[2024-01-24 10:58:06,473] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:58:06,475] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:58:06,476] [INFO] DQC Reference Directory: /var/lib/cwl/stg9a57c0c9-9190-4b22-b86b-e6bb679ed1a4/dqc_reference
[2024-01-24 10:58:09,633] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:58:09,634] [INFO] Task started: Prodigal
[2024-01-24 10:58:09,634] [INFO] Running command: gunzip -c /var/lib/cwl/stg8c59ef86-ef6c-4ad1-8130-4b96f1bb31be/GCF_003315175.1_ASM331517v1_genomic.fna.gz | prodigal -d GCF_003315175.1_ASM331517v1_genomic.fna/cds.fna -a GCF_003315175.1_ASM331517v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:58:25,912] [INFO] Task succeeded: Prodigal
[2024-01-24 10:58:25,912] [INFO] Task started: HMMsearch
[2024-01-24 10:58:25,913] [INFO] Running command: hmmsearch --tblout GCF_003315175.1_ASM331517v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9a57c0c9-9190-4b22-b86b-e6bb679ed1a4/dqc_reference/reference_markers.hmm GCF_003315175.1_ASM331517v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:58:26,269] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:58:26,271] [INFO] Found 6/6 markers.
[2024-01-24 10:58:26,313] [INFO] Query marker FASTA was written to GCF_003315175.1_ASM331517v1_genomic.fna/markers.fasta
[2024-01-24 10:58:26,314] [INFO] Task started: Blastn
[2024-01-24 10:58:26,314] [INFO] Running command: blastn -query GCF_003315175.1_ASM331517v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a57c0c9-9190-4b22-b86b-e6bb679ed1a4/dqc_reference/reference_markers.fasta -out GCF_003315175.1_ASM331517v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:27,177] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:27,180] [INFO] Selected 14 target genomes.
[2024-01-24 10:58:27,180] [INFO] Target genome list was writen to GCF_003315175.1_ASM331517v1_genomic.fna/target_genomes.txt
[2024-01-24 10:58:27,189] [INFO] Task started: fastANI
[2024-01-24 10:58:27,189] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c59ef86-ef6c-4ad1-8130-4b96f1bb31be/GCF_003315175.1_ASM331517v1_genomic.fna.gz --refList GCF_003315175.1_ASM331517v1_genomic.fna/target_genomes.txt --output GCF_003315175.1_ASM331517v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:40,527] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:40,528] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9a57c0c9-9190-4b22-b86b-e6bb679ed1a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:40,528] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9a57c0c9-9190-4b22-b86b-e6bb679ed1a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:40,546] [INFO] Found 14 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 10:58:40,546] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:40,546] [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
Eoetvoesia caeni	strain=DSM 25520	GCA_003315175.1	645616	645616	type	True	100.0	1557	1557	95	conclusive
Eoetvoesia caeni	strain=PB3-7B	GCA_022688825.1	645616	645616	type	True	99.9982	1555	1557	95	conclusive
Eoetvoesia caeni	strain=PB3-7B	GCA_013416545.1	645616	645616	type	True	99.9975	1551	1557	95	conclusive
Parapusillimonas granuli	strain=DSM 18079	GCA_014202705.1	380911	380911	type	True	79.7373	411	1557	95	below_threshold
Parapusillimonas granuli	strain=LMG 24012	GCA_013416525.1	380911	380911	type	True	79.6692	420	1557	95	below_threshold
Achromobacter veterisilvae	strain=LMG 30378	GCA_900496975.1	2069367	2069367	type	True	78.8022	377	1557	95	below_threshold
Candidimonas nitroreducens	strain=SC-089	GCA_002209565.1	683354	683354	type	True	78.5381	393	1557	95	below_threshold
Pusillimonas minor	strain=YC-7-48	GCA_014237865.1	2697024	2697024	type	True	78.5224	302	1557	95	below_threshold
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	78.4843	405	1557	95	below_threshold
Candidimonas humi	strain=DSM 25336	GCA_019166065.1	683355	683355	type	True	78.4502	403	1557	95	below_threshold
Bordetella pertussis	strain=18323	GCA_000306945.1	520	520	type	True	77.9062	303	1557	95	below_threshold
Bordetella pertussis	strain=FDAARGOS_1543	GCA_020736265.1	520	520	type	True	77.8511	305	1557	95	below_threshold
Bordetella bronchiseptica	strain=CCUG 219	GCA_021391275.1	518	518	suspected-type	True	77.8127	306	1557	95	below_threshold
Achromobacter insolitus	strain=NCTC 13520	GCA_024168865.1	217204	217204	type	True	77.5255	325	1557	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:40,548] [INFO] DFAST Taxonomy check result was written to GCF_003315175.1_ASM331517v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:40,549] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:40,549] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:40,549] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9a57c0c9-9190-4b22-b86b-e6bb679ed1a4/dqc_reference/checkm_data
