[2024-01-24 12:14:33,752] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:33,754] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:33,754] [INFO] DQC Reference Directory: /var/lib/cwl/stg7039bc0f-9b42-435e-b820-f6127e78b83a/dqc_reference
[2024-01-24 12:14:35,039] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:35,040] [INFO] Task started: Prodigal
[2024-01-24 12:14:35,041] [INFO] Running command: gunzip -c /var/lib/cwl/stgb717951a-c784-4892-92d5-6e9b071c5613/GCF_019049855.1_ASM1904985v1_genomic.fna.gz | prodigal -d GCF_019049855.1_ASM1904985v1_genomic.fna/cds.fna -a GCF_019049855.1_ASM1904985v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:42,496] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:42,497] [INFO] Task started: HMMsearch
[2024-01-24 12:14:42,497] [INFO] Running command: hmmsearch --tblout GCF_019049855.1_ASM1904985v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7039bc0f-9b42-435e-b820-f6127e78b83a/dqc_reference/reference_markers.hmm GCF_019049855.1_ASM1904985v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:42,760] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:42,762] [INFO] Found 6/6 markers.
[2024-01-24 12:14:42,830] [INFO] Query marker FASTA was written to GCF_019049855.1_ASM1904985v1_genomic.fna/markers.fasta
[2024-01-24 12:14:42,831] [INFO] Task started: Blastn
[2024-01-24 12:14:42,831] [INFO] Running command: blastn -query GCF_019049855.1_ASM1904985v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7039bc0f-9b42-435e-b820-f6127e78b83a/dqc_reference/reference_markers.fasta -out GCF_019049855.1_ASM1904985v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:43,533] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:43,540] [INFO] Selected 14 target genomes.
[2024-01-24 12:14:43,540] [INFO] Target genome list was writen to GCF_019049855.1_ASM1904985v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:43,547] [INFO] Task started: fastANI
[2024-01-24 12:14:43,548] [INFO] Running command: fastANI --query /var/lib/cwl/stgb717951a-c784-4892-92d5-6e9b071c5613/GCF_019049855.1_ASM1904985v1_genomic.fna.gz --refList GCF_019049855.1_ASM1904985v1_genomic.fna/target_genomes.txt --output GCF_019049855.1_ASM1904985v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:50,462] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:50,462] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7039bc0f-9b42-435e-b820-f6127e78b83a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:50,463] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7039bc0f-9b42-435e-b820-f6127e78b83a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:50,472] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:14:50,473] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:50,473] [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
Hydrogenophilus thiooxidans	strain=SS56	GCA_019049855.1	2820326	2820326	type	True	100.0	734	738	95	conclusive
Hydrogenophilus thermoluteolus	strain=TH-1	GCA_003574215.1	297	297	type	True	94.0023	658	738	95	below_threshold
Tepidiphilus thermophilus	strain=JCM 19170	GCA_001517365.1	876478	876478	suspected-type	True	77.2789	161	738	95	below_threshold
Tepidiphilus thermophilus	strain=JCM 19170	GCA_001418245.1	876478	876478	suspected-type	True	77.2789	161	738	95	below_threshold
Tepidiphilus margaritifer	strain=DSM 15129	GCA_000425565.1	203471	203471	type	True	77.0388	142	738	95	below_threshold
Tepidiphilus baoligensis	strain=B18-69	GCA_012911495.1	2698687	2698687	type	True	77.0057	141	738	95	below_threshold
Thauera aromatica	strain=K172	GCA_003030465.1	59405	59405	type	True	76.4524	88	738	95	below_threshold
Aromatoleum toluvorans	strain=Td21	GCA_012910905.1	92002	92002	type	True	76.2666	88	738	95	below_threshold
Crenobacter cavernae	strain=K1W11S-77	GCA_003355495.1	2290923	2290923	type	True	75.941	53	738	95	below_threshold
Crenobacter sedimenti	strain=HX-7-9	GCA_010435965.1	2705474	2705474	type	True	75.7473	56	738	95	below_threshold
Crenobacter intestini	strain=GY 70310	GCA_004919095.1	2563443	2563443	type	True	75.6749	58	738	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:50,475] [INFO] DFAST Taxonomy check result was written to GCF_019049855.1_ASM1904985v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:50,475] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:50,476] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:50,476] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7039bc0f-9b42-435e-b820-f6127e78b83a/dqc_reference/checkm_data
[2024-01-24 12:14:50,477] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:50,508] [INFO] Task started: CheckM
[2024-01-24 12:14:50,508] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019049855.1_ASM1904985v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019049855.1_ASM1904985v1_genomic.fna/checkm_input GCF_019049855.1_ASM1904985v1_genomic.fna/checkm_result
[2024-01-24 12:15:18,630] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:18,632] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:18,655] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:18,656] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:18,656] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019049855.1_ASM1904985v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:18,657] [INFO] Task started: Blastn
[2024-01-24 12:15:18,657] [INFO] Running command: blastn -query GCF_019049855.1_ASM1904985v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7039bc0f-9b42-435e-b820-f6127e78b83a/dqc_reference/reference_markers_gtdb.fasta -out GCF_019049855.1_ASM1904985v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:19,683] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:19,687] [INFO] Selected 17 target genomes.
[2024-01-24 12:15:19,687] [INFO] Target genome list was writen to GCF_019049855.1_ASM1904985v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:19,700] [INFO] Task started: fastANI
[2024-01-24 12:15:19,701] [INFO] Running command: fastANI --query /var/lib/cwl/stgb717951a-c784-4892-92d5-6e9b071c5613/GCF_019049855.1_ASM1904985v1_genomic.fna.gz --refList GCF_019049855.1_ASM1904985v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019049855.1_ASM1904985v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:28,168] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:28,185] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:28,185] [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_019049855.1	s__Hydrogenophilus sp019049855	100.0	734	738	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Hydrogenophilus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003574215.1	s__Hydrogenophilus thermoluteolus	94.0023	658	738	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Hydrogenophilus	95.0	98.30	98.30	0.97	0.97	2	-
GCF_006503695.1	s__Tepidiphilus succinatimandens	77.2581	155	738	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Tepidiphilus	95.0	98.86	98.78	0.95	0.95	4	-
GCF_012911495.1	s__Tepidiphilus baoligensis	77.0229	140	738	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Tepidiphilus	95.0	97.01	96.91	0.89	0.87	3	-
GCA_016235745.1	s__Tepidiphilus sp016235745	76.9415	124	738	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Tepidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002872475.1	s__Azoarcus_D pumilus	76.4876	65	738	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003030465.1	s__Thauera aromatica	76.4524	88	738	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012910905.1	s__Aromatoleum toluvorans	76.2879	87	738	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302295.1	s__Thauera sp017302295	76.0298	79	738	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003265685.1	s__Piscinibacter caeni	75.7471	79	738	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:28,187] [INFO] GTDB search result was written to GCF_019049855.1_ASM1904985v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:28,187] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:28,191] [INFO] DFAST_QC result json was written to GCF_019049855.1_ASM1904985v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:28,192] [INFO] DFAST_QC completed!
[2024-01-24 12:15:28,192] [INFO] Total running time: 0h0m54s