[2024-01-25 20:02:35,550] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:02:35,551] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:02:35,552] [INFO] DQC Reference Directory: /var/lib/cwl/stgfd9fca89-27ea-41b8-ad64-d21a8448f3e3/dqc_reference
[2024-01-25 20:02:36,644] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:02:36,645] [INFO] Task started: Prodigal
[2024-01-25 20:02:36,645] [INFO] Running command: gunzip -c /var/lib/cwl/stg1e1ded8c-7a15-4f19-8558-395295dc2879/GCF_000425565.1_ASM42556v1_genomic.fna.gz | prodigal -d GCF_000425565.1_ASM42556v1_genomic.fna/cds.fna -a GCF_000425565.1_ASM42556v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:02:42,827] [INFO] Task succeeded: Prodigal
[2024-01-25 20:02:42,828] [INFO] Task started: HMMsearch
[2024-01-25 20:02:42,828] [INFO] Running command: hmmsearch --tblout GCF_000425565.1_ASM42556v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfd9fca89-27ea-41b8-ad64-d21a8448f3e3/dqc_reference/reference_markers.hmm GCF_000425565.1_ASM42556v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:02:43,029] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:02:43,030] [INFO] Found 6/6 markers.
[2024-01-25 20:02:43,051] [INFO] Query marker FASTA was written to GCF_000425565.1_ASM42556v1_genomic.fna/markers.fasta
[2024-01-25 20:02:43,052] [INFO] Task started: Blastn
[2024-01-25 20:02:43,052] [INFO] Running command: blastn -query GCF_000425565.1_ASM42556v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd9fca89-27ea-41b8-ad64-d21a8448f3e3/dqc_reference/reference_markers.fasta -out GCF_000425565.1_ASM42556v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:02:43,816] [INFO] Task succeeded: Blastn
[2024-01-25 20:02:43,818] [INFO] Selected 5 target genomes.
[2024-01-25 20:02:43,818] [INFO] Target genome list was writen to GCF_000425565.1_ASM42556v1_genomic.fna/target_genomes.txt
[2024-01-25 20:02:43,823] [INFO] Task started: fastANI
[2024-01-25 20:02:43,824] [INFO] Running command: fastANI --query /var/lib/cwl/stg1e1ded8c-7a15-4f19-8558-395295dc2879/GCF_000425565.1_ASM42556v1_genomic.fna.gz --refList GCF_000425565.1_ASM42556v1_genomic.fna/target_genomes.txt --output GCF_000425565.1_ASM42556v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:02:46,829] [INFO] Task succeeded: fastANI
[2024-01-25 20:02:46,830] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfd9fca89-27ea-41b8-ad64-d21a8448f3e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:02:46,830] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfd9fca89-27ea-41b8-ad64-d21a8448f3e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:02:46,835] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:02:46,835] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:02:46,835] [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
Tepidiphilus margaritifer	strain=DSM 15129	GCA_000425565.1	203471	203471	type	True	100.0	729	730	95	conclusive
Tepidiphilus baoligensis	strain=B18-69	GCA_012911495.1	2698687	2698687	type	True	91.5642	598	730	95	below_threshold
Tepidiphilus olei	strain=J18	GCA_006980705.1	2502184	2502184	type	True	91.5139	579	730	95	below_threshold
Tepidiphilus thermophilus	strain=JCM 19170	GCA_001418245.1	876478	876478	suspected-type	True	91.4457	623	730	95	below_threshold
Tepidiphilus thermophilus	strain=JCM 19170	GCA_001517365.1	876478	876478	suspected-type	True	91.3982	625	730	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:02:46,836] [INFO] DFAST Taxonomy check result was written to GCF_000425565.1_ASM42556v1_genomic.fna/tc_result.tsv
[2024-01-25 20:02:46,837] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:02:46,837] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:02:46,837] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfd9fca89-27ea-41b8-ad64-d21a8448f3e3/dqc_reference/checkm_data
[2024-01-25 20:02:46,838] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:02:46,862] [INFO] Task started: CheckM
[2024-01-25 20:02:46,863] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000425565.1_ASM42556v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000425565.1_ASM42556v1_genomic.fna/checkm_input GCF_000425565.1_ASM42556v1_genomic.fna/checkm_result
[2024-01-25 20:03:09,947] [INFO] Task succeeded: CheckM
[2024-01-25 20:03:09,948] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:03:09,970] [INFO] ===== Completeness check finished =====
[2024-01-25 20:03:09,971] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:03:09,971] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000425565.1_ASM42556v1_genomic.fna/markers.fasta)
[2024-01-25 20:03:09,971] [INFO] Task started: Blastn
[2024-01-25 20:03:09,971] [INFO] Running command: blastn -query GCF_000425565.1_ASM42556v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd9fca89-27ea-41b8-ad64-d21a8448f3e3/dqc_reference/reference_markers_gtdb.fasta -out GCF_000425565.1_ASM42556v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:03:11,310] [INFO] Task succeeded: Blastn
[2024-01-25 20:03:11,312] [INFO] Selected 10 target genomes.
[2024-01-25 20:03:11,313] [INFO] Target genome list was writen to GCF_000425565.1_ASM42556v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:03:11,332] [INFO] Task started: fastANI
[2024-01-25 20:03:11,332] [INFO] Running command: fastANI --query /var/lib/cwl/stg1e1ded8c-7a15-4f19-8558-395295dc2879/GCF_000425565.1_ASM42556v1_genomic.fna.gz --refList GCF_000425565.1_ASM42556v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000425565.1_ASM42556v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:03:18,229] [INFO] Task succeeded: fastANI
[2024-01-25 20:03:18,236] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:03:18,237] [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_000425565.1	s__Tepidiphilus margaritifer	100.0	729	730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Tepidiphilus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_012911495.1	s__Tepidiphilus baoligensis	91.5642	598	730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Tepidiphilus	95.0	97.01	96.91	0.89	0.87	3	-
GCF_006503695.1	s__Tepidiphilus succinatimandens	91.4826	620	730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Tepidiphilus	95.0	98.86	98.78	0.95	0.95	4	-
GCA_016235745.1	s__Tepidiphilus sp016235745	88.8009	526	730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Tepidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003034845.1	s__Thauera_A sp003034845	78.1831	240	730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001591165.1	s__Thauera butanivorans	77.8838	245	730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001922305.1	s__Thauera chlorobenzoica	77.8433	236	730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	97.93	95.88	0.91	0.86	3	-
GCA_003963015.1	s__Thauera sp003963015	77.7934	275	730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302295.1	s__Thauera sp017302295	77.622	228	730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016192825.1	s__SG8-41 sp016192825	75.9592	106	730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-41;g__SG8-41	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:03:18,238] [INFO] GTDB search result was written to GCF_000425565.1_ASM42556v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:03:18,239] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:03:18,243] [INFO] DFAST_QC result json was written to GCF_000425565.1_ASM42556v1_genomic.fna/dqc_result.json
[2024-01-25 20:03:18,243] [INFO] DFAST_QC completed!
[2024-01-25 20:03:18,243] [INFO] Total running time: 0h0m43s