[2024-01-24 11:34:55,023] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:55,026] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:55,026] [INFO] DQC Reference Directory: /var/lib/cwl/stg08aa79b7-691f-4049-aa91-225bd7c9ba4b/dqc_reference
[2024-01-24 11:34:56,589] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:56,589] [INFO] Task started: Prodigal
[2024-01-24 11:34:56,590] [INFO] Running command: gunzip -c /var/lib/cwl/stgb694482b-5b93-4d11-98c3-3e4fedd3144c/GCF_013416545.1_ASM1341654v1_genomic.fna.gz | prodigal -d GCF_013416545.1_ASM1341654v1_genomic.fna/cds.fna -a GCF_013416545.1_ASM1341654v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:12,135] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:12,135] [INFO] Task started: HMMsearch
[2024-01-24 11:35:12,136] [INFO] Running command: hmmsearch --tblout GCF_013416545.1_ASM1341654v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg08aa79b7-691f-4049-aa91-225bd7c9ba4b/dqc_reference/reference_markers.hmm GCF_013416545.1_ASM1341654v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:12,443] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:12,446] [INFO] Found 6/6 markers.
[2024-01-24 11:35:12,487] [INFO] Query marker FASTA was written to GCF_013416545.1_ASM1341654v1_genomic.fna/markers.fasta
[2024-01-24 11:35:12,488] [INFO] Task started: Blastn
[2024-01-24 11:35:12,488] [INFO] Running command: blastn -query GCF_013416545.1_ASM1341654v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg08aa79b7-691f-4049-aa91-225bd7c9ba4b/dqc_reference/reference_markers.fasta -out GCF_013416545.1_ASM1341654v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:13,295] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:13,298] [INFO] Selected 14 target genomes.
[2024-01-24 11:35:13,299] [INFO] Target genome list was writen to GCF_013416545.1_ASM1341654v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:13,302] [INFO] Task started: fastANI
[2024-01-24 11:35:13,303] [INFO] Running command: fastANI --query /var/lib/cwl/stgb694482b-5b93-4d11-98c3-3e4fedd3144c/GCF_013416545.1_ASM1341654v1_genomic.fna.gz --refList GCF_013416545.1_ASM1341654v1_genomic.fna/target_genomes.txt --output GCF_013416545.1_ASM1341654v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:26,075] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:26,076] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg08aa79b7-691f-4049-aa91-225bd7c9ba4b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:26,077] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg08aa79b7-691f-4049-aa91-225bd7c9ba4b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:26,092] [INFO] Found 14 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 11:35:26,093] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:26,093] [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=PB3-7B	GCA_013416545.1	645616	645616	type	True	100.0	1561	1564	95	conclusive
Eoetvoesia caeni	strain=PB3-7B	GCA_022688825.1	645616	645616	type	True	99.9958	1557	1564	95	conclusive
Eoetvoesia caeni	strain=DSM 25520	GCA_003315175.1	645616	645616	type	True	99.9802	1544	1564	95	conclusive
Parapusillimonas granuli	strain=DSM 18079	GCA_014202705.1	380911	380911	type	True	79.6916	415	1564	95	below_threshold
Parapusillimonas granuli	strain=LMG 24012	GCA_013416525.1	380911	380911	type	True	79.6484	422	1564	95	below_threshold
Achromobacter veterisilvae	strain=LMG 30378	GCA_900496975.1	2069367	2069367	type	True	78.987	372	1564	95	below_threshold
Pusillimonas minor	strain=YC-7-48	GCA_014237865.1	2697024	2697024	type	True	78.8032	298	1564	95	below_threshold
Candidimonas nitroreducens	strain=SC-089	GCA_002209565.1	683354	683354	type	True	78.5129	396	1564	95	below_threshold
Candidimonas humi	strain=DSM 25336	GCA_019166065.1	683355	683355	type	True	78.4957	387	1564	95	below_threshold
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	78.4175	409	1564	95	below_threshold
Bordetella pertussis	strain=FDAARGOS_1543	GCA_020736265.1	520	520	type	True	77.914	299	1564	95	below_threshold
Bordetella pertussis	strain=18323	GCA_000306945.1	520	520	type	True	77.8913	299	1564	95	below_threshold
Bordetella bronchiseptica	strain=CCUG 219	GCA_021391275.1	518	518	suspected-type	True	77.7586	310	1564	95	below_threshold
