25 19:52:28,190] [INFO] Found 6 fastANI hits (3 hits with ANI > circumscription radius)
[2024-01-25 19:52:28,190] [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_003722315.1	s__Thermoanaerobacter ethanolicus	98.2575	742	846	d__Bacteria;p__Firmicutes_A;c__Thermoanaerobacteria;o__Thermoanaerobacterales;f__Thermoanaerobacteraceae;g__Thermoanaerobacter	96.9409	98.23	97.61	0.86	0.74	8	inconclusive
GCF_000147695.2	s__Thermoanaerobacter wiegelii	97.2436	740	846	d__Bacteria;p__Firmicutes_A;c__Thermoanaerobacteria;o__Thermoanaerobacterales;f__Thermoanaerobacteraceae;g__Thermoanaerobacter	96.9409	N/A	N/A	N/A	N/A	1	inconclusive
GCA_000445185.1	s__Thermoanaerobacter sp000445185	95.8356	618	846	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_014896455.1	s__Thermoanaerobacter sp014896455	95.6405	599	846	d__Bacteria;p__Firmicutes_A;c__Thermoanaerobacteria;o__Thermoanaerobacterales;f__Thermoanaerobacteraceae;g__Thermoanaerobacter	95.6271	N/A	N/A	N/A	N/A	1	inconclusive
GCF_000019085.1	s__Thermoanaerobacter pseudethanolicus	94.8127	617	846	d__Bacteria;p__Firmicutes_A;c__Thermoanaerobacteria;o__Thermoanaerobacterales;f__Thermoanaerobacteraceae;g__Thermoanaerobacter	95.1128	98.35	97.55	0.89	0.81	10	-
GCF_900129115.1	s__Thermoanaerobacter uzonensis	94.4111	652	846	d__Bacteria;p__Firmicutes_A;c__Thermoanaerobacteria;o__Thermoanaerobacterales;f__Thermoanaerobacteraceae;g__Thermoanaerobacter	95.0	96.59	96.59	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:52:28,192] [INFO] GTDB search result was written to GCF_000262445.1_ASM26244v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:52:28,192] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:52:28,194] [INFO] DFAST_QC result json was written to GCF_000262445.1_ASM26244v1_genomic.fna/dqc_result.json
[2024-01-25 19:52:28,195] [INFO] DFAST_QC completed!
[2024-01-25 19:52:28,195] [INFO] Total running time: 0h0m37s