[2024-01-24 10:58:40,550] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:40,598] [INFO] Task started: CheckM
[2024-01-24 10:58:40,599] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003315175.1_ASM331517v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003315175.1_ASM331517v1_genomic.fna/checkm_input GCF_003315175.1_ASM331517v1_genomic.fna/checkm_result
[2024-01-24 10:59:26,827] [INFO] Task succeeded: CheckM
[2024-01-24 10:59:26,828] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:59:26,842] [INFO] ===== Completeness check finished =====
[2024-01-24 10:59:26,842] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:59:26,843] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003315175.1_ASM331517v1_genomic.fna/markers.fasta)
[2024-01-24 10:59:26,843] [INFO] Task started: Blastn
[2024-01-24 10:59:26,843] [INFO] Running command: blastn -query GCF_003315175.1_ASM331517v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a57c0c9-9190-4b22-b86b-e6bb679ed1a4/dqc_reference/reference_markers_gtdb.fasta -out GCF_003315175.1_ASM331517v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:59:28,299] [INFO] Task succeeded: Blastn
[2024-01-24 10:59:28,304] [INFO] Selected 15 target genomes.
[2024-01-24 10:59:28,304] [INFO] Target genome list was writen to GCF_003315175.1_ASM331517v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:59:28,322] [INFO] Task started: fastANI
[2024-01-24 10:59:28,324] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c59ef86-ef6c-4ad1-8130-4b96f1bb31be/GCF_003315175.1_ASM331517v1_genomic.fna.gz --refList GCF_003315175.1_ASM331517v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003315175.1_ASM331517v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:41,953] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:41,969] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:59:41,970] [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_003315175.1	s__Eoetvoesia caeni	100.0	1557	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Eoetvoesia	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_003545815.1	s__Pusillimonas caeni	79.6803	535	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013416525.1	s__Parapusillimonas granuli	79.6574	419	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Parapusillimonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900129885.1	s__Candidimonas_A bauzanensis	79.644	443	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013416435.1	s__Parapusillimonas sp013416435	79.0807	327	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Parapusillimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004022565.1	s__Pusillimonas_D thiosulfatoxidans	78.9269	331	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_D	95.0	97.98	97.65	0.84	0.81	3	-
GCF_900496975.1	s__Achromobacter veterisilvae	78.8282	376	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339425.1	s__Candidimonas_A sp004339425	78.526	308	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002209565.1	s__Candidimonas nitroreducens	78.5173	395	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019166065.1	s__Candidimonas humi	78.4401	404	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004322135.1	s__Eoetvoesia sp004322135	78.4355	391	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Eoetvoesia	95.0	99.95	99.95	0.92	0.92	2	-
GCF_004216695.1	s__Pigmentiphaga kullae	78.4225	308	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pigmentiphaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017356245.1	s__Bordetella_A petrii_D	78.2681	368	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000306945.1	s__Bordetella pertussis	77.9062	303	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	99.42	95.13	0.93	0.83	983	-
GCA_009360345.1	s__Pigmentiphaga sp009360345	77.3345	240	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pigmentiphaga	95.0	99.85	99.84	0.97	0.96	3	-
--------------------------------------------------------------------------------
[2024-01-24 10:59:41,972] [INFO] GTDB search result was written to GCF_003315175.1_ASM331517v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:41,976] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:41,981] [INFO] DFAST_QC result json was written to GCF_003315175.1_ASM331517v1_genomic.fna/dqc_result.json
[2024-01-24 10:59:41,981] [INFO] DFAST_QC completed!
[2024-01-24 10:59:41,981] [INFO] Total running time: 0h1m36s