Achromobacter insolitus	strain=NCTC 13520	GCA_024168865.1	217204	217204	type	True	77.6044	322	1564	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:26,095] [INFO] DFAST Taxonomy check result was written to GCF_013416545.1_ASM1341654v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:26,095] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:26,095] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:26,096] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg08aa79b7-691f-4049-aa91-225bd7c9ba4b/dqc_reference/checkm_data
[2024-01-24 11:35:26,097] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:26,144] [INFO] Task started: CheckM
[2024-01-24 11:35:26,144] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013416545.1_ASM1341654v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013416545.1_ASM1341654v1_genomic.fna/checkm_input GCF_013416545.1_ASM1341654v1_genomic.fna/checkm_result
[2024-01-24 11:36:11,915] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:11,917] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:11,940] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:11,940] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:11,941] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013416545.1_ASM1341654v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:11,941] [INFO] Task started: Blastn
[2024-01-24 11:36:11,941] [INFO] Running command: blastn -query GCF_013416545.1_ASM1341654v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg08aa79b7-691f-4049-aa91-225bd7c9ba4b/dqc_reference/reference_markers_gtdb.fasta -out GCF_013416545.1_ASM1341654v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:13,385] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:13,389] [INFO] Selected 15 target genomes.
[2024-01-24 11:36:13,389] [INFO] Target genome list was writen to GCF_013416545.1_ASM1341654v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:13,399] [INFO] Task started: fastANI
[2024-01-24 11:36:13,399] [INFO] Running command: fastANI --query /var/lib/cwl/stgb694482b-5b93-4d11-98c3-3e4fedd3144c/GCF_013416545.1_ASM1341654v1_genomic.fna.gz --refList GCF_013416545.1_ASM1341654v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013416545.1_ASM1341654v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:26,974] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:26,993] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:26,994] [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	99.9802	1544	1564	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_900129885.1	s__Candidimonas_A bauzanensis	79.7321	449	1564	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_003545815.1	s__Pusillimonas caeni	79.7141	543	1564	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	79.6603	421	1564	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Parapusillimonas	95.0	100.00	100.00	0.99	0.99	2	-
GCA_013416435.1	s__Parapusillimonas sp013416435	78.9925	332	1564	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Parapusillimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900496975.1	s__Achromobacter veterisilvae	78.9689	373	1564	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004022565.1	s__Pusillimonas_D thiosulfatoxidans	78.9162	336	1564	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_002209565.1	s__Candidimonas nitroreducens	78.5252	396	1564	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216695.1	s__Pigmentiphaga kullae	78.4876	301	1564	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pigmentiphaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019166065.1	s__Candidimonas humi	78.4857	388	1564	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	78.4775	383	1564	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Eoetvoesia	95.0	99.95	99.95	0.92	0.92	2	-
GCF_004339425.1	s__Candidimonas_A sp004339425	78.4619	305	1564	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_017356245.1	s__Bordetella_A petrii_D	78.2899	361	1564	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	77.903	298	1564	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	77.4854	230	1564	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 11:36:26,995] [INFO] GTDB search result was written to GCF_013416545.1_ASM1341654v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:26,996] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:26,999] [INFO] DFAST_QC result json was written to GCF_013416545.1_ASM1341654v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:27,000] [INFO] DFAST_QC completed!
[2024-01-24 11:36:27,000] [INFO] Total running time: 0h1m32s