[2024-01-24 13:50:11,002] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:50:11,003] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:50:11,004] [INFO] DQC Reference Directory: /var/lib/cwl/stg55235968-b238-4c93-9b8b-69ce59763695/dqc_reference
[2024-01-24 13:50:12,302] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:50:12,303] [INFO] Task started: Prodigal
[2024-01-24 13:50:12,303] [INFO] Running command: gunzip -c /var/lib/cwl/stg5405218f-d2be-44e4-9459-80e82617a7a4/GCF_012911495.1_ASM1291149v1_genomic.fna.gz | prodigal -d GCF_012911495.1_ASM1291149v1_genomic.fna/cds.fna -a GCF_012911495.1_ASM1291149v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:19,455] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:19,456] [INFO] Task started: HMMsearch
[2024-01-24 13:50:19,456] [INFO] Running command: hmmsearch --tblout GCF_012911495.1_ASM1291149v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg55235968-b238-4c93-9b8b-69ce59763695/dqc_reference/reference_markers.hmm GCF_012911495.1_ASM1291149v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:19,717] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:19,718] [INFO] Found 6/6 markers.
[2024-01-24 13:50:19,761] [INFO] Query marker FASTA was written to GCF_012911495.1_ASM1291149v1_genomic.fna/markers.fasta
[2024-01-24 13:50:19,762] [INFO] Task started: Blastn
[2024-01-24 13:50:19,762] [INFO] Running command: blastn -query GCF_012911495.1_ASM1291149v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg55235968-b238-4c93-9b8b-69ce59763695/dqc_reference/reference_markers.fasta -out GCF_012911495.1_ASM1291149v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:20,670] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:20,674] [INFO] Selected 7 target genomes.
[2024-01-24 13:50:20,675] [INFO] Target genome list was writen to GCF_012911495.1_ASM1291149v1_genomic.fna/target_genomes.txt
[2024-01-24 13:50:20,680] [INFO] Task started: fastANI
[2024-01-24 13:50:20,681] [INFO] Running command: fastANI --query /var/lib/cwl/stg5405218f-d2be-44e4-9459-80e82617a7a4/GCF_012911495.1_ASM1291149v1_genomic.fna.gz --refList GCF_012911495.1_ASM1291149v1_genomic.fna/target_genomes.txt --output GCF_012911495.1_ASM1291149v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:25,226] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:25,227] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg55235968-b238-4c93-9b8b-69ce59763695/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:25,227] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg55235968-b238-4c93-9b8b-69ce59763695/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:25,235] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:50:25,235] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:50:25,235] [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 baoligensis	strain=B18-69	GCA_012911495.1	2698687	2698687	type	True	100.0	725	729	95	inconclusive
Tepidiphilus olei	strain=J18	GCA_006980705.1	2502184	2502184	type	True	96.8643	636	729	95	inconclusive
Tepidiphilus margaritifer	strain=DSM 15129	GCA_000425565.1	203471	203471	type	True	91.5788	589	729	95	below_threshold
Tepidiphilus thermophilus	strain=JCM 19170	GCA_001517365.1	876478	876478	suspected-type	True	89.9511	594	729	95	below_threshold
Tepidiphilus thermophilus	strain=JCM 19170	GCA_001418245.1	876478	876478	suspected-type	True	89.9407	595	729	95	below_threshold
Burkholderia thailandensis	strain=E264; ATCC 700388	GCA_000012365.1	57975	57975	type	True	76.0657	122	729	95	below_threshold
Burkholderia thailandensis	strain=ATCC 700388	GCA_000152285.1	57975	57975	type	True	75.8462	110	729	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:25,236] [INFO] DFAST Taxonomy check result was written to GCF_012911495.1_ASM1291149v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:25,237] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:25,237] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:25,237] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg55235968-b238-4c93-9b8b-69ce59763695/dqc_reference/checkm_data
[2024-01-24 13:50:25,238] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:25,267] [INFO] Task started: CheckM
[2024-01-24 13:50:25,267] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012911495.1_ASM1291149v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012911495.1_ASM1291149v1_genomic.fna/checkm_input GCF_012911495.1_ASM1291149v1_genomic.fna/checkm_result
[2024-01-24 13:50:51,635] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:51,637] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:51,652] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:51,653] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:51,653] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012911495.1_ASM1291149v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:51,654] [INFO] Task started: Blastn
[2024-01-24 13:50:51,654] [INFO] Running command: blastn -query GCF_012911495.1_ASM1291149v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg55235968-b238-4c93-9b8b-69ce59763695/dqc_reference/reference_markers_gtdb.fasta -out GCF_012911495.1_ASM1291149v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:53,122] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:53,125] [INFO] Selected 11 target genomes.
[2024-01-24 13:50:53,126] [INFO] Target genome list was writen to GCF_012911495.1_ASM1291149v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:53,156] [INFO] Task started: fastANI
[2024-01-24 13:50:53,156] [INFO] Running command: fastANI --query /var/lib/cwl/stg5405218f-d2be-44e4-9459-80e82617a7a4/GCF_012911495.1_ASM1291149v1_genomic.fna.gz --refList GCF_012911495.1_ASM1291149v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012911495.1_ASM1291149v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:00,156] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:00,166] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:00,166] [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_012911495.1	s__Tepidiphilus baoligensis	100.0	725	729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Tepidiphilus	95.0	97.01	96.91	0.89	0.87	3	conclusive
GCF_000425565.1	s__Tepidiphilus margaritifer	91.5788	589	729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Tepidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006503695.1	s__Tepidiphilus succinatimandens	89.8461	593	729	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	87.9798	497	729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Tepidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003963015.1	s__Thauera sp003963015	77.9067	250	729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003034845.1	s__Thauera_A sp003034845	77.7955	240	729	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_001922305.1	s__Thauera chlorobenzoica	77.7646	237	729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	97.93	95.88	0.91	0.86	3	-
GCF_012910905.1	s__Aromatoleum toluvorans	77.4891	211	729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240585.1	s__Thauera sp018240585	77.4637	201	729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156155.1	s__Aromatoleum tolulyticum	77.292	207	729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011526165.1	s__Desulfobacillus sp011526165	77.0981	158	729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Desulfobacillus	95.0	98.84	98.84	0.79	0.79	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:00,168] [INFO] GTDB search result was written to GCF_012911495.1_ASM1291149v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:00,168] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:00,172] [INFO] DFAST_QC result json was written to GCF_012911495.1_ASM1291149v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:00,172] [INFO] DFAST_QC completed!
[2024-01-24 13:51:00,172] [INFO] Total running time: 0h0m